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Pathogens, microbiome and the host: emergence of the ecological Koch's postulates

Pathogens, microbiome and the host: emergence of the ecological Koch's postulates Abstract Even though tremendous progress has been made in the last decades to elucidate the mechanisms of intestinal homeostasis, dysbiosis and disease, we are only at the beginning of understanding the complexity of the gut ecosystem and the underlying interaction networks. We are also only starting to unravel the mechanisms that pathogens have evolved to overcome the barriers imposed by the microbiota and host to exploit the system to their own benefit. Recent work in these domains clearly indicates that the ‘traditional Koch's postulates’, which state that a given pathogen leads to a distinct disease, are not valid for all ‘infectious’ diseases, but that a more complete and complex interpretation of Koch's postulates is needed in order to understand and explain them. This review summarises the current understanding of what defines a healthy gut ecosystem and highlights recent progress in uncovering the interplay between the host, its microbiota and invading intestinal pathogens. Based on these recent findings, we propose a new interpretation of Koch's postulates that we term ‘ecological Koch's postulates’. microbiota, Koch's postulates, pathogen, host INTRODUCTION Traditionally, pathogens have been viewed as armed warriors, fighting against the host (Sansonetti 2004). However, it is well established that not everyone that has ingested a typical infectious dose of a given pathogen, for example Salmonella typhimurium, Helicobacter pylori or Campylobacter jejuni, will develop disease. There also is increasing evidence for asymptomatic carriage of enteric pathogens (Kotloff et al.2013; Breurec et al.2016; Randremanana et al.2016). In addition, it is also known that antibiotic use leads to an increased susceptibility to infection by enteropathogens (Bohnhoff, Drake and Miller 1954; Miller, Bohnhoff and Drake 1954; Barthel et al.2003; Sekirov et al.2008; Van der Waaij, Berghuis-de Vries and Lekkerkerk-van der Wees 2009). These observations led to an extended concept that acknowledged the role of the microbiota in protecting the host against pathogens, referred to first as ‘microbial barrier’ and later as ‘colonisation resistance’. Bacteria can have an inhibitory effect on phylogenetically unrelated species/groups of bacteria (interspecies barrier effect). This was demonstrated as early as the late 1970s through work showing that the pre-colonisation of axenic mice with Escherichia coli could inhibit the colonisation of Shigella flexneri (Ducluzeau et al.1977). Furthermore, bacteria from the same species/group can have an inhibitory effect on the installation of their peers (intra-species barrier effect). This concept was shown in the 1980s in studies using closely related Clostridium species (Corthier and Muller 1988). Several studies have also assessed the role of the prokaryotic microbiota on the susceptibility to viral infections. Indeed, susceptibility to rota- and norovirus seems to depend, at least in part, on the composition of a host's prokaryotic microbiota (Rodríguez-Díaz et al.2017), as do sexually transmitted diseases, such as for example Human Immunodeficiency Virus (Nunn et al.2015), Cervical Human Papillomavirus (Shannon et al.2017b) or Herpes Simplex Virus (Shannon et al.2017a), in the context of a changed vaginal microbiota. For many years, the exact mechanisms underlying the phenomenon of colonisation resistance remained unclear. However, work over the last decades has demonstrated that the microbiota forms a complex ecosystem and interacts with the host and invading pathogens in a dynamic manner. The intestinal microbiota is composed of trillions of organisms belonging to hundreds of different species (Eckburg et al.2005; Yatsunenko et al.2012), reviewed in (Cho and Blaser 2012). While the majority belongs to the prokaryota (bacteria and archae), it also comprises viruses (including phages) and different eukaryotes, especially yeasts and protists (Parfrey, Walters and Knight 2011; Clemente et al.2012; Ursell et al.2012; Parfrey et al.2014; Hamad, Raoult and Bittar 2016). Members of the gram-negative Bacteroidetes and the gram-positive Firmicutes dominate the bacterial community residing in the gut. Less abundant groups include members of the Proteobacteria, the Verrucomicrobia, the Tenericutes, the Defferibacteres and the Fusobacteria (Eckburg et al.2005; Yatsunenko et al.2012). In areas of the world without developed water supplies, the intestinal microbiota can also include multicellular organisms, for example helminths (Giacomin, Agha and Loukas 2016). Several different ecosystems formed by microbial communities in and on the body (e.g. the skin microbiota, the gastric microbiota and the vaginal microbiota) engage in a constant crosstalk with the human host (Costello et al.2009). The microbes belonging to each of these communities are often specific and adapted to living in their particular environment (e.g. anaerobic bacteria in the gut). This review will focus on the interactions found in the intestine, relying mainly on data gathered in laboratory mice. Even though similar mechanisms are at work in all ecosystems found in and on the human host, a complete description would go beyond the scope of this review. In this review, we will summarise the current understanding of what defines a healthy gut ecosystem and highlight recent progress in uncovering the interplay between the hosts, its microbiota and invading intestinal pathogens. THE GUT ECOSYSTEM- SPECIES ABUNDANCE, CHANCE AND THE ENVIRONMENT It has been hypothesised that at least some of the gut microbes have co-evolved and/or co-speciated with mammals (Groussin et al.2017). However, co-occurrence of microbes and their host, even if they affect each others’ fitness, does not necessarily mean a shared evolutionary history but can also be forged by numerous other mechanisms, including unidirectional selection (Moran and Sloan 2015). Regardless of their evolutionary origin, most mammals have a distinct assembly of microorganisms organised into a complex social network, which is remarkably robust and resilient to aggressions from, for example, allogenic/pathogenic intruders. Two major competing ecological theories have been proposed to explain how microbial communities are organised and maintained, i.e. how communities are assembled. The first, termed niche theory (Chase and Leibold 2004), is based on deterministic processes and assumes that each species occupies a given realised niche (i.e. a particular position in the abiotic and biotic space) due to its species-specific properties that define its fundamental niche. The grounding of this theory for microbes lies in the work of Martinus Willem Beijerinck (1851–1931) and in the famous statement: ‘Everything is everywhere, but the environment selects’ (O’Malley 2007). On the other hand, the ‘neutral theory’ is based only on stochastic processes and was proposed at the beginning of the century by Hubbell (2001) (The Unified Neutral Theory of Biodiversity and Biogeography, Princeton University Press, Princeton, NJ, USA.). The theory suggests that local communities are assembled independently of species fitness differences, hence assuming that all individual have the same fitness. Furthermore, the neutral theory claims that the fitness differences between species are not larger than the fitness differences within a given species. Competition is therefore not the driving factor of the observed community structure (all species are equivalent; they have the same chance of immigration, extinction and speciation). Of course, these two theories are not mutually exclusive and can act in parallel to drive microbial community assembly at (i) different spatial scales (e.g. at different locations in the intestine) or (ii) in different environments e.g. in different location on or in our body. Testing the fit of both theories on intestinal microbial communities has been hampered by the inability to culture many of the present species and hence define the composition of the microbial communities. With the rise of advanced sequencing methodologies and the decreasing associated costs, large datasets have been put together that now allow testing of these theories on highly complex communities, for example the intestinal microbiota. In studies conducted in the past few years, evidence is emerging that the intestine is not only an ecosystem based on Hubbell's ‘neutral theory’ where each member has the same fitness (Costello et al.2012). Indeed the Human Microbiome Project, which screened several hundred stool samples from individuals residing in the United States, revealed that the microbiota of only one individual showed a composition structure consistent primarily with the ‘neutral theory’ (Li and Ma 2016). Instead, modelling confirmed that the microbiota is governed mainly by deterministic processes, including environmental factors (Li and Ma 2016). This, however, does not exclude that both processes are shaping the communities at the same time, and clearly more work is needed to elucidate these questions. The microbiome is shaped by different deterministic forces, including maternal transmission at birth (Dogra et al.2015; Frese and Mills 2015; Rutayisire et al.2016; Stokholm et al.2016; Edwards 2017), nutrition (Turnbaugh et al.2006; De Filippo et al.2010; Muegge et al.2011; David et al.2014; Donovan and Comstock 2016; Kashtanova et al.2016; Araújo et al.2017; Donovan 2017; Edwards 2017), host genetics (Leamy et al.2014; Camarinha-Silva et al.2017), the use of different food additives or drugs (Dethlefsen et al.2008; Modi, Collins and Relman 2014; Chassaing et al.2015, 2017; Namasivayam et al.2017; Pourabedin et al.2017; Uebanso et al.2017) and infection (Hoffmann et al.2009; Hill et al.2010; Braun et al.2017). The immune system's dynamic IgA host response to the microbiota (Suzuki et al.2004; Peterson et al.2007; Macpherson, Geuking and Slack 2012; Slack et al.2012; Pabst, Cerovic and Hornef 2016; Moor et al.2017) and its action to hamper bacteria from interacting with the gut tissue (immune exclusion) and to grow (enchained growth; Moor et al.2017), as well as other innate and adaptive immune mechanisms, also have an important role in controlling the microbiota and shaping the community structure (Ivanov et al.2009; Slack et al.2009; Macpherson, Geuking and McCoy 2012; Schnupf, Gaboriau-Routhiau and Cerf-Bensussan 2013; Goto et al.2014; Kato et al.2014; Rescigno 2014; Spasova and Surh 2014; Atarashi et al.2015; Dowds, Blumberg and Zeissig 2015; Furusawa, Obata and Hase 2015; Ivanov 2017). The different environments that individuals and their gut ecosystem experience therefore select for a particular set of strains within the microbiota. However, a core bacterial genetic pool can be defined that is common to all individuals (Ley et al.2006; Qin et al.2010). Scarce resources such as nutrients and access to a given niche are limiting factors for growth in this confined ecosystem (reviewed in Stecher and Hardt 2011). These thoughts were already, in part, formulated earlier in the ‘nutrient niche theory’, a refined niche theory established by Freter et al. (1983a, 1983b, 1983c). The ‘nutrient niche theory’ or ‘niche co-existence theory’ stresses that ecological niches are defined by the available nutrients. Furthermore, Freter asserted that a given species can only establish itself if it is using at least one of the limiting nutrients in the most efficient way. He also hypothesised that only a few nutrients are responsible for shaping the whole community as they limit the growth potential of the whole ecological niche (Freter et al.1983a, 1983b, 1983c). Although Freter's classic ‘nutrient niche theory’ is useful to understand some of the mechanisms occurring in the gut ecosystem, it is not reflective of the entire complexity observed. Indeed, several cases of mixed-substrate utilisation and metabolic flexibility have been described. For example, E. coli and Salmonella spp., can thrive on tetrathionate, nitrate, succinate, 1,2-propanediol, or ethanolamines among others, and therefore rapidly adapt to a changing environment in the intestine during inflammation (Thiennimitr et al.2011; Winter et al. 2013b; Rivera-Chávez et al.2016a; Faber et al.2017; Spiga et al.2017). There are also a few examples of nutritional cooperation between gut microbes described (Rakoff-Nahoum, Foster and Comstock 2016). To date, the complexity of the gut ecosystem and the underlying interaction networks are only beginning to be understood. We are also only starting to unravel the mechanisms that pathogens have evolved to overcome the barriers imposed by the microbiota and host to exploit the system to their own benefit. HALLMARKS OF HOMEOSTASIS Intestinal pathogens are mainly ingested through the consumption of contaminated food or water. During their travel to their preferred ‘niche’, they encounter several obstacles and barriers imposed by the members of the ecosystem, which impede colonisation and invasion by intruders. Most pathogens must replicate in the gut lumen in order to elicit disease (Ackermann et al.2008). Below, we discuss the primary mechanisms in a healthy host that hamper pathogens from overcoming these obstacles and cause disease (see Fig. 1). Figure 1. View largeDownload slide Homeostatic gut environment (A) versus a dysbiotic gut environment (B). Scheme of an intestine in homeostasis (left) and in dysbiosis upon invasion of a pathogen (depicted in red). Upon dysbiosis, the mucus layer is thinner, larger amounts of antimicrobial peptides are secreted (e.g. C-type lectins as Reg3γ) to prevent bacteria breach the barrier and get access to the underlying tissue. This leads to villous blunting, influx of inflammatory cells into the lamina propria and depletion of members of the microbiota, leading to a changed composition and lower diversity of the resident microbiota. Figure 1. View largeDownload slide Homeostatic gut environment (A) versus a dysbiotic gut environment (B). Scheme of an intestine in homeostasis (left) and in dysbiosis upon invasion of a pathogen (depicted in red). Upon dysbiosis, the mucus layer is thinner, larger amounts of antimicrobial peptides are secreted (e.g. C-type lectins as Reg3γ) to prevent bacteria breach the barrier and get access to the underlying tissue. This leads to villous blunting, influx of inflammatory cells into the lamina propria and depletion of members of the microbiota, leading to a changed composition and lower diversity of the resident microbiota. Stomach acidity and bile acids After ingestion and resisting salivary enzymes, the first major barrier to infection is the low pH environment of the stomach. Indeed, pharmacological perturbation of stomach acidity through the use of proton-pump inhibitors leads to an increased pH and greater susceptibility to enteric infections (reviewed in Eusebi et al.2017). After surviving the stomach, the pathogen then enters the duodenum, where it is exposed to the massive influx of bile acids that are produced by the liver and released by the gall bladder. The primary bile acids are involved in lipid absorption from food. They also show toxicity towards given groups of bacteria. For example, in rats treated with cholic acid, phylum-level alterations in the composition of the gut microbiota were observed with an increase in Firmicutes and a concomitant decrease in Bacteroidetes. Cholic acid feeding also led to a less complex composition of the microbiota with overrepresentation of members of the classes Clostridia and Erysipelotrichi (Islam et al.2011). Therefore, bile acids shape the resident bacterial community by promoting the growth of bile acid-metabolising bacteria and by inhibiting in turn, the growth of bile-sensitive bacteria. Several studies in patients suffering from biliary obstruction, who display blocked bile flow into the small intestine, have shown an association with bacterial overgrowth and translocation of bacteria in the small intestine (Clements et al.1996). It was also shown that this phenotype can be reversed by the administration of bile acids (Lorenzo-Zúñiga et al.2003). Bile acids thus play an important role in regulating the microbiota in the small intestine. Over the length of the intestinal tract, these primary bile acids are metabolised by the microbiota to over 50 different secondary bile acids. One of the possible transformations is the deconjugation of bile acids through extracellular bile salt hydrolases (BSHs). BSHs are encoded by different members of the microbiota, especially in members of the Firmicutes, Bacteroidetes and some Actinobacteria. The deconjugated secondary bile acids show less toxicity towards the microbiota than the primary bile acids. Bile acids can also be oxidised and epimerised (transformation in between two stereoisomers) at specific hydroxyl-groups through transformation by 3-α, 7-α, or 12-α hydroxysteroid dehydrogenases. The secondary bile acids have an important role in gut homeostasis by inhibiting inflammation (reviewed in Ridlon et al.2014; Wahlström et al.2016; Winston and Theriot 2016). A recent study has shown that disuccinimidyl suberate (DSS)-mediated colitis was ameliorated in the presence of ursodeoxycholic acid or its taurine- or glycine-conjugated derivatives. Even though daily administration of these bile acids did not restore the full diversity of the microbiota to pre-DSS levels, specific species, such as Akkermansia muciniphila and the Clostridium cluster XIVa, were less depleted upon DSS treatment and the ratio of Firmicutes to Bacteroidetes remained normal (Van den Bossche et al.2017). Secondary bile acids have also been implicated in colony resistance, for example resistance against infection by Clostridium difficile (Winston and Theriot 2016; Van den Bossche et al.2017). Reducing the pool of secondary bile acids through antibiotic treatment relieves colonisation resistance towards C. difficile and enhances spore germination. A later study demonstrated that the colonisation resistance was mediated by a close relative, Clostridium scindens, through the production of the 7-α- dehydroxylated bile acids lithocholic acid and deoxycholic acid (Studer et al.2016). Box 1. Colonisation resistance. Colonisation resistance describes a phenomenon, observed in the human gut as well as in many other ecosystems that invading pathogens (and other organisms) face resistance against establishing themselves in this densely populated space. This ‘colonisation resistance’ is due to several factors, namely competition for nutrients or direct inhibition by chemical compounds or ‘molecular weapons’, for example Type 6 secretion systems and translocated toxins or other toxins. Colonisation resistance can be breached by interfering with the equilibrium of the ecosystem, for example by the administration of antibiotics or by infection. Short-chain fatty acids and other mechanisms of colony resistance through direct inhibition In the colon, complex carbohydrates present in the food or eaten in the form of prebiotics are metabolised by the resident microbiota into short chain fatty acids (SCFA), the three most abundant being acetate, propionate and butyrate. Acetate and propionate are produced mainly by members of the Lactobacilli and Bifidobacteriae. Butyrate is produced by bacteria of the phylum Firmicutes, for example Roseburia spp. and Faecalibacterium prausnitzii, or different members of the genus Clostridium (Ramirez-Farias et al.2009; Rivière et al.2016). Acetate triggers anti-inflammatory and anti-apoptotic responses in host epithelial cells, which leads to protection in the gut against colonisation with pathogenic bacteria like Enterobacteriaceae and Clostridiae (Fukuda et al.2011). Recently, butyrate production by Clostridia species has been implicated in colonisation resistance against S. typhimurium (Rivera-Chávez et al.2016b). The authors show that either through antibiotic treatment or, to a lesser extent, through Salmonella infection and the action of the Salmonella type three secretion system (T3SS) and associated virulence factors a depletion of butyrate-producing Clostridia species occurs in the intestine of affected mice. This then leads to an increased epithelial oxygenation and subsequently aerobic expansion of S. typhimurium. The colonisation resistance against Salmonella, alongside an anaerobic epithelial environment, could be restored through gavage of the mice with tributyrin, a butyrate metabolic precursor, clearly demonstrating the inhibitory role of butyrate on Salmonella invasion. Colonisation resistance and maintenance of the ecosystem through competition and cooperation In addition to direct inhibition, invading bacteria must also contend with limited available nutrient resources. Nutrient availability in the gut varies with food intake and time of day. Therefore, the microbiota faces a constantly changing environment. In a healthy, fully established intestine, all nutrient niches are occupied and incoming species must utilise methods to displace resident species from their established niches in order to create their own niche. A recent study analysing the gene expression of co-occurring human gut microbes showed that for 41% of all co-occurring species the presence of one of the organisms was associated with an altered transcriptional profile in the other, the most affected genes being involved in nutrient uptake and anaerobic respiration (Plichta et al.2016). This suggests that nutrient niche partitioning is prevalent within the gut ecosystem. Furthermore, early in development or after a destabilisation of the equilibrium, e.g. by an infection or antibiotic treatment, the microbiota has to re-establish itself. In this context, the so-called priority effect is observed, whereby the first re-colonising species establish a large colony that hampers the subsequent re-establishment of otherwise fully adapted species to the other's niche (Fukami and Nakajima 2011) (reviewed in Pereira and Berry 2017). This leads to fierce competition for nutrients within the microbiota and by invading pathogens. It also suggests that most of the interactions in the gut are based on competition. To date, cooperation is a type of interaction only very rarely described and does not seem to be as successful as competition in a crowded and competitive environment such as the intestine (Foster and Bell 2012). In one study of cooperation within the gut microbiota, Bacteroides ovatus was shown to produce two outer surface glycoside hydrolases, which digest complex carbohydrates, for example inulin. However, these two hydrolases are not necessary for B. ovatus to grow on inulin. Rather, other members of the microbiota, such as Bacteroides vulgatus, grow on the inulin breakdown products produced by B. ovatus. Bacteroides ovatus then uses products produced by B. vulgatus and both species flourish (Rakoff-Nahoum, Foster and Comstock 2016). Despite the rare documented cases of cooperation, most microbial interactions in the intestine are indeed competitive. The metabolic landscape is shaped by a few so-called keystone species or keystone taxa, which have a large impact on the rest of the community by degrading initial substrates and making these accessible to many other species. Keystone species may only be detectable in very low relative abundance; however their outsized effect on the global microbial composition makes them a ‘keystone’ of the microbiota (reviewed in Pereira and Berry 2017). One example of ‘keystone species’ is Akkermansia muciniphila, which degrades secreted host mucus into products that are then accessible to other bacteria, such as B. vulgatus (Png et al.2010). Hydrogen and sulphate/sulphite consuming species represent an example of a ‘keystone taxa’ due to their regulatory effect on the fermentative activity of other species (Carbonero et al.2012; Rey et al.2013). Yet, some of these taxa, for example Ruminococcus, have evolved to degrade mucin without giving other species access to the degradation products. The intramolecular transsialidase produced by R. gnavus releases 2,7-anhydro- Neu5Ac instead of sialic acid from mucin and other glycoproteins, a product that cannot be utilised by other species (Tailford et al.2015b; reviewed in Tailford et al.2015a). This nutritional limitation represents a strong barrier for the niche establishment of invading species. Box 2. The concept of the nutritional/dietary niche. A nutritional niche describes the nutrient sources which are available to, and usable by, a given set of organisms at a given time and space. The nutritional niche therefore defines if an organism is capable of establishing itself in a given place or not. The concept of the nutritional niche is a sub-definition of the ecological niche concept. The concept has been first proposed by Rolf Freter (Freter's nutritional niche theory) and has subsequently been adapted to take into account the instable flux of nutrients in given ecosystems, for example the intestine, and to take into account the co-existence of other microorganisms utilising the same nutrients either at different geographic locations in the intestine or at different time points. The theory also has been expanded to take into account the metabolic flexibility and mixed-substrate utilisation that most microorganisms exhibit. The process by which a given organism changes its ecological niche is known as ‘niche construction’. (See Pereira and Berry 2017, for an extended review of the topic.) Mucus layer The mucus layer forms a physical barrier to the microbiota, preventing direct interaction with the epithelium (reviewed in McGuckin et al.2011; Pelaseyed et al.2014). In the gut, the goblet cells are responsible for the secretion of the mucin MUC2, which forms a disulphide cross-linked network. This network is comprised of an inner layer, which is tightly attached to the epithelium and mainly impenetrable to bacteria, as well as a looser, outer layer. This outer layer harbours a specific community of bacteria, feeding on the mucus (Li et al.2015) and attaching to its o-glycosylated side-chains (Johansson, Larsson and Hansson 2011). Mucus production is dynamic and depends on the presence of bacterial stimuli, especially lipopolysaccharide and peptidoglycan as reported in an elegant study using germ-free mice (Petersson et al.2011). It has also been known for a long time that SCFAs are involved in mucus secretion from goblet cells into the gut lumen (Shimotoyodome et al.2000; Willemsen et al.2003). Homeostasis of mucus production is regulated by two complementary bacteria, Bacteroides thetaiotaomicron (stimulating mucus production through increased goblet cell differentiation) and F. prausnitzii (inhibiting goblet cell proliferation and mucus glycosylation; Wrzosek et al.2013). A preponderance of evidence shows that mucus composition and structure directly depends on the interplay between resident microbiota and epithelial tissues (Jakobsson et al.2015). Several studies have also linked reduced or aberrant O-glycosylation of mucin to the development of intestinal inflammation (Fu et al.2011; Larsson et al.2011; Sommer et al.2014). Other studies have shown the penetration of commensal bacteria into the inner mucus layer in the context of colitis (Johansson et al.2014). The mucus layer thickness is also related to nutrition, especially dietary intake, as it has been shown recently that low-fibre diets increase mucus-eroding bacteria communities, leading to greater access for pathogens at the epithelial surface and subsequently increased susceptibility to infection (Desai et al.2016). Furthermore, the attachment of the mucus layer to the epithelium is dependent on the microbiota. Meprin β, a host-derived zinc-dependent metalloprotease induced by the microbiota, is needed to detach the mucus in the small intestine and to subsequently release it into the intestinal lumen (Schütte et al.2014). A healthy mucus layer is therefore essential to protect the underlying epithelium from the dense bacterial population and to physically separate this population from immune cells in the underlying tissue in order to prevent exaggerated immune activation. Mucosal immune system Prokaryotic microbiota and the immune system It is now well established that the immune system relies on the microbiota for proper maturation (reviewed in Schnupf, Gaboriau-Routhiau and Cerf-Bensussan 2013; Spasova and Surh 2014; Turfkruyer and Verhasselt 2015; Donovan and Comstock 2016; Torow and Hornef 2017). Different bacterial species guide the development of specific cell subsets; for example, segmented filamentous bacteria induce the development of TH17 cells (Gaboriau-Routhiau et al.2009; Ivanov et al.2009; Goto et al.2014; reviewed in Ivanov 2017; Schnupf et al.2017), and Bacteroides fragilis has been shown to induce Treg proliferation and to act on the T(H)1/T(H)2 balance (Mazmanian et al.2005; Round and Mazmanian 2010). Faecalibacterium prausnitzii increases antigen-specific T cells and decreases the number of IFN-γ(+) T cells (Rossi et al.2016) and other Clostridia species induce different Treg subsets (Atarashi et al.2011). Additionally, short chained fatty acids derived from bacteria regulate Treg numbers in the intestine (Geuking et al.2011; Smith et al.2013; Furusawa, Obata and Hase 2015) and have a direct impact on overall IgA levels (Kim et al.2016; reviewed in Velasquez-Manoff 2015). Mucosal IgA plays a crucial role in gut homeostasis (Macpherson and Slack 2007; Peterson et al.2007; Pabst, Cerovic and Hornef 2016). It is known to protect the gut mucosa from the access of bacteria (immune exclusion) and to inhibit bacterial replication in the gut lumen (enchained growth; Moor et al.2017). Through these mechanisms, IgA regulates the composition and dynamics of the gut microbiota. IgA and the microbiota therefore regulate each other, leading to a delicate homeostatic balance between stimulation and control (reviewed in Macpherson and Slack 2007; Peterson et al.2007; Macpherson, Geuking and Slack 2012; Slack et al.2012; Pabst, Cerovic and Hornef 2016). The microbiota's effect on the mucosal immune system is not limited to regulatory T cells and IgA secretion. It also plays a major role in inducing production of antimicrobial peptides (AMPs), which concentrate at the interphase between the thick, tightly formed, mucus layer and the more dispersed outer layer (reviewed in Lehrer, Lichtenstein and Ganz 1993; Salzman et al.2010)(Meyer-Hoffert et al.2008; Vaishnava et al.2011). AMPs include the defensins, the Reg-protein family and several other proteins, which act directly on the bacteria by targeting the bacterial cell wall. In addition, other host factors with antimicrobial activity include lipocalin2/NGAL, which chelates bacterial siderophores involved in iron acquisition, as well as calprotectin, which leads to the chelation of two other essential trace elements, zinc and manganese. Eukaryotic microbiota and the immune system The intestinal microbiota is not only composed of bacteria, but also harbours a whole array of archae, viruses and eukaryotes. It has been shown that the presence of helminths, through their effect on the host immune system (Walsh et al.2009; Finlay, Walsh and Mills 2014; Finlay et al.2016; Ramanan et al.2016), can have profound effects on the microbiota composition in the intestine (Walk et al.2010; Broadhurst et al.2012; Giacomin et al.2015; McKenney et al.2015; Li et al.2016; Ramanan et al.2016; Guernier et al.2017; reviewed in Gause and Maizels 2016) as well as on disease susceptibility within the intestine (Reynolds et al.2017) and at distant sites, e.g. the respiratory system (McFarlane et al.2017). However, alterations in the microbiota composition due to the presence of helminths are not generalisable, as changes were observed in a first study of 51 persons infected with Trichuris trichiuria in Malaysia (Lee et al.2014), but no changes were found in a second study in 97 children from Ecuador (Cooper et al.2013) nor in 8 persons living in Australia infected experimentally by Necator americanus (Cantacessi et al.2014). Helminths have also been shown to attenuate the effect of intestinal bowel disease by restoring the number of goblet cells and preventing outgrowth of B. vulgatus in the context of Nod2−/− mice and associated intestinal inflammation (Ramanan et al.2016). For some of the observed immune changes, the helminth-induced changes seem to be mediated through the prokaryotic microbiota (Zaiss et al.2015). For other effects, they seem to be independent from the microbiota (Osborne et al.2014), highlighting the complex interplay found within the gut ecosystem. Very recently, a member of the eukaryome, Tritrichomonas musculis, was shown to activate the epithelial inflammasome and to induce protection against bacterial mucosal infection (Chudnovskiy et al.2016). Other protists, such as Giardia (Barash et al.2017) and possibly Blastocystis (Audebert et al.2016; Siegwald et al.2017), have also been shown to change the resident prokaryotic microbiota. However, data remain conflicting, pointing towards the fact that shifts in the microbiota through given eukaryotes might be strain specific. Due to incomplete databases, it is currently difficult to determine the exact strain of a eukaryotic organism by comparison against the database. More work in curating these databases is therefore needed to better appreciate the influence that specific eukaryotes might have on the prokaryotic microbiota. More work is also needed to unravel the triad of eukaryotes, prokaryotes and the immune system to better understand the mutual interactions that take place. Taken together, the microbiota and the development and proper function of the mucosal immune system are exquisitely intertwined. Thus, perturbations on either side of this ecosystem can deregulate the balance and leave the host open to infection or inflammatory diseases (Clarke 2014). FRIEND OR FOE: PATHOGENS FACING THE MICROBIOTA AND THE HOST As discussed, the host and its microbiota have set up a tightly regulated network of mutual control. Invading pathogens therefore have several barriers to overcome in order to establish themselves and cause disease (see Fig. 2). Figure 2. View largeDownload slide Mechanisms evolved by pathogen to combat the resident microbiota and the host. Pathogens have evolved several mechanisms to overcome the barrier imposed by the resident microbiota and the host. These include direct (bacteriocins, microcins, T6SS) and indirect (nutrient restriction) inhibition of members of the microbiota, the use of alternative energy sources as well as different mechanisms to overcome the barriers imposed by the hosts (mucinases, T3SS and other virulence factors acting on the host). Figure 2. View largeDownload slide Mechanisms evolved by pathogen to combat the resident microbiota and the host. Pathogens have evolved several mechanisms to overcome the barrier imposed by the resident microbiota and the host. These include direct (bacteriocins, microcins, T6SS) and indirect (nutrient restriction) inhibition of members of the microbiota, the use of alternative energy sources as well as different mechanisms to overcome the barriers imposed by the hosts (mucinases, T3SS and other virulence factors acting on the host). Within the last decade, much progress has been made in understanding the ‘ménage à trois’ of the microbiota, the host and pathogens. In this section, we will discuss the mechanisms that have evolved in pathogens to overcome the protective environment arising from homeostasis and summarise the complex interactions that take place between pathogens, the microbrobiota and their host. Combatting the resident microbiota by direct killing or by inhibition Small antibacterial toxins A number of small, mainly plasmid-encoded, antibacterial peptides, termed bacteriocins or microcins, are produced and secreted by a broad range of bacteria, including the Bifidobacteria (reviewed in Martinez et al.2013; Alvarez-Sieiro et al.2016), Lactobacilli (Collins et al.2017), Enterococci (Kommineni et al.2015) and many more. It has been demonstrated that bacteriocin production leads to a niche advantage for the bacteria expressing them (Riley and Wertz 2002; Kommineni et al.2015). Some of the bacteriocins and microcins have been shown to act against pathogenic strains (Kommineni et al.2015; Sassone-Corsi et al.2016b), thereby augmenting colonisation resistance and mediating resistance to invading pathogens. One bacteriocin subclass produced by Enterobacteriaceae and termed colicins are encoded by several pathogenic strains including S. typhimurium (Nedialkova et al.2014) and Shigella sonnei (Anderson et al.2017; Calcuttawala et al.2017). It has been shown recently that S. typhimurium expresses colicin Ib (ColIB), giving it a fitness advantage over the closely related E. coli, which blooms simultaneously in the gut upon Salmonella-induced intestinal inflammation. ColIb is regulated through the SOS-response and iron-limitation and upregulated in the context of inflammation (Nedialkova et al.2014). Therefore, the carriage and induced upregulation of colicins seems to be an evolutionary adaption of enteropathogens in order to have a selective advantage in the ecological niche they share with commensal E. coli in the inflamed gut. Type 6 secretion system (T6SS) T6SS are encoded by a substantial number of gram-negative pathogens, as diverse as Helicobacter hepaticus (Chow and Mazmanian 2010), S. typhimurium (Sana et al.2016), S. sonnei (Anderson et al.2017), Pseudomonas aeruginosa (Mougous et al.2006), enteroaggregative E. coli (Dudley et al.2006), Vibrio cholera (Pukatzki et al.2006) and B. fragilis (Chatzidaki-Livanis, Geva-Zatorsky and Comstock 2016; Hecht et al.2016) to name a few. Indeed, T6SS homologous have been described in up to 25% of all sequenced gram-negative genomes. While some bacteria use their T6SS to interfere with host processes (Brodmann et al.2017), alter the immune response upon infection (Chow and Mazmanian 2010; Aubert et al.2016; Hachani, Wood and Filloux 2016; Chen et al.2017), or modulate virulence (Bladergroen, Badelt and Spaink 2003; Parsons and Heffron 2005; Pukatzki et al.2006), growing evidence suggests that T6SS are also used to attack the resident microbiota and to confer the bacteria expressing them with a competitive advantage (Russell et al.2014; Unterweger et al.2014; Chatzidaki-Livanis, Geva-Zatorsky and Comstock 2016; Sana et al.2016; Anderson et al.2017; Bernal et al.2017; Kim et al.2017; Tian et al.2017). Indeed, Shigella, which encodes a T6SS had a selective advantage in colonisation of the mouse gut compared to S. flexneri or E. coli, a phenomenon which was shown to be largely due to the T6SS (Anderson et al.2017). In B. fragilis, this could also be observed at the strain level, where symbiotic, non-toxic B. fragilis was shown to outcompete a pathogenic strain in a T6SS-dependent manner (Chatzidaki-Livanis, Geva-Zatorsky and Comstock 2016; Hecht et al.2016). The T6SS is also implicated in other important tasks that confer the bacterium harbouring it a selective advantage over the resident microbiota. These include iron acquisition (Lin et al.2017) as well as different mechanisms to handle oxidative stress induced by the host (Wang et al.2015; Si et al.2017; Wan et al.2017). It has been shown recently in marine bacteria that T6SS are horizontally shared between different species (Salomon et al.2015). Furthermore, in V. cholera, the T6SS was shown to be able to foster horizontal gene transfer (Borgeaud et al.2015). Clearly, the last few years have seen strong advancements in the understanding of T6SS contributions to microbial life cycles (Filloux 2013), while more work is needed in order to fully understand the full scope of T6SS functions. Exploiting nutrients to gain a selective advantage over the resident microbiota The most limiting nutrients in the gut are micronutrients, especially iron, as well as general energy sources, such as carbohydrates. Bacterial pathogens have evolved a number of strategies to selectively acquire nutrients over the resident microbiota in the race for these resources. Iron scavenging and use of specific siderophores The host has evolved sophisticated strategies termed ‘nutritional immunity’ to limit the amount of available iron that the microbiota has access to (reviewed in Cassat and Skaar 2013; Kortman et al.2014). Bacteria have responded by maximising their ability to uptake iron through the secretion of iron-scavenging molecules, termed siderophores, which give them a selective advantage over strains lacking the scavenging capability (Niehus et al.2017). Lipocalin2 (NGAL in humans) is a potent antimicrobial factor secreted by the host whose function is to sequester iron bound siderophores (Flo et al.2004). Bacteria do not only have to compete with the host for iron, but also with the resident members of the microbiota. Indeed, many microbes encode species-specific siderophores that require specific re-uptake machinery to bind and import the iron-siderophore complex (reviewed in Miethke and Marahiel 2007). Many enteropathogens have also evolved specific strategies to more efficiently scavenge any available iron. Salmonella typhimurium for example secretes Salmochelin, which is not recognised by lipocalin2/NGAL (Raffatellu et al.2009). Using Salmochelin, S. typhimurium is able to obtain enough iron to overcome iron-restriction, leading to a selective growth advantage over neighbouring bacteria. This proves especially important in the context of the inflamed intestine where Salmonella thrives amidst large quantities of Lipocalin2 secreted mainly by recruited neutrophils. Use of alternative energy sources Salmonella typhimurium is a useful model pathogen to illustrate the basic mechanisms that pathogens employ to bypass the metabolic environment established by the microbiota. Initial replication of Salmonella in the yet undisturbed gut depends on hydrogen gas, an important intermediate in microbiota metabolism (Maier et al.2013). Once Salmonella has invaded the gut mucosa and induced inflammation, other energy sources become available and are exploited by the pathogen. One of these is the aerobic and anaerobic respiration of 1, 2-propanediol generated by the resident microbiota (demonstrated in mono-associated mice using B. fragilis and B. thetaiotaomicron) through fermentation of fucose or rhamnose in the inflamed intestine (Faber et al.2017). Salmonella can also thrive by oxidative respiration on succinate, which is released by the resident microbiota (Spiga et al.2017). As an alternative energy source, Salmonella is also capable of using galactarate and glucarate, generated by the microbiota after antibiotic treatment. This metabolic versatility, especially in an oxidative environment as is found in the inflamed intestine, is likely the basis of the long known condition of antibiotic-mediated Salmonella expansion (Faber et al.2016). Another nutrient source is siacylic acid, liberated from the breakdown of sialyated mucins by B. thetaiotaomicron and other microbiota members. Bacteroides thetaiotaomicron secretes a sialidase but lacks the ability to use the freed siacylic acid itself. In turn, this acid is metabolised by C. difficile and S. typhimurium as an alternative nutrient source giving them a selective nutritional advantage over neighbouring bacteria (Ng et al.2013; Huang et al.2015). Differential energy utilisation has also been recently shown in some E. coli species, which use microbiota-derived formate as an alternative energy source to increase their advantage over other resident species (Hughes et al.2017). Several enteropathogens, including Citrobacter rodentium, C. jejuni and S. typhimurium, induce acute intestinal inflammation through their virulence factors (reviewed in Winter et al.2010a). The inflammation provides these pathogens with an advantage over the resident microbiota by transforming the intestine into an aerobic environment. Niche creation can be exemplified by the widely studied enteropathogen S. typhimurium (reviewed in Winter, Lopez and Bäumler 2013a; Winter and Bäumler 2014a). It is likely that similar mechanisms that have evolved in Salmonella have also evolved in other enteropathogens, for example E. coli and Shigella spp. and together contribute to the ‘enterobacterial bloom’ that is observed in the inflamed gut (Lupp et al.2007; Stecher et al.2010; reviewed in Winter and Bäumler 2014a). Inflammation leads to the production of respiratory electron acceptors, for example nitrogen species and reactive oxygen species. These products are converted in the intestine to nitrate. Nitrate can be used by Salmonella spp., E. coli and potentially other facultative anaerobe members of the Enterobacteriaceae as an alternative electron acceptor, giving them a selective advantage over other resident bacteria, which rely mainly on anaerobic fermentation of carbohydrates (Lopez et al.2012; Spees et al.2013; Winter et al. 2013a). Salmonella has also been shown to use other electron acceptors, for example S-oxides, ethanolamine or tetrathionate, which are present in larger amounts in the inflamed intestine (Winter et al.2010b; Thiennimitr et al.2011). In a recent study, it could be shown that Salmonella T3SS activation leads to a depletion of Clostridium species, which in turn leads to a decrease in butyrate levels. Butyrate is the most important energy source of colonocytes and butyrate oxidation to carbon dioxide leads to the consumption of local oxygen and the generation of an anaerobic environment. The lack of butyrate therefore increases tissue oxygenation, generating a favourable niche for Salmonella's aerobic expansion in the gut lumen (Rivera-Chávez et al.2016b). Under physiological conditions, the microbiota induces expression of PPARγ, resulting in an increase in β-oxidation of the colonocytes and hence an anoxic environment. In the context of antibiotic treatment, PPARγ-induction is inhibited and the colonocytes switch to anaerobic glucose oxidation. This then leads to increased availability of nitrate and allows for aerobic expansion of Enterobacteriaceae (Byndloss et al.2017). Inflammation also leads to the outgrowth of other bacterial species, for example B. vulgatus (Huang et al.2015). Through its sialidase activity, B. vulgatus releases sialic acid from the intestinal tissue, supporting the growth of E. coli. Bacteroides vulgatus thereby contributes to the occurrence of the ‘enterobacterial blooms’ observed during inflammation. Conversely, enterobacterial blooms during infection are abrogated when sialidase inhibitors are administered (Huang et al.2015). Gut inflammation can also boost horizontal gene transfer, either between pathogenic and commensal enteropathogens or between dense populations of enteropathogens in the context of the so-called enterobacterial booms (see text above). This has been shown for the transfer of a colicin-carrying plasmid p2 (Stecher et al.2012) as well as of temperate phages (Diard et al.2017). Enterobacterial blooms can therefore contribute to pathogen evolution of some species. Virulence genes Once in contact with the host, pathogens have developed different strategies to influence the host and exploit it to their own benefit. This is mainly achieved through the so-called virulence factors. First and foremost, pathogens express ‘classical’ virulence factors, for example toxins and the T3SS and their associated effector proteins. The function and specific role of these virulence factors have been discussed in detail elsewhere (Puhar and Sansonetti 2014; Qiu and Luo 2017; and many others for specific pathogens). The expression of these virulence factors can be constitutive. However, with the immense fitness cost virulence gene expression imparts on the pathogen, virulence gene expression is often regulated by environmental cues. This means that the bacterium only expresses the virulence genes once it is in close contact with the host and at the right location along the gastrointestinal tract. Induction of pathogen virulence genes by cues from the host Different host cues allow invading pathogens to pinpoint their position within their host and to regulate virulence genes only once the appropriate location has been reached. Host cues for virulence regulation include bile acids (Antunes et al.2012; Brotcke Zumsteg et al.2014; Eade et al.2016), pH (Behari, Stagon and Calderwood 2001), temperature (Elhadad et al.2015; Nuss et al.2015; Fraser and Brown 2017), nutrient availability (reviewed in Porcheron, Schouler and Dozois 2016), and oxygen levels (Marteyn et al.2010; Fraser and Brown 2017; reviewed in Marteyn et al.2011; Marteyn, Gazi and Sansonetti 2012). Oxygen levels are dynamic within the intestine and even within the anoxic colon an oxygen tension gradient is present in close proximity to the epithelial surface. Shigella flexneri has adapted to this gradient by repressing its T3SS in response to reduced oxygen levels encountered in the lumen of the intestine. The key outcome is to conserve metabolic resources in this energy and nutrient depleted environment. This regulation has the added benefit of more closely aligning the expression of virulence factors to the site of infection at the epithelial layer, where they are actually used. The suppression of the T3SS system is mediated by the oxygen sensitive regulator gene fnr. When oxygen pressure increases near the epithelium, the anaerobic block on the master regulators of the T3SS, spa32 and spa33 is released and the genes of the T3SS can be expressed (Marteyn et al.2010). Another example of regulated virulence is the bile salt-mediated activation of virulence in V. cholerae. It was recently shown through a series of elegant in vitro experiments in a tissue model of infection that virulence genes of V. cholerae are induced by the bile salt taurocholate, glyocholate and cholate, but not the deconjugated deoxycholate or chenodeoxycholate. This virulence activation is mediated through the dimerisation of the transcription factor TcpP by disulphide bond formation. Consequently, a V. cholerae strain mutated in the respective cysteine is unable to respond to the bile salts, leading to a competitive disadvantage compared to the wild-type strain in an infant mouse model of colonisation. This colonisation difference was abolished when a bile-salt sequestering resine, cholestyramine, was co-administered, confirming the crucial role of bile acids in the observed colonisation defect (Yang et al.2013). A third example is the regulation of virulence genes in Enterotoxigenic E. coli (ETEC) and its close relative, the mouse pathogen C. rodentium in the intestine. A recent study has shown that the two neurotransmitters epinephrine and norepinephrine that are produced by the endocrine cells localised in the intestine are needed for the full expression of virulence/colonisation genes (Moreira et al.2016). Together, these observations show that pathogens have evolved varied and complex mechanisms to tightly regulate their virulence attributes. This helps pathogens avoid unnecessary energetic costs that may lead to a loss of fitness in the highly competitive gut environment (see Diard and Hardt 2017, for a recent review on the evolution of bacterial virulence). Induction of pathogens's virulence genes by members of the microbiota We previously discussed the cues from the host that lead to the induction of virulence genes expression in the invading pathogens. Beside this host-mediated induction, some virulence genes are also controlled by sensing metabolites derived from the microbiota, for example SCFAs (butyrate, actetate, lactate and propionate). A recent study has shown that microbiota-derived SCFAs modulate the expression of virulence genes in C. jejuni. The authors discovered that the gradient of SCFAs butyrate, acetate, and lactate along the intestinal tract guide expression of genes involved in virulence and commensalism of C. jejuni. Lactate, which is abundant in the upper intestinal tract, suppresses production of C. jejuni virulence genes, while acetate and butyrate, two SCFAs that are mostly produced in the lower intestinal tract, activate virulence pathways (Luethy et al.2017). Expression of the Salmonella pathogenicity island 1 (SPI-1) is inhibited in the presence of propionate, an SCFA that is produced mainly by Lactobacilli and Bifidobacteria and is more abundant in the upper gastrointestinal tract. Propionate acts through posttranslational modification on HilD, the master regulator of the Salmonella SPI-1 (Hung et al.2013). This inhibition ensures that the coordinated expression of SPI-1 genes starts only in the distal small intestine, the main site of Salmonella infection. Another example of microbiota-mediated virulence gene expression is the enhancement of enterohemorraghic E. coli (EHEC) T3SS by B. thetaiotaomicron. Bacteroides thetaiotaomicron is an abundant member of the gut microbiota metabolising complex polysaccharides into monosaccharides that can be further processed by a number of other bacteria. The presence of B. thetaiotaomicron leads to a local increase in the levels of succinate, which is sensed by the transcription factor Cra of EHEC. Cra activation leads to an increase in the expression of the genes encoding EHECs T3SS while leaving the general growth of the pathogen unaffected (Curtis et al.2014). Induction of AMP's by pathogens to inhibit microbiota competition Some pathogens have evolved mechanisms to exploit the host's own antibacterial defences. By developing countermeasures against host AMPs, pathogens can rely on the host response to combat the resident microbiota and gain a selective advantage. Salmonella typhimurium for example uses an alternative siderophore (Salmochelin, described above), which is resistant to chelation by Lipocalin2. Salmonella has also evolved strategies to resist against calprotectin-induced sequestration of zinc and manganese (Liu et al.2012), giving Salmonella a selective advantage over the majority of microbiota members that do not have the necessary tools to survive in the inflamed gut. Salmonella infection induces the cytokine IL-22, which in turn activates AMPs (Behnsen et al.2014). One of the proteins induced is the AMP Reg3beta. Previously, Stelter et al. (2011) and Miki, Holst and Hardt 2012 showed that the induction of this AMP inhibits the competing microbiota, while having no effect on the resistant S. typhimurium. In a new study, Miki and collaborators could show that Reg3beta extends gut colonisation by S. typhimurium through the prolonged induction of a pro-inflammatory environment and changes to the microbiota, especially an inhibition of Bacteroides species. The alteration of the microbiota also leads to profound changes in the metabolic landscape with metabolites of Vitamin B6 being the most affected. The authors could show that the re-insertion of Bacteroides species or supplementation of Vitamin B6 alone was able to accelerate clearance of Salmonella from infected mice (Miki et al.2017). A recent study in Ixodes scacpularis ticks showed a similar mechanism whereby Anaplasma phagocytophilum infection induced Ixodes anti-freeze glycoprotein (Iafgp), which alters biofilm formation in the Ixodes gut to destabilise the resident microbiota and facilitate niche construction of A. phagocytophilum. It is likely that many pathogens have evolved similar mechanisms to take the advantage of host defence mechanisms to facilitate niche construction and induce a host-derived selective advantage over the resident microbiota. Evolutionary adaptions of pathogens to overcome homeostasis: penetrating the mucus layer As described previously, the mucus layer constitutes a thick, protective layer between the gut lumen and the epithelium. To get access to the epithelium, pathogens have evolved strategies to penetrate the mucus layer and enter the underlying epithelium. Porphyromonas gingivalis, a pathogen found mostly in the oral cavity, secretes a cysteine protease (RgpB), which leads to Muc2 cleavage (van der Post et al.2013). Mucinases also play an important role in the colonisation and fitness of pathogenic E. coli (Valeri et al.2015), an E. coli strain associated with Crohn's disease (Gibold et al.2016), and also eukaryotic pathogens such as Candida albicans (Colina et al.1996) or Entamoeba histolytica (Lidell et al.2006). It is likely that other enteropathogens also express mucinases to gain access to the underlying epithelium although more research is needed to fully address the scope of mucinase secretion and usage by pathogens. Mechanisms established by the microbiota to clear off invading pathogen after infection The microbiota not only plays an important role in preventing the colonisation of pathogens, but also in the pathogen clearing from the gut upon resolution of the inflammation. The mechanisms underlying this process differ from those governing colonisation resistance as the mucosa and the microbiota have both been affected and therefore need to return to homeostasis (Endt et al.2010). In the case of S. typhimurium infection it was shown that recovery is mainly mediated by the microbiota and was largely independent of the IgA pool (Endt et al.2010). Mechanistic insights on the underlying causes of clearance were elucidated in a study on V. cholera infection, showing an increase in Ruminococcus obeum upon infection of mice with the pathogen. The same was also observed in a cohort of infected humans from Bangladesh recovering from the disease. In elegant mouse studies, the authors showed that R. obeum, through the expression of the luxS gene (autoinducer-2 synthase), promotes quorum sensing-mediated restriction of virulence gene expression in V. cholerae, leading to a decrease in host symptoms (Hsiao et al.2014). DYSBIOSIS: TOWARDS A NEW INTERPRETATION OF KOCH'S POSTULATES It is now common knowledge that the gut is a complex ecosystem with different interacting entities and that infections must be understood in this context rather than isolated as a pathogen and a host. In consequence, for these complex diseases, neither Koch's postulates (a pathogen, a disease) nor the molecular Koch's postulates as proposed by Stanley Falkow (a virulence gene, a disease; Falkow 1988) are sufficient. In a very recent review by Neville and collaborators, a third interpretation of Koch's postulates, the commensal Koch's postulates, was proposed (a beneficial microbe, an ameliorated disease state). The authors infer a new framework for establishing causation in microbiome studies where they use the commensal Koch's postulates to test if a given microorganism is able to ameliorate a disease state in a reproducible manner (Neville, Forster and Lawley 2017). As in the original Koch's postulates, they propose that for inferring causation, the ‘beneficial’ commensals need to be isolated in pure cultures before they are re-introduced and tested in a host for their capacity to mitigate disease. We propose yet another interpretation of Koch’ postulates, which we have termed ‘ecological Koch's postulates (a gut ecosystem state, a disease). Underlying these postulates is the fact that the gut harbours a full ecosystem, rather than an isolated bacterium or pathogen. This means that rather than an isolated microorganism or group of microorganisms, a whole ecosystem, including the microbiota, the genetic make-up of the host as well as nutrition, age, etc., form an entity, which can ultimately lead to disease (see Fig. 3 and Box 3). Figure 3. View largeDownload slide The evolution of Koch's postulates. In recent years, the original Koch's postulates (‘a pathogen, a disease’) have been extended to the molecular Koch's postulates (Stanley Falkow, ‘a virulence genes, a disease’) and here to the ecological Koch's postulates (‘a dysbiosis, a disease’). Figure 3. View largeDownload slide The evolution of Koch's postulates. In recent years, the original Koch's postulates (‘a pathogen, a disease’) have been extended to the molecular Koch's postulates (Stanley Falkow, ‘a virulence genes, a disease’) and here to the ecological Koch's postulates (‘a dysbiosis, a disease’). Box 3. Postulates for defining a disease-promoting ecosystem (dysbiosis). Ecological Koch's postulates The dysbiotic microbiota is found in similar composition/with similar characteristics in all affected individuals. The dysbiotic microbiota can be retrieved from the affected host. Gavaging of germ-free hosts with this retrieved microbiota leads, in combination with a similar environment (ex. genetic make-up of the host, nutrition, age), to similar symptoms as in the affected individual. The dysbiotic microbiota composition remains fairly stable in the newly affected host. Original Koch's postulates The microorganism must be present in all diseased individuals. The microorganism must be isolated from the diseased host and be grown in a pure culture. The re-inoculation of a naïve host with this pure culture must lead to the same disease as in the original host. The microorganism must be recovered from the newly diseased host. The ecological Koch's postulates are based on two major observations, both pointing towards the fact that the clear distinction between a pathogen and a commensal are probably too simple of a model to explain complex disease states. Not every person infected with a ‘pathogen’ will manifest disease. Therefore, host susceptibility not only from a genetic point of view, but also from the resident microbiota, the nutrition, earlier infections, or other insults to the microbiota, plays as much of a role in the manifestation of disease as does the presence of given virulence factors in an aggressing pathogen. The pathogens not only need to be present and harbour the virulence genes, but they also need to express these genes and be able to establish a niche for themselves within the competitive environment of the already established microbial community in order to replicate and then cause disease. In the last years, several gastrointestinal diseases have emerged, which are not associated with an overt pathogen, but where the microbial community as a whole seems to mediate the disease. Examples are intestinal bowel disease, colorectal cancer, obesity, and different states of malnutrition. Indeed, depending on the microbial community pathogens find themselves in, bacteria, which normally do behave as commensals may become invasive and cause disease. For all of these diseases, a decrease in the composition complexity of the microbiota leads to dysbiosis and an oxidation of the gut environment as well as an increase in aeortolerant species such as Enterobacteriaceae (Rivera-Chávez, Lopez and Bäumler 2017). These disturbances in the ecosystem lead to a lowered resilience and increased susceptibility to pathogens and other, normally commensal, bacteria with potential harmful properties (often called pathobionts). Indeed, these diseases are characterised by the fact that the wrong bacteria are in wrong proportions, in wrong ‘company’ (Huang et al.2015) or in the wrong ‘place’ (Brown et al.2015; Tomas et al.2016). The presence of commensal bacteria near the epithelial surface has been put in relation with the breakdown of gut homeostasis and emergence of pathological states in the context of environmental enteropathy (Brown et al.2015) or in a pre-diabetic state (Tomas et al.2016). In the ecological Koch's postulates, a dysbiotic community, including or not ‘classical pathogens’ or pathobionts therefore represents a disease. The entity of transmission is the complete dysbiotic microbiota rather than a pathogen (Koch's postulates), a virulence gene (molecular Koch's postulates) or a commensal (commensal Koch's postulates). In accordance to the other Koch's postulates, the ecological Koch's postulates are proven through the fact that a given entity (here the dysbiotic microbiota) from a diseased individual can provoke disease in a formerly healthy individual. To prove this hypothesis, one hence has to transmit the microbiota from a diseased individual into a germfree individual/mouse and this transplanted individual subsequently has to develop the signs of the disease. This transfer can either be performed in (I) ‘standard’ conditions, using a ‘wild-type, normally fed’ germ-free host (showing a direct effect of the microbiota on disease), or, else, in (II) a ‘pre-fragilised’ host, as an example in a mouse exhibiting a mutation in a given gene or eating a specific chow. In syndromes, which do need a pre-fragilised host, the dysbiotic microbiota contributes to disease, without however being the only cause for it. As stated earlier, several inflammatory, gastrointestinal diseases can be explained through the ecological Koch's postulates, including obesity. Indeed, if a microbiota from obese mice is transplanted into lean mice, the transplanted mice showed increased fat deposition (Turnbaugh et al.2006; Ridaura et al.2013). The same could also be proven for kwashiorkor, the oedematous form of acute undernutrition (Smith et al.2013) as well as for environmental enteropathy (Brown et al.2015). On the other hand, it is well known that mutations in nod2 facilitate and support the onset of IBD (Cho 2001). Therefore, to prove the contribution of the microbiota in IBD, a susceptible host, mutated for nod2, should be transplanted with the dysbiotic microbiota and this transplanted microbiota should worsen the disease state. An instructive example of a ‘pathological dysbiosis’ and hence a disease following the ecological Koch's postulates is chronic and acute malnutrition coupled to associated environmental enteropathy. Several reports have shown evidence that children suffering from one of these two syndromes have an altered colonic microbiota (Smith et al.2013; Subramanian et al.2014; Gough et al.2015; Blanton et al.2016a, 2016b) and increased abundance of asymptomatic pathogen carriage, including enteroaggregative E. coli (Havt et al.2017), Campylobacter spp. and Giardia spp. (Platts-Mills et al.2017). Furthermore, a recent study sequencing cultured microbes from two Bangladeshi children suffering or not of undernutrition showed that the B. fragilis strain found in the undernourished child is enterotoxic, while the strains found within the normally nourished child were not. When transplanting the native community into germfree mice and infecting with the enterotoxigenic B. fragilis strain, the authors could show that the enterotoxigenic strain causally led to malnutrition and associated pathophysiological disturbances only in its native community, but not when administered to mice harbouring the microbiota of the healthy child (Wagner et al.2016). These observations put forward the hypotheses that (I) even subclinical infections with enteropathogens can have negative effects on gut health and that (II) pathogens or pathobionts, depending on the community they dwell in, might have negative effects on host homeostasis or not. This indeed supports the concept of the ‘ecological Koch's postulates’, stating that the whole ecosystem, rather than an isolated element contributes to morbidity. Overall, we are only beginning to understand the complex relationships and interactions within the gut ecosystem and more research is needed in order to elucidate the origin and pathophysiological effect of the different dysbiotic communities and to understand the crosstalk they have between each other as well as with the host. CONCLUSION Infection biology has been moving in the last decades from the original Koch's postulates looking at pathogens, to molecular Koch's postulates looking at virulence factors, to the newly proposed ecological Koch's postulates looking at dysbiosis. Indeed, infection biology has shifted towards an integrated approach of systems biology, ecology and evolution. This increasing complexity makes it more and more difficult to untangle the causative effects of disease states and asks for imaginative and sophisticated designs of experiments to explain the underlying pathophysiological mechanisms. Particularly, experiments need to take into account the physiological and pathophysiological state of the infected host, for example the microbiota and the exact nutrition the model animals are receiving. In recent years, several initiatives have been launched to standardise the microbiota of model animals (Brugiroux et al.2016) or at least to meticulously report, not only the exact strain of pathogen used and the genetics of the mouse model, but also the microbiota composition, as well as the food composition of the animal models used (Ma et al.2012; Macpherson and McCoy 2015). This will prove indispensable in the future in order to compare different studies and explain the pathophysiological mechanisms underlying the complex interplay between pathogens, the microbiota, and their host. To date, we are only at the beginning of understanding the interactions within these ecosystems, the perturbations, which can be induced, and their effect on pathogen susceptibility and disease. The widely available techniques of sequencing, especially of metagenomics, metatranscriptomics and metabolomics, will prove essential in this endeavour. Special attention should also be paid to not forget that the microbiota harbours other organisms than prokaryotes, first and foremost viruses (including phages and prophages), and eukaryotes. Only an integrated view of the gut ecosystem, including the host, the pro- and eukaryome and virome as well as the pathogens will allow us to move forward in our understanding of which mechanisms are governing infection. The scientific community is on the verge of experiencing another revolution in understanding the complex network of gut interactions. This will surely open the way for more targeted and personalised interventions to infectious diseases based on interference or corrections to the misbalances in the gut ecosystem and restoration of gut homeostasis. This could include siderophore-based immunisation strategies (Mike et al.2016; Sassone-Corsi et al.2016a), probiotic bacteria (e.g. E. coli strain Nissle) using similar iron-scavenging mechanisms than the invading pathogen (Deriu et al.2013), probiotic strains consuming H2 and hence restricting the use of this energy source for invading pathogens (Maier et al.2013), the development of probiotic strains expressing bacteriocins or microcins targeting the pathogen (Kommineni et al.2015; Hegarty et al.2016; Sassone-Corsi et al.2016b), expressing iron-sequestering mechanisms to inhibit invading pathogens (Vazquez-Gutierrez et al.2016), siacylidase inhibitors (Huang et al.2015) or inhibitors of anaerobic respiration (Winter and Bäumler 2014b) (see Table 1). There are certainly many other possible intervention strategies yet to be discovered. The generated knowledge will therefore prove very important in paving the way to propose other intervention strategies, which do not rely on antibiotics. In a world where antibiotic resistance is on a constant rise this aspect will be of utmost importance. Table 1. Possible new intervention strategies intervening with the gut ecosystem to target diseases related to dysbioses-induced enteropathogenic blooms. Intervention strategy Evidence for intervention References Siderophore-based immunisation strategies Mice immunised mice with siderophores conjugated to an immunogenic carrier protein were able to elicit a potent immune response and to protect against urinary tract infections. Mike et al. (2016) and Sassone-Corsi et al. (2016a) Mice immunised with a cholera toxin β-siderophore conjugate show a potent immune response and are able to protect against infection with Salmonella typhimurium. Probiotic strains with similar or more efficient iron-sequestering mechanisms inhibiting invading pathogens Oral gavage with Escherichia coli strain Nissle 1917 reduces S. typhimurium colonisation in mouse models of acute colitis or chronic persistent infection. The observed probiotic activity depends on the iron-sequestering mechanisms of E. coli Nissle, which is highly similar to the one found in Salmonella typhimurium. Deriu et al. (2013) and Vazquez-Gutierrez et al. (2016) The two bifidobacterial strains Bifidobacterium pseudolongum PV8-2 (Bp PV8-2) and Bifidobacterium kashiwanohense PV20-2 (Bk PV20-2) are able to inhibit growth of S. typhimurium and E. coli O157:H45 (EHEC) in in vitro co-culture experiments and are able to displace the pathogens on mucus-producing HT29-MTX cell lines. Probiotic strains consuming H2 to prevent initial ecosystem invasion In a non-inflamed intestine, S. typhimurium relies on H2 metabolisms for invasion. Introducing H2-consuming bacteria into the microbiota reduces hyb-dependent S. typhimurium growth. Maier et al. (2013) Probiotic strains producing butyrate Oral gavage of mice with tributyrin reduces growth of S. typhimurium in the inflamed intestine. Rivera-Chávez et al. (2016b) Probiotic strains expressing bacteriocins or microcins targeting the pathogen Colonisation of mice with a bacteriocin-carrying E. faecalis strain defective for conjugation leads to clearance of vancomycin resistant enterococci. Kommineni et al. (2015), Hegarty et al. (2016) and Sassone-Corsi et al. (2016b) Microcin-producing E. coli Nissle is able to limit the growth of commensal E. coli, adherent–invasive E. coli and Salmonella enterica in the inflamed intestine. Siacylidase inhibitors Oral administration of sialidase inhibitors decreases outgrowth of E. coli as well as the severity of colitis in a mouse model. (Huang et al. (2015) Inhibitors of aerobic respiration Aerobic respiration is used by Salmonella spp and other Enterobacteriaceae to thrive in the inflamed intestine. Winter and Bäumler (2014b) Sustaining PPAR-γ signalling PPAR-γ signalling in the homeostatic intestine leads to β-oxidation in the colonocytes and hence an anoxic environment limiting nitrate availability and outgrowth of Enterobacteriaceae Byndloss et al. (2017) Intervention strategy Evidence for intervention References Siderophore-based immunisation strategies Mice immunised mice with siderophores conjugated to an immunogenic carrier protein were able to elicit a potent immune response and to protect against urinary tract infections. Mike et al. (2016) and Sassone-Corsi et al. (2016a) Mice immunised with a cholera toxin β-siderophore conjugate show a potent immune response and are able to protect against infection with Salmonella typhimurium. Probiotic strains with similar or more efficient iron-sequestering mechanisms inhibiting invading pathogens Oral gavage with Escherichia coli strain Nissle 1917 reduces S. typhimurium colonisation in mouse models of acute colitis or chronic persistent infection. The observed probiotic activity depends on the iron-sequestering mechanisms of E. coli Nissle, which is highly similar to the one found in Salmonella typhimurium. Deriu et al. (2013) and Vazquez-Gutierrez et al. (2016) The two bifidobacterial strains Bifidobacterium pseudolongum PV8-2 (Bp PV8-2) and Bifidobacterium kashiwanohense PV20-2 (Bk PV20-2) are able to inhibit growth of S. typhimurium and E. coli O157:H45 (EHEC) in in vitro co-culture experiments and are able to displace the pathogens on mucus-producing HT29-MTX cell lines. Probiotic strains consuming H2 to prevent initial ecosystem invasion In a non-inflamed intestine, S. typhimurium relies on H2 metabolisms for invasion. Introducing H2-consuming bacteria into the microbiota reduces hyb-dependent S. typhimurium growth. Maier et al. (2013) Probiotic strains producing butyrate Oral gavage of mice with tributyrin reduces growth of S. typhimurium in the inflamed intestine. Rivera-Chávez et al. (2016b) Probiotic strains expressing bacteriocins or microcins targeting the pathogen Colonisation of mice with a bacteriocin-carrying E. faecalis strain defective for conjugation leads to clearance of vancomycin resistant enterococci. Kommineni et al. (2015), Hegarty et al. (2016) and Sassone-Corsi et al. (2016b) Microcin-producing E. coli Nissle is able to limit the growth of commensal E. coli, adherent–invasive E. coli and Salmonella enterica in the inflamed intestine. Siacylidase inhibitors Oral administration of sialidase inhibitors decreases outgrowth of E. coli as well as the severity of colitis in a mouse model. (Huang et al. (2015) Inhibitors of aerobic respiration Aerobic respiration is used by Salmonella spp and other Enterobacteriaceae to thrive in the inflamed intestine. Winter and Bäumler (2014b) Sustaining PPAR-γ signalling PPAR-γ signalling in the homeostatic intestine leads to β-oxidation in the colonocytes and hence an anoxic environment limiting nitrate availability and outgrowth of Enterobacteriaceae Byndloss et al. (2017) View Large Table 1. Possible new intervention strategies intervening with the gut ecosystem to target diseases related to dysbioses-induced enteropathogenic blooms. Intervention strategy Evidence for intervention References Siderophore-based immunisation strategies Mice immunised mice with siderophores conjugated to an immunogenic carrier protein were able to elicit a potent immune response and to protect against urinary tract infections. Mike et al. (2016) and Sassone-Corsi et al. (2016a) Mice immunised with a cholera toxin β-siderophore conjugate show a potent immune response and are able to protect against infection with Salmonella typhimurium. Probiotic strains with similar or more efficient iron-sequestering mechanisms inhibiting invading pathogens Oral gavage with Escherichia coli strain Nissle 1917 reduces S. typhimurium colonisation in mouse models of acute colitis or chronic persistent infection. The observed probiotic activity depends on the iron-sequestering mechanisms of E. coli Nissle, which is highly similar to the one found in Salmonella typhimurium. Deriu et al. (2013) and Vazquez-Gutierrez et al. (2016) The two bifidobacterial strains Bifidobacterium pseudolongum PV8-2 (Bp PV8-2) and Bifidobacterium kashiwanohense PV20-2 (Bk PV20-2) are able to inhibit growth of S. typhimurium and E. coli O157:H45 (EHEC) in in vitro co-culture experiments and are able to displace the pathogens on mucus-producing HT29-MTX cell lines. Probiotic strains consuming H2 to prevent initial ecosystem invasion In a non-inflamed intestine, S. typhimurium relies on H2 metabolisms for invasion. Introducing H2-consuming bacteria into the microbiota reduces hyb-dependent S. typhimurium growth. Maier et al. (2013) Probiotic strains producing butyrate Oral gavage of mice with tributyrin reduces growth of S. typhimurium in the inflamed intestine. Rivera-Chávez et al. (2016b) Probiotic strains expressing bacteriocins or microcins targeting the pathogen Colonisation of mice with a bacteriocin-carrying E. faecalis strain defective for conjugation leads to clearance of vancomycin resistant enterococci. Kommineni et al. (2015), Hegarty et al. (2016) and Sassone-Corsi et al. (2016b) Microcin-producing E. coli Nissle is able to limit the growth of commensal E. coli, adherent–invasive E. coli and Salmonella enterica in the inflamed intestine. Siacylidase inhibitors Oral administration of sialidase inhibitors decreases outgrowth of E. coli as well as the severity of colitis in a mouse model. (Huang et al. (2015) Inhibitors of aerobic respiration Aerobic respiration is used by Salmonella spp and other Enterobacteriaceae to thrive in the inflamed intestine. Winter and Bäumler (2014b) Sustaining PPAR-γ signalling PPAR-γ signalling in the homeostatic intestine leads to β-oxidation in the colonocytes and hence an anoxic environment limiting nitrate availability and outgrowth of Enterobacteriaceae Byndloss et al. (2017) Intervention strategy Evidence for intervention References Siderophore-based immunisation strategies Mice immunised mice with siderophores conjugated to an immunogenic carrier protein were able to elicit a potent immune response and to protect against urinary tract infections. Mike et al. (2016) and Sassone-Corsi et al. (2016a) Mice immunised with a cholera toxin β-siderophore conjugate show a potent immune response and are able to protect against infection with Salmonella typhimurium. Probiotic strains with similar or more efficient iron-sequestering mechanisms inhibiting invading pathogens Oral gavage with Escherichia coli strain Nissle 1917 reduces S. typhimurium colonisation in mouse models of acute colitis or chronic persistent infection. The observed probiotic activity depends on the iron-sequestering mechanisms of E. coli Nissle, which is highly similar to the one found in Salmonella typhimurium. Deriu et al. (2013) and Vazquez-Gutierrez et al. (2016) The two bifidobacterial strains Bifidobacterium pseudolongum PV8-2 (Bp PV8-2) and Bifidobacterium kashiwanohense PV20-2 (Bk PV20-2) are able to inhibit growth of S. typhimurium and E. coli O157:H45 (EHEC) in in vitro co-culture experiments and are able to displace the pathogens on mucus-producing HT29-MTX cell lines. Probiotic strains consuming H2 to prevent initial ecosystem invasion In a non-inflamed intestine, S. typhimurium relies on H2 metabolisms for invasion. Introducing H2-consuming bacteria into the microbiota reduces hyb-dependent S. typhimurium growth. Maier et al. (2013) Probiotic strains producing butyrate Oral gavage of mice with tributyrin reduces growth of S. typhimurium in the inflamed intestine. Rivera-Chávez et al. (2016b) Probiotic strains expressing bacteriocins or microcins targeting the pathogen Colonisation of mice with a bacteriocin-carrying E. faecalis strain defective for conjugation leads to clearance of vancomycin resistant enterococci. Kommineni et al. (2015), Hegarty et al. (2016) and Sassone-Corsi et al. (2016b) Microcin-producing E. coli Nissle is able to limit the growth of commensal E. coli, adherent–invasive E. coli and Salmonella enterica in the inflamed intestine. Siacylidase inhibitors Oral administration of sialidase inhibitors decreases outgrowth of E. coli as well as the severity of colitis in a mouse model. (Huang et al. (2015) Inhibitors of aerobic respiration Aerobic respiration is used by Salmonella spp and other Enterobacteriaceae to thrive in the inflamed intestine. Winter and Bäumler (2014b) Sustaining PPAR-γ signalling PPAR-γ signalling in the homeostatic intestine leads to β-oxidation in the colonocytes and hence an anoxic environment limiting nitrate availability and outgrowth of Enterobacteriaceae Byndloss et al. (2017) View Large Acknowledgements We would like to thank Pamela Schnupf, Kelsey Huus and Florent Mazel for fruitful discussions and critical reading of the manuscript. PV was supported by an Early.PostdocMobility Fellowship form the Swiss National Science Foundation, a Roux-Cantarini Postdoctoral Fellowship as well as a L'Oréal-UNESCO for Women in Science France Fellowship. PJS is an HHMI Senior Foreign Scholar and CIFAR scholar in the human microbiome consortium. FUNDING Work in PJS's group is supported by European Research Council (ERC) Grant No. 339579 (DECRYPT) . Conflict of interest. None declared. REFERENCES Ackermann M , Stecher B , Freed NE et al. Self-destructive cooperation mediated by phenotypic noise . Nature 2008 ; 454 : 987 – 90 . Google Scholar CrossRef Search ADS PubMed Alvarez-Sieiro P , Montalbán-López M , Mu D et al. Bacteriocins of lactic acid bacteria: extending the family . Appl Microbiol Biotechnol 2016 ; 100 : 2939 – 51 . Google Scholar CrossRef Search ADS PubMed Anderson MC , Vonaesch P , Saffarian A et al. Shigella sonnei encodes a functional T6SS used for interbacterial competition and niche occupancy . Cell Host Microbe 2017 ; 21 : 769 – 76 . e3 . Google Scholar CrossRef Search ADS PubMed Antunes LCM , Wang M , Andersen SK et al. Repression of Salmonella enterica phoP expression by small molecules from physiological bile. J Bacteriol . American Society for Microbiology ; 2012 ; 194 : 2286 – 96 . Araújo JR , Tomas J , Brenner C et al. Impact of high-fat diet on the intestinal microbiota and small intestinal physiology before and after the onset of obesity . Biochimie . 2017 ; 141 : 97 – 106 . Google Scholar CrossRef Search ADS PubMed Atarashi K , Tanoue T , Ando M et al. Th17 cell induction by adhesion of microbes to intestinal epithelial cells . Cell 2015 ; 163 : 367 – 80 . Google Scholar CrossRef Search ADS PubMed Atarashi K , Tanoue T , Shima T et al. Induction of colonic regulatory T cells by indigenous Clostridium species . Science 2011 ; 331 : 337 – 41 . Google Scholar CrossRef Search ADS PubMed Aubert DF , Xu H , Yang J et al. A Burkholderia type VI effector deamidates Rho GTPases to activate the pyrin inflammasome and trigger inflammation . Cell Host Microbe 2016 ; 19 : 664 – 74 . Google Scholar CrossRef Search ADS PubMed Audebert C , Even G , Cian A et al. Colonization with the enteric protozoa Blastocystis is associated with increased diversity of human gut bacterial microbiota . Sci Rep 2016 ; 6 : 25255 . Google Scholar CrossRef Search ADS PubMed Barash NR , Maloney JG , Singer SM et al. Giardia alters commensal microbial diversity throughout the murine gut . Infect Immun 2017 ; 85 : e00948 – 16 . Google Scholar CrossRef Search ADS PubMed Barthel M , Hapfelmeier S , Quintanilla-Martínez L et al. Pretreatment of mice with streptomycin provides a Salmonella enterica serovar Typhimurium colitis model that allows analysis of both pathogen and host . Infect Immun 2003 ; 71 : 2839 – 58 . Google Scholar CrossRef Search ADS PubMed Behari J , Stagon L , Calderwood SB . pepA, a gene mediating pH regulation of virulence genes in Vibrio cholerae. J Bacteriol . American Society for Microbiology ; 2001 ; 183 : 178 – 88 . Behnsen J , Jellbauer S , Wong CP et al. The cytokine IL-22 promotes pathogen colonization by suppressing related commensal bacteria . Immunity 2014 ; 40 : 262 – 73 . Google Scholar CrossRef Search ADS PubMed Bernal P , Allsopp LP , Filloux A et al. The Pseudomonas putida T6SS is a plant warden against phytopathogens . ISME J 2017 ; 11 : 972 – 87 . Google Scholar CrossRef Search ADS PubMed Bladergroen MR , Badelt K , Spaink HP . Infection-blocking genes of a symbiotic Rhizobium leguminosarum strain that are involved in temperature-dependent protein secretion . Mol Plant Microbe Interact 2003 ; 16 : 53 – 64 . Google Scholar CrossRef Search ADS PubMed Blanton LV , Barratt MJ , Charbonneau MR et al. Childhood undernutrition, the gut microbiota, and microbiota-directed therapeutics . Science 2016a ; 352 : 1533 – 3 . Google Scholar CrossRef Search ADS Blanton LV , Charbonneau MR , Salih T et al. Gut bacteria that prevent growth impairments transmitted by microbiota from malnourished children . Science 2016b ; 351 , DOI: https://doi.org/10.1126/science.aad3311 . Bohnhoff M , Drake BL , Miller CP . Effect of streptomycin on susceptibility of intestinal tract to experimental Salmonella infection . Proc Soc Exp Biol Med 1954 ; 86 : 132 – 7 . Google Scholar CrossRef Search ADS PubMed Borgeaud S , Metzger LC , Scrignari T et al. The type VI secretion system of Vibrio cholerae fosters horizontal gene transfer . Science 2015 ; 347 : 63 – 7 . Google Scholar CrossRef Search ADS PubMed Braun T , Di Segni A , BenShoshan M et al. Fecal microbial characterization of hospitalized patients with suspected infectious diarrhea shows significant dysbiosis . Sci Rep 2017 ; 7 : 1088 . Google Scholar CrossRef Search ADS PubMed Breurec S , Vanel N , Bata P et al. Etiology and epidemiology of diarrhea in hospitalized children from low income country: a matched case-control study in central african republic . PLoS Negl Trop Dis 2016 ; 10 : e0004283 . Google Scholar CrossRef Search ADS PubMed Broadhurst MJ , Ardeshir A , Kanwar B et al. Therapeutic helminth infection of macaques with idiopathic chronic diarrhea alters the inflammatory signature and mucosal microbiota of the colon . PLoS Pathog 2012 ; 8 : e1003000 . Google Scholar CrossRef Search ADS PubMed Brodmann M , Dreier RF , Broz P et al. Francisella requires dynamic type VI secretion system and ClpB to deliver effectors for phagosomal escape . Nat Commun 2017 ; 8 : 15853 . Google Scholar CrossRef Search ADS PubMed Brotcke Zumsteg A , Goosmann C , Brinkmann V et al. IcsA is a Shigella flexneri adhesin regulated by the type III secretion system and required for pathogenesis . Cell Host & Microbe . 2014 ; 15 : 435 – 45 . Google Scholar CrossRef Search ADS PubMed Brown EM , Wlodarska M , Willing BP et al. Diet and specific microbial exposure trigger features of environmental enteropathy in a novel murine model . Nat Commun 2015 ; 6 : 7806 . Google Scholar CrossRef Search ADS PubMed Brugiroux S , Beutler M , Pfann C et al. Genome-guided design of a defined mouse microbiota that confers colonization resistance against Salmonella enterica serovar Typhimurium . Nat Microbiol 2016 ; 2 : 16215 . Google Scholar CrossRef Search ADS PubMed Byndloss MX , Olsan EE , Rivera-Chávez F et al. Microbiota-activated PPAR-γ signaling inhibits dysbiotic Enterobacteriaceae expansion . Science 2017 ; 357 : 570 – 5 . Google Scholar CrossRef Search ADS PubMed Calcuttawala F , Hariharan C , Pazhani GP et al. Characterization of E-type colicinogenic plasmids from Shigella sonnei . FEMS Microbiol Lett 2017 ; 364 , DOI: https://doi.org/10.1093/femsle/fnx060 . Camarinha-Silva A , Maushammer M , Wellmann R et al. Host genome influence on gut microbial composition and microbial prediction of complex traits in pigs . Genetics 2017 ; 206 : 1637 – 44 . Google Scholar CrossRef Search ADS PubMed Cantacessi C , Giacomin P , Croese J et al. Impact of experimental hookworm infection on the human gut microbiota . J Infect Dis 2014 ; 210 : 1431 – 4 . Google Scholar CrossRef Search ADS PubMed Carbonero F , Benefiel AC , Alizadeh-Ghamsari AH et al. Microbial pathways in colonic sulfur metabolism and links with health and disease . Front Physiol 2012 ; 3 : 448 . Google Scholar CrossRef Search ADS PubMed Cassat JE , Skaar EP . Iron in infection and immunity . Cell Host Microbe 2013 ; 13 : 509 – 19 . Google Scholar CrossRef Search ADS PubMed Chase JM , Leibold MA . Ecological niches: linking classical and contemporary approaches . Biodivers Conserv 2004 ; 13 : 1791 – 3 . Google Scholar CrossRef Search ADS Chassaing B , Koren O , Goodrich JK et al. Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome . Nature 2015 ; 519 : 92 – 6 . Google Scholar CrossRef Search ADS PubMed Chassaing B , Van de Wiele T , De Bodt J et al. Dietary emulsifiers directly alter human microbiota composition and gene expression ex vivo potentiating intestinal inflammation . Gut 2017 ; 66 : 1414 – 27 . Google Scholar CrossRef Search ADS PubMed Chatzidaki-Livanis M , Geva-Zatorsky N , Comstock LE . Bacteroides fragilis type VI secretion systems use novel effector and immunity proteins to antagonize human gut Bacteroidales species . Proc Natl Acad Sci USA 2016 ; 113 : 3627 – 32 . Google Scholar CrossRef Search ADS PubMed Chen H , Yang D , Han F et al. The bacterial T6SS effector EvpP prevents NLRP3 inflammasome activation by inhibiting the Ca(2+)-dependent MAPK-Jnk pathway . Cell Host Microbe 2017 ; 21 : 47 – 58 . Google Scholar CrossRef Search ADS PubMed Cho I , Blaser MJ . The human microbiome: at the interface of health and disease . Nat Rev Genet 2012 ; 13 : 260 – 70 . Google Scholar CrossRef Search ADS PubMed Cho JH. Update on the genetics of inflammatory bowel disease . Curr Gastroenterol Rep 2001 ; 3 : 458 – 63 . Google Scholar CrossRef Search ADS PubMed Chow J , Mazmanian SK . A pathobiont of the microbiota balances host colonization and intestinal inflammation . Cell Host Microbe 2010 ; 7 : 265 – 76 . Google Scholar CrossRef Search ADS PubMed Chudnovskiy A , Mortha A , Kana V et al. Host-protozoan interactions protect from mucosal infections through activation of the inflammasome . Cell 2016 ; 167 : 444 – 56 . e14 . Google Scholar CrossRef Search ADS PubMed Clarke TB. Microbial programming of systemic innate immunity and resistance to infection . PLoS Pathog 2014 ; 10 : e1004506 . Google Scholar CrossRef Search ADS PubMed Clemente JC , Ursell LK , Parfrey LW et al. The impact of the gut microbiota on human health: an integrative view . Cell 2012 ; 148 : 1258 – 70 . Google Scholar CrossRef Search ADS PubMed Clements WD , Parks R , Erwin P et al. Role of the gut in the pathophysiology of extrahepatic biliary obstruction . Gut 1996 ; 39 : 587 – 93 . Google Scholar CrossRef Search ADS PubMed Colina AR , Aumont F , Deslauriers N et al. Evidence for degradation of gastrointestinal mucin by Candida albicans secretory aspartyl proteinase . Infect Immun 1996 ; 64 : 4514 – 9 . Google Scholar PubMed Collins FWJ , O’Connor PM , O'Sullivan O et al. Bacteriocin gene-trait matching across the complete Lactobacillus pan-genome . Sci Rep 2017 ; 7 : 3481 . Google Scholar CrossRef Search ADS PubMed Cooper P , Walker AW , Reyes J et al. Patent human infections with the whipworm, Trichuris trichiura, are not associated with alterations in the faecal microbiota . PLoS ONE 2013 ; 8 : e76573 . Google Scholar CrossRef Search ADS PubMed Corthier G , Muller MC . Emergence in gnotobiotic mice of nontoxinogenic clones of Clostridium difficile from a toxinogenic one . Infect Immun 1988 ; 56 : 1500 – 4 . Google Scholar PubMed Costello EK , Lauber CL , Hamady M et al. Bacterial community variation in human body habitats across space and time . Science 2009 ; 326 : 1694 – 7 . Google Scholar CrossRef Search ADS PubMed Costello EK , Stagaman K , Dethlefsen L et al. The application of ecological theory toward an understanding of the human microbiome . Science 2012 ; 336 : 1255 – 62 . Google Scholar CrossRef Search ADS PubMed Curtis MM , Hu Z , Klimko C et al. The gut commensal Bacteroides thetaiotaomicron exacerbates enteric infection through modification of the metabolic landscape . Cell Host Microbe 2014 ; 16 : 759 – 69 . Google Scholar CrossRef Search ADS PubMed David LA , Maurice CF , Carmody RN et al. Diet rapidly and reproducibly alters the human gut microbiome . Nature 2014 ; 505 : 559 – 63 . Google Scholar CrossRef Search ADS PubMed De Filippo C , Cavalieri D , Di Paola M et al. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa . Proc Natl Acad Sci USA 2010 ; 107 : 14691 – 6 . Google Scholar CrossRef Search ADS PubMed Deriu E , Liu JZ , Pezeshki M et al. Probiotic bacteria reduce Salmonella typhimurium intestinal colonization by competing for iron . Cell Host Microbe 2013 ; 14 : 26 – 37 . Google Scholar CrossRef Search ADS PubMed Desai MS , Seekatz AM , Koropatkin NM et al. A dietary fiber-deprived gut microbiota degrades the colonic mucus barrier and enhances pathogen susceptibility . Cell 2016 ; 167 : 1339 – 53 . e21 . Google Scholar CrossRef Search ADS PubMed Dethlefsen L , Huse S , Sogin ML et al. The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing . PLoS Biol 2008 ; 6 : e280 . Google Scholar CrossRef Search ADS PubMed Diard M , Bakkeren E , Cornuault JK et al. Inflammation boosts bacteriophage transfer between Salmonella spp . Science 2017 ; 355 : 1211 – 5 . Google Scholar CrossRef Search ADS PubMed Diard M , Hardt W-D . Evolution of bacterial virulence . FEMS Microbiol Rev 2017 ; 41 : 679 – 97 . Google Scholar CrossRef Search ADS PubMed Dogra S , Sakwinska O , Soh S-E et al. Dynamics of infant gut microbiota are influenced by delivery mode and gestational duration and are associated with subsequent adiposity . MBio 2015 ; 6 : e02419 – 14 . Google Scholar CrossRef Search ADS PubMed Donovan SM , Comstock SS . Human milk oligosaccharides influence neonatal mucosal and systemic immunity . Ann Nutr Metab 2016 ; 69 Suppl 2 : 42 – 51 . Google Scholar CrossRef Search ADS PubMed Donovan SM. Introduction to the special focus issue on the impact of diet on gut microbiota composition and function and future opportunities for nutritional modulation of the gut microbiome to improve human health . Gut Microbes 2017 ; 8 : 75 – 81 . Google Scholar CrossRef Search ADS PubMed Dowds CM , Blumberg RS , Zeissig S . Control of intestinal homeostasis through crosstalk between natural killer T cells and the intestinal microbiota . Clin Immunol 2015 ; 159 : 128 – 33 . Google Scholar CrossRef Search ADS PubMed Ducluzeau R , Ladire M , Callut C et al. Antagonistic effect of extremely oxygen-sensitive clostridia from the microflora of conventional mice and of Escherichia coli against Shigella flexneri in the digestive tract of gnotobiotic mice . Infect Immun 1977 ; 17 : 415 – 24 . Google Scholar PubMed Dudley EG , Thomson NR , Parkhill J et al. Proteomic and microarray characterization of the AggR regulon identifies a pheU pathogenicity island in enteroaggregative Escherichia coli . Mol Microbiol 2006 ; 61 : 1267 – 82 . Google Scholar CrossRef Search ADS PubMed Eade CR , Hung C-C , Bullard B et al. Bile Acids Function Synergistically To Repress Invasion Gene Expression in Salmonella by Destabilizing the Invasion Regulator HilD. Payne SM, editor. Infect Immun . American Society for Microbiology ; 2016 ; 84 : 2198 – 208 . Eckburg PB , Bik EM , Bernstein CN et al. Diversity of the human intestinal microbial flora . Science 2005 ; 308 : 1635 – 8 . Google Scholar CrossRef Search ADS PubMed Edwards CA . Determinants and duration of impact of early gut bacterial colonization . Ann Nutr Metab 2017 ; 70 : 246 – 50 . Google Scholar CrossRef Search ADS PubMed Elhadad D , McClelland M , Rahav G et al. Feverlike Temperature is a Virulence Regulatory Cue Controlling the Motility and Host Cell Entry of Typhoidal Salmonella . J INFECT DIS . 2015 ; 212 : 147 – 56 . Google Scholar CrossRef Search ADS PubMed Endt K , Stecher B , Chaffron S et al. The microbiota mediates pathogen clearance from the gut lumen after non-typhoidal Salmonella diarrhea . PLoS Pathog 2010 ; 6 : e1001097 . Google Scholar CrossRef Search ADS PubMed Eusebi LH , Rabitti S , Artesiani ML et al. Proton pump inhibitors: risks of long-term use . J Gastroenterol Hepatol 2017 ; 32 : 1295 – 302 . Google Scholar CrossRef Search ADS PubMed Faber F , Thiennimitr P , Spiga L et al. Respiration of microbiota-derived 1,2-propanediol drives Salmonella expansion during colitis . PLoS Pathog 2017 ; 13 : e1006129 . Google Scholar CrossRef Search ADS PubMed Faber F , Tran L , Byndloss MX et al. Host-mediated sugar oxidation promotes post-antibiotic pathogen expansion . Nature 2016 ; 534 : 697 – 9 . Google Scholar CrossRef Search ADS PubMed Falkow S. Molecular Koch's postulates applied to microbial pathogenicity . Rev Infect Dis 1988 ; 10 Suppl 2 : S274 – 6 . Google Scholar CrossRef Search ADS PubMed Filloux A. The rise of the type VI secretion system . F1000Prime Rep 2013 ; 5 : 52 . Google Scholar CrossRef Search ADS PubMed Finlay CM , Stefanska AM , Walsh KP et al. Helminth products protect against autoimmunity via innate type 2 cytokines IL-5 and IL-33, which promote eosinophilia . J Immunol 2016 ; 196 : 703 – 14 . Google Scholar CrossRef Search ADS PubMed Finlay CM , Walsh KP , Mills KHG . Induction of regulatory cells by helminth parasites: exploitation for the treatment of inflammatory diseases . Immunol Rev 2014 ; 259 : 206 – 30 . Google Scholar CrossRef Search ADS PubMed Flo TH , Smith KD , Sato S et al. Lipocalin 2 mediates an innate immune response to bacterial infection by sequestrating iron . Nature 2004 ; 432 : 917 – 21 . Google Scholar CrossRef Search ADS PubMed Foster KR , Bell T . Competition, not cooperation, dominates interactions among culturable microbial species . Curr Biol 2012 ; 22 : 1845 – 50 . Google Scholar CrossRef Search ADS PubMed Fraser T , Brown PD . Temperature and Oxidative Stress as Triggers for Virulence Gene Expression in Pathogenic Leptospira spp . Front Microbiol . 2017 ; 8 : 783 . Google Scholar CrossRef Search ADS PubMed Frese SA , Mills DA . Birth of the infant gut microbiome: moms deliver twice! Cell Host Microbe 2015 ; 17 : 543 – 4 . Google Scholar CrossRef Search ADS PubMed Freter R , Brickner H , Botney M et al. Mechanisms that control bacterial populations in continuous-flow culture models of mouse large intestinal flora . Infect Immun 1983a ; 39 : 676 – 85 . Freter R , Brickner H , Fekete J et al. Survival and implantation of Escherichia coli in the intestinal tract . Infect Immun 1983b ; 39 : 686 – 703 . Freter R , Stauffer E , Cleven D et al. Continuous-flow cultures as in vitro models of the ecology of large intestinal flora . Infect Immun 1983c ; 39 : 666 – 75 . Fu J , Wei B , Wen T et al. Loss of intestinal core 1-derived O-glycans causes spontaneous colitis in mice . J Clin Invest 2011 ; 121 : 1657 – 66 . Google Scholar CrossRef Search ADS PubMed Fukami T , Nakajima M . Community assembly: alternative stable states or alternative transient states? Ecol Lett 2011 ; 14 : 973 – 84 . Google Scholar CrossRef Search ADS PubMed Fukuda S , Toh H , Hase K et al. Bifidobacteria can protect from enteropathogenic infection through production of acetate . Nature 2011 ; 469 : 543 – 7 . Google Scholar CrossRef Search ADS PubMed Furusawa Y , Obata Y , Hase K . Commensal microbiota regulates T cell fate decision in the gut . Semin Immunopathol 2015 ; 37 : 17 – 25 . Google Scholar CrossRef Search ADS PubMed Gaboriau-Routhiau V , Rakotobe S , Lécuyer E et al. The key role of segmented filamentous bacteria in the coordinated maturation of gut helper T cell responses . Immunity 2009 ; 31 : 677 – 89 . Google Scholar CrossRef Search ADS PubMed Gause WC , Maizels RM . Macrobiota - helminths as active participants and partners of the microbiota in host intestinal homeostasis . Curr Opin Microbiol 2016 ; 32 : 14 – 8 . Google Scholar CrossRef Search ADS PubMed Geuking MB , Cahenzli J , Lawson MAE et al. Intestinal bacterial colonization induces mutualistic regulatory T cell responses . Immunity 2011 ; 34 : 794 – 806 . Google Scholar CrossRef Search ADS PubMed Giacomin P , Agha Z , Loukas A . Helminths and intestinal flora team up to improve gut health . Trends Parasitol 2016 ; 32 : 664 – 6 . Google Scholar CrossRef Search ADS PubMed Giacomin P , Zakrzewski M , Croese J et al. Experimental hookworm infection and escalating gluten challenges are associated with increased microbial richness in celiac subjects . Sci Rep 2015 ; 5 : 13797 . Google Scholar CrossRef Search ADS PubMed Gibold L , Garenaux E , Dalmasso G et al. The Vat-AIEC protease promotes crossing of the intestinal mucus layer by Crohn's disease-associated Escherichia coli . Cell Microbiol 2016 ; 18 : 617 – 31 . Google Scholar CrossRef Search ADS PubMed Goto Y , Panea C , Nakato G et al. Segmented filamentous bacteria antigens presented by intestinal dendritic cells drive mucosal Th17 cell differentiation . Immunity 2014 ; 40 : 594 – 607 . Google Scholar CrossRef Search ADS PubMed Gough EK , Stephens DA , Moodie EEM et al. Linear growth faltering in infants is associated with Acidaminococcus sp. and community-level changes in the gut microbiota . Microbiome 2015 ; 3 : 24 . Google Scholar CrossRef Search ADS PubMed Groussin M , Mazel F , Sanders JG et al. Unraveling the processes shaping mammalian gut microbiomes over evolutionary time . Nat Commun 2017 ; 8 : 14319 . Google Scholar CrossRef Search ADS PubMed Guernier V , Brennan B , Yakob L et al. Gut microbiota disturbance during helminth infection: can it affect cognition and behaviour of children? BMC Infect Dis 2017 ; 17 : 58 . Google Scholar CrossRef Search ADS PubMed Hachani A , Wood TE , Filloux A . Type VI secretion and anti-host effectors . Curr Opin Microbiol 2016 ; 29 : 81 – 93 . Google Scholar CrossRef Search ADS PubMed Hamad I , Raoult D , Bittar F . Repertory of eukaryotes (eukaryome) in the human gastrointestinal tract: taxonomy and detection methods . Parasite Immunol 2016 ; 38 : 12 – 36 . Google Scholar CrossRef Search ADS PubMed Havt A , Lima IF , Medeiros PH et al. Prevalence and virulence gene profiling of enteroaggregative Escherichia coli in malnourished and nourished Brazilian children . Diagn Microbiol Infect Dis 2017 ; 89 : 98 – 105 . Google Scholar CrossRef Search ADS PubMed Hecht AL , Casterline BW , Earley ZM et al. Strain competition restricts colonization of an enteric pathogen and prevents colitis . EMBO Rep 2016 ; 17 : 1281 – 91 . Google Scholar CrossRef Search ADS PubMed Hegarty JW , Guinane CM , Ross RP et al. Bacteriocin production: a relatively unharnessed probiotic trait? F1000Res 2016 ; 5 : 2587 . Google Scholar CrossRef Search ADS PubMed Hill DA , Hoffmann C , Abt MC et al. Metagenomic analyses reveal antibiotic-induced temporal and spatial changes in intestinal microbiota with associated alterations in immune cell homeostasis . Mucosal Immunol 2010 ; 3 : 148 – 58 . Google Scholar CrossRef Search ADS PubMed Hoffmann C , Hill DA , Minkah N et al. Community-wide response of the gut microbiota to enteropathogenic Citrobacter rodentium infection revealed by deep sequencing . Infect Immun 2009 ; 77 : 4668 – 78 . Google Scholar CrossRef Search ADS PubMed Hsiao A , Ahmed AMS , Subramanian S et al. Members of the human gut microbiota involved in recovery from Vibrio cholerae infection . Nature 2014 ; 515 : 423 – 6 . Google Scholar CrossRef Search ADS PubMed Huang Y-L , Chassard C , Hausmann M et al. Sialic acid catabolism drives intestinal inflammation and microbial dysbiosis in mice . Nat Commun 2015 ; 6 : 8141 . Google Scholar CrossRef Search ADS PubMed Hughes ER , Winter MG , Duerkop BA et al. Microbial respiration and formate oxidation as metabolic signatures of inflammation-associated dysbiosis . Cell Host Microbe 2017 ; 21 : 208 – 19 . Google Scholar CrossRef Search ADS PubMed Hung C-C , Garner CD , Slauch JM et al. The intestinal fatty acid propionate inhibits Salmonella invasion through the post-translational control of HilD . Mol Microbiol 2013 ; 87 : 1045 – 60 . Google Scholar CrossRef Search ADS PubMed Islam KBMS , Fukiya S , Hagio M et al. Bile acid is a host factor that regulates the composition of the cecal microbiota in rats . Gastroenterology 2011 ; 141 : 1773 – 81 . Google Scholar CrossRef Search ADS PubMed Ivanov II , Atarashi K , Manel N et al. Induction of intestinal Th17 cells by segmented filamentous bacteria . Cell 2009 ; 139 : 485 – 98 . Google Scholar CrossRef Search ADS PubMed Ivanov II . Microbe hunting hits home . Cell Host Microbe 2017 ; 21 : 282 – 5 . Google Scholar CrossRef Search ADS PubMed Jakobsson HE , Rodríguez-Piñeiro AM , Schütte A et al. The composition of the gut microbiota shapes the colon mucus barrier . EMBO Rep 2015 ; 16 : 164 – 77 . Google Scholar CrossRef Search ADS PubMed Johansson MEV , Gustafsson JK , Holmén-Larsson J et al. Bacteria penetrate the normally impenetrable inner colon mucus layer in both murine colitis models and patients with ulcerative colitis . Gut 2014 ; 63 : 281 – 91 . Google Scholar CrossRef Search ADS PubMed Johansson MEV , Larsson JMH , Hansson GC . The two mucus layers of colon are organized by the MUC2 mucin, whereas the outer layer is a legislator of host-microbial interactions . Proc Natl Acad Sci USA 2011 ; 108 Suppl 1 : 4659 – 65 . Google Scholar CrossRef Search ADS PubMed Kashtanova DA , Popenko AS , Tkacheva ON et al. Association between the gut microbiota and diet: fetal life, early childhood, and further life . Nutrition 2016 ; 32 : 620 – 7 . Google Scholar CrossRef Search ADS PubMed Kato LM , Kawamoto S , Maruya M et al. The role of the adaptive immune system in regulation of gut microbiota . Immunol Rev 2014 ; 260 : 67 – 75 . Google Scholar CrossRef Search ADS PubMed Kim J , Lee J-Y , Lee H et al. Microbiological features and clinical impact of the type VI secretion system (T6SS) in Acinetobacter baumannii isolates causing bacteremia . Virulence 2017 ; 8 : 1378 – 89 . Google Scholar CrossRef Search ADS PubMed Kim M , Qie Y , Park J et al. Gut microbial metabolites fuel host antibody responses . Cell Host Microbe 2016 ; 20 : 202 – 14 . Google Scholar CrossRef Search ADS PubMed Kommineni S , Bretl DJ , Lam V et al. Bacteriocin production augments niche competition by enterococci in the mammalian gastrointestinal tract . Nature 2015 ; 526 : 719 – 22 . Google Scholar CrossRef Search ADS PubMed Kortman GAM , Raffatellu M , Swinkels DW et al. Nutritional iron turned inside out: intestinal stress from a gut microbial perspective . FEMS Microbiol Rev 2014 ; 38 : 1202 – 34 . Google Scholar CrossRef Search ADS PubMed Kotloff KL , Nataro JP , Blackwelder WC et al. Burden and aetiology of diarrhoeal disease in infants and young children in developing countries (the Global Enteric Multicenter Study, GEMS): a prospective, case-control study . Lancet 2013 ; 382 : 209 – 22 . Google Scholar CrossRef Search ADS PubMed Larsson JMH , Karlsson H , Crespo JG et al. Altered O-glycosylation profile of MUC2 mucin occurs in active ulcerative colitis and is associated with increased inflammation . Inflamm Bowel Dis 2011 ; 17 : 2299 – 307 . Google Scholar CrossRef Search ADS PubMed Leamy LJ , Kelly SA , Nietfeldt J et al. Host genetics and diet, but not immunoglobulin A expression, converge to shape compositional features of the gut microbiome in an advanced intercross population of mice . Genome Biol 2014 ; 15 : 552 . Google Scholar CrossRef Search ADS PubMed Lee SC , Tang MS , Lim YAL et al. Helminth colonization is associated with increased diversity of the gut microbiota . PLoS Negl Trop Dis 2014 ; 8 : e2880 . Google Scholar CrossRef Search ADS PubMed Lehrer RI , Lichtenstein AK , Ganz T . Defensins: antimicrobial and cytotoxic peptides of mammalian cells . Annu Rev Immunol 1993 ; 11 : 105 – 28 . Google Scholar CrossRef Search ADS PubMed Ley RE , Turnbaugh PJ , Klein S et al. Microbial ecology: human gut microbes associated with obesity . Nature 2006 ; 444 : 1022 – 3 . Google Scholar CrossRef Search ADS PubMed Li H , Limenitakis JP , Fuhrer T et al. The outer mucus layer hosts a distinct intestinal microbial niche . Nat Commun 2015 ; 6 : 8292 . Google Scholar CrossRef Search ADS PubMed Li L , Ma ZS . Testing the neutral theory of biodiversity with human microbiome datasets . Sci Rep 2016 ; 6 : 31448 . Google Scholar CrossRef Search ADS PubMed Li RW , Li W , Sun J et al. The effect of helminth infection on the microbial composition and structure of the caprine abomasal microbiome . Sci Rep 2016 ; 6 : 20606 . Google Scholar CrossRef Search ADS PubMed Lidell ME , Moncada DM , Chadee K et al. Entamoeba histolytica cysteine proteases cleave the MUC2 mucin in its C-terminal domain and dissolve the protective colonic mucus gel . Proc Natl Acad Sci USA 2006 ; 103 : 9298 – 303 . Google Scholar CrossRef Search ADS PubMed Lin J , Zhang W , Cheng J et al. A pseudomonas T6SS effector recruits PQS-containing outer membrane vesicles for iron acquisition . Nat Commun 2017 ; 8 : 14888 . Google Scholar CrossRef Search ADS PubMed Liu JZ , Jellbauer S , Poe AJ et al. Zinc sequestration by the neutrophil protein calprotectin enhances Salmonella growth in the inflamed gut . Cell Host Microbe 2012 ; 11 : 227 – 39 . Google Scholar CrossRef Search ADS PubMed Lopez CA , Winter SE , Rivera-Chávez F et al. Phage-mediated acquisition of a type III secreted effector protein boosts growth of Salmonella by nitrate respiration . MBio 2012 ; 3 : e00143 – 12 . Google Scholar CrossRef Search ADS PubMed Lorenzo-Zúñiga V , Bartolí R , Planas R et al. Oral bile acids reduce bacterial overgrowth, bacterial translocation, and endotoxemia in cirrhotic rats . Hepatology 2003 ; 37 : 551 – 7 . Google Scholar CrossRef Search ADS PubMed Luethy PM , Huynh S , Ribardo DA et al. Microbiota-derived short-chain fatty acids modulate expression of Campylobacter jejuni determinants required for commensalism and virulence . MBio 2017 ; 8 : e00407 – 17 . Google Scholar CrossRef Search ADS PubMed Lupp C , Robertson ML , Wickham ME et al. Host-mediated inflammation disrupts the intestinal microbiota and promotes the overgrowth of Enterobacteriaceae . Cell Host Microbe 2007 ; 2 : 204 . Google Scholar CrossRef Search ADS PubMed Ma BW , Bokulich NA , Castillo PA et al. Routine habitat change: a source of unrecognized transient alteration of intestinal microbiota in laboratory mice . PLoS One 2012 ; 7 : e47416 . Google Scholar CrossRef Search ADS PubMed Macpherson AJ , Geuking MB , McCoy KD . Innate and adaptive immunity in host-microbiota mutualism . Front Biosci (Schol Ed) 2012 ; 4 : 685 – 98 . Google Scholar PubMed Macpherson AJ , Geuking MB , Slack E et al. The habitat, double life, citizenship, and forgetfulness of IgA . Immunol Rev 2012 ; 245 : 132 – 46 . Google Scholar CrossRef Search ADS PubMed Macpherson AJ , McCoy KD . Standardised animal models of host microbial mutualism . Mucosal Immunol 2015 ; 8 : 476 – 86 . Google Scholar CrossRef Search ADS PubMed Macpherson AJ , Slack E . The functional interactions of commensal bacteria with intestinal secretory IgA . Curr Opin Gastroenterol 2007 ; 23 : 673 – 8 . Google Scholar CrossRef Search ADS PubMed Maier L , Vyas R , Cordova CD et al. Microbiota-derived hydrogen fuels Salmonella typhimurium invasion of the gut ecosystem . Cell Host Microbe 2013 ; 14 : 641 – 51 . Google Scholar CrossRef Search ADS PubMed Marteyn B , Gazi A , Sansonetti P . Shigella: a model of virulence regulation in vivo . Gut Microbes . Taylor & Francis ; 2012 ; 3 : 104 – 20 . Marteyn B , Scorza FB , Sansonetti PJ et al. Breathing life into pathogens: the influence of oxygen on bacterial virulence and host responses in the gastrointestinal tract . Cell Microbiol . Blackwell Publishing Ltd ; 2011 ; 13 : 171 – 6 . Google Scholar CrossRef Search ADS PubMed Marteyn B , West NP , Browning DF et al. Modulation of Shigella virulence in response to available oxygen in vivo . Nature ; 2010 ; 465 : 355 – 8 . Google Scholar CrossRef Search ADS PubMed Martinez FAC , Balciunas EM , Converti A et al. Bacteriocin production by Bifidobacterium spp. A review . Biotechnol Adv 2013 ; 31 : 482 – 8 . Google Scholar CrossRef Search ADS PubMed Mazmanian SK , Liu CH , Tzianabos AO et al. An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system . Cell 2005 ; 122 : 107 – 18 . Google Scholar CrossRef Search ADS PubMed McFarlane AJ , McSorley HJ , Davidson DJ et al. Enteric helminth-induced type I interferon signaling protects against pulmonary virus infection through interaction with the microbiota . J Allergy Clin Immunol . 2017 ; 140 : 1068 – 1078.e6 . Google Scholar CrossRef Search ADS PubMed McGuckin MA , Lindén SK , Sutton P et al. Mucin dynamics and enteric pathogens . Nat Rev Microbiol 2011 ; 9 : 265 – 78 . Google Scholar CrossRef Search ADS PubMed McKenney EA , Williamson L , Yoder AD et al. Alteration of the rat cecal microbiome during colonization with the helminth Hymenolepis diminuta . Gut Microbes 2015 ; 6 : 182 – 93 . Google Scholar CrossRef Search ADS PubMed Meyer-Hoffert U , Hornef MW , Henriques-Normark B et al. Secreted enteric antimicrobial activity localises to the mucus surface layer . Gut 2008 ; 57 : 764 – 71 . Google Scholar CrossRef Search ADS PubMed Miethke M , Marahiel MA . Siderophore-based iron acquisition and pathogen control . Microbiol Mol Biol Rev 2007 ; 71 : 413 – 51 . Google Scholar CrossRef Search ADS PubMed Mike LA , Smith SN , Sumner CA et al. Siderophore vaccine conjugates protect against uropathogenic Escherichia coli urinary tract infection . Proc Natl Acad Sci USA 2016 ; 113 : 13468 – 73 . Google Scholar CrossRef Search ADS PubMed Miki T , Goto R , Fujimoto M et al. The bactericidal lectin RegIIIβ prolongs gut colonization and enteropathy in the streptomycin mouse model for Salmonella diarrhea . Cell Host Microbe 2017 ; 21 : 195 – 207 . Google Scholar CrossRef Search ADS PubMed Miki T , Holst O , Hardt W-D . The bactericidal activity of the C-type lectin RegIIIβ against gram-negative bacteria involves binding to lipid A . J Biol Chem 2012 ; 287 : 34844 – 55 . Google Scholar CrossRef Search ADS PubMed Miller CP , Bohnhoff M , Drake BL . The effect of antibiotic therapy on susceptibility to an experimental enteric infection . Trans Assoc Am Physicians 1954 ; 67 : 156 – 61 . Google Scholar PubMed Modi SR , Collins JJ , Relman DA . Antibiotics and the gut microbiota . J Clin Invest 2014 ; 124 : 4212 – 8 . Google Scholar CrossRef Search ADS PubMed Moor K , Diard M , Sellin ME et al. High-avidity IgA protects the intestine by enchaining growing bacteria . Nature 2017 ; 544 : 498 – 502 . Google Scholar CrossRef Search ADS PubMed Moran NA , Sloan DB . The hologenome concept: helpful or hollow? PLoS Biol 2015 ; 13 : e1002311 . Google Scholar CrossRef Search ADS PubMed Moreira CG , Russell R , Mishra AA et al. Bacterial adrenergic sensors regulate virulence of enteric pathogens in the gut . MBio 2016 ; 7 : e00826 – 16 . Google Scholar CrossRef Search ADS PubMed Mougous JD , Cuff ME , Raunser S et al. A virulence locus of Pseudomonas aeruginosa encodes a protein secretion apparatus . Science 2006 ; 312 : 1526 – 30 . Google Scholar CrossRef Search ADS PubMed Muegge BD , Kuczynski J , Knights D et al. Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans . Science 2011 ; 332 : 970 – 4 . Google Scholar CrossRef Search ADS PubMed Namasivayam S , Maiga M , Yuan W et al. Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy . Microbiome 2017 ; 5 : 71 . Google Scholar CrossRef Search ADS PubMed Nedialkova LP , Denzler R , Koeppel MB et al. Inflammation fuels colicin Ib-dependent competition of Salmonella Serovar Typhimurium and E. coli in enterobacterial blooms. Galán JE, editor . PLoS Pathog . 2014 ; 10 : e1003844 . Google Scholar CrossRef Search ADS PubMed Neville BA , Forster SC , Lawley TD . Commensal Koch's postulates: establishing causation in human microbiota research . Curr Opin Microbiol 2017 ; 42 : 47 – 52 . Google Scholar CrossRef Search ADS PubMed Ng KM , Ferreyra JA , Higginbottom SK et al. Microbiota-liberated host sugars facilitate post-antibiotic expansion of enteric pathogens . Nature 2013 ; 502 : 96 – 9 . Google Scholar CrossRef Search ADS PubMed Niehus R , Picot A , Oliveira NM et al. The evolution of siderophore production as a competitive trait . Evolution 2017 ; 71 : 1443 – 55 . Google Scholar CrossRef Search ADS PubMed Nunn KL , Wang Y-Y , Harit D et al. Enhanced trapping of HIV-1 by human cervicovaginal mucus is associated with Lactobacillus crispatus-dominant microbiota . MBio 2015 ; 6 : e01084 – 15 . Google Scholar CrossRef Search ADS PubMed O’Malley MA. The nineteenth century roots of “everything is everywhere.” Nat Rev Microbiol 2007 ; 5 : 647 – 51 . Google Scholar CrossRef Search ADS PubMed Nuss AM , Heroven AK , Waldmann B et al. Transcriptomic profiling of Yersinia pseudotuberculosis reveals reprogramming of the Crp regulon by temperature and uncovers Crp as a master regulator of small RNAs. Sharma CM, editor. PLoS Genet . Public Library of Science ; 2015 ; 11 : e1005087 . Osborne LC , Monticelli LA , Nice TJ et al. Coinfection. Virus-helminth coinfection reveals a microbiota-independent mechanism of immunomodulation . Science 2014 ; 345 : 578 – 82 . Google Scholar CrossRef Search ADS PubMed Pabst O , Cerovic V , Hornef M . Secretory IgA in the coordination of establishment and maintenance of the microbiota . Trends Immunol 2016 ; 37 : 287 – 96 . Google Scholar CrossRef Search ADS PubMed Parfrey LW , Walters WA , Knight R . Microbial eukaryotes in the human microbiome: ecology, evolution, and future directions . Front Microbiol 2011 ; 2 : 153 . Google Scholar CrossRef Search ADS PubMed Parfrey LW , Walters WA , Lauber CL et al. Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity . Front Microbiol 2014 ; 5 : 298 . Google Scholar CrossRef Search ADS PubMed Parsons DA , Heffron F . sciS, an icmF homolog in Salmonella enterica serovar Typhimurium, limits intracellular replication and decreases virulence . Infect Immun 2005 ; 73 : 4338 – 45 . Google Scholar CrossRef Search ADS PubMed Pelaseyed T , Bergström JH , Gustafsson JK et al. The mucus and mucins of the goblet cells and enterocytes provide the first defense line of the gastrointestinal tract and interact with the immune system . Immunol Rev 2014 ; 260 : 8 – 20 . Google Scholar CrossRef Search ADS PubMed Pereira FC , Berry D . Microbial nutrient niches in the gut . Environ Microbiol 2017 ; 19 : 1366 – 78 . Google Scholar CrossRef Search ADS PubMed Peterson DA , McNulty NP , Guruge JL et al. IgA response to symbiotic bacteria as a mediator of gut homeostasis . Cell Host Microbe 2007 ; 2 : 328 – 39 . Google Scholar CrossRef Search ADS PubMed Petersson J , Schreiber O , Hansson GC et al. Importance and regulation of the colonic mucus barrier in a mouse model of colitis . Am J Physiol Gastrointest Liver Physiol 2011 ; 300 : G327 – 33 . Google Scholar CrossRef Search ADS PubMed Platts-Mills JA , Taniuchi M , Uddin MJ et al. Association between enteropathogens and malnutrition in children aged 6–23 mo in Bangladesh: a case-control study . Am J Clin Nutr 2017 ; 105 : 1132 – 8 . Google Scholar CrossRef Search ADS PubMed Plichta DR , Juncker AS , Bertalan M et al. Transcriptional interactions suggest niche segregation among microorganisms in the human gut . Nat Microbiol 2016 ; 1 : 16152 . Google Scholar CrossRef Search ADS PubMed Png CW , Lindén SK , Gilshenan KS et al. Mucolytic bacteria with increased prevalence in IBD mucosa augment in vitro utilization of mucin by other bacteria . Am J Gastroenterol 2010 ; 105 : 2420 – 8 . Google Scholar CrossRef Search ADS PubMed Porcheron G , Schouler C , Dozois CM . Survival games at the dinner table: regulation of Enterobacterial virulence through nutrient sensing and acquisition . Curr Opin Microbiol . 2016 ; 30 : 98 – 106 . Google Scholar CrossRef Search ADS PubMed Pourabedin M , Chen Q , Yang M et al. Mannan- and xylooligosaccharides modulate caecal microbiota and expression of inflammatory-related cytokines and reduce caecal Salmonella enteritidis colonisation in young chickens . FEMS Microbiol Ecol 2017 ; 93 : fiw226 . Google Scholar CrossRef Search ADS PubMed Puhar A , Sansonetti PJ . Type III secretion system . Curr Biol 2014 ; 24 : R784 – 91 . Google Scholar CrossRef Search ADS PubMed Pukatzki S , Ma AT , Sturtevant D et al. Identification of a conserved bacterial protein secretion system in Vibrio cholerae using the Dictyostelium host model system . Proc Natl Acad Sci USA 2006 ; 103 : 1528 – 33 . Google Scholar CrossRef Search ADS PubMed Qin J , Li R , Raes J et al. A human gut microbial gene catalogue established by metagenomic sequencing . Nature 2010 ; 464 : 59 – 65 . Google Scholar CrossRef Search ADS PubMed Qiu J , Luo Z-Q . Legionella and Coxiella effectors: strength in diversity and activity . Nat Rev Microbiol 2017 ; 23 : 274 . Raffatellu M , George MD , Akiyama Y et al. Lipocalin-2 resistance confers an advantage to Salmonella enterica serotype Typhimurium for growth and survival in the inflamed intestine . Cell Host Microbe 2009 ; 5 : 476 – 86 . Google Scholar CrossRef Search ADS PubMed Rakoff-Nahoum S , Foster KR , Comstock LE . The evolution of cooperation within the gut microbiota . Nature 2016 ; 533 : 255 – 9 . Google Scholar CrossRef Search ADS PubMed Ramanan D , Bowcutt R , Lee SC et al. Helminth infection promotes colonization resistance via type 2 immunity . Science 2016 ; 352 : 608 – 12 . Google Scholar CrossRef Search ADS PubMed Ramirez-Farias C , Slezak K , Fuller Z et al. Effect of inulin on the human gut microbiota: stimulation of Bifidobacterium adolescentis and Faecalibacterium prausnitzii . Br J Nutr 2009 ; 101 : 541 – 50 . Google Scholar CrossRef Search ADS PubMed Randremanana RV , Razafindratsimandresy R , Andriatahina T et al. Etiologies, risk factors and impact of severe diarrhea in the under-fives in Moramanga and Antananarivo, Madagascar . PLoS One 2016 ; 11 : e0158862 . Google Scholar CrossRef Search ADS PubMed Rescigno M. Intestinal microbiota and its effects on the immune system . Cell Microbiol 2014 ; 16 : 1004 – 13 . Google Scholar CrossRef Search ADS PubMed Rey FE , Gonzalez MD , Cheng J et al. Metabolic niche of a prominent sulfate-reducing human gut bacterium . Proc Natl Acad Sci USA 2013 ; 110 : 13582 – 7 . Google Scholar CrossRef Search ADS PubMed Reynolds LA , Redpath SA , Yurist-Doutsch S et al. Enteric helminths promote Salmonella coinfection by altering the intestinal metabolome . J Infect Dis 2017 ; 215 : 1245 – 54 . Google Scholar CrossRef Search ADS PubMed Ridaura VK , Faith JJ , Rey FE et al. Gut microbiota from twins discordant for obesity modulate metabolism in mice . Science 2013 ; 341 : 1241214 – 4 . Google Scholar CrossRef Search ADS PubMed Ridlon JM , Kang DJ , Hylemon PB et al. Bile acids and the gut microbiome . Curr Opin Gastroenterol 2014 ; 30 : 332 – 8 . Google Scholar CrossRef Search ADS PubMed Riley MA , Wertz JE . Bacteriocins: evolution, ecology, and application . Annu Rev Microbiol 2002 ; 56 : 117 – 37 . Google Scholar CrossRef Search ADS PubMed Rivera-Chávez F , Lopez CA , Bäumler AJ . Oxygen as a driver of gut dysbiosis . Free Radic Biol Med 2017 ; 105 : 93 – 101 . Google Scholar CrossRef Search ADS PubMed Rivera-Chávez F , Lopez CA , Zhang LF et al. Energy taxis toward host-derived nitrate supports a Salmonella pathogenicity island 1-independent mechanism of invasion . MBio 2016a ; 7 : e00960 – 16 . Google Scholar CrossRef Search ADS Rivera-Chávez F , Zhang LF , Faber F et al. Depletion of butyrate-producing clostridia from the gut microbiota drives an aerobic luminal expansion of Salmonella . Cell Host Microbe 2016b ; 19 : 443 – 54 . Google Scholar CrossRef Search ADS Rivière A , Selak M , Lantin D et al. Bifidobacteria and butyrate-producing colon bacteria: importance and strategies for their stimulation in the human gut . Front Microbiol 2016 ; 7 : 979 . Google Scholar CrossRef Search ADS PubMed Rodríguez-Díaz J , García-Mantrana I , Vila-Vicent S et al. Relevance of secretor status genotype and microbiota composition in susceptibility to rotavirus and norovirus infections in humans . Sci Rep 2017 ; 7 : 45559 . Google Scholar CrossRef Search ADS PubMed Rossi O , van Berkel LA , Chain F et al. Faecalibacterium prausnitzii A2-165 has a high capacity to induce IL-10 in human and murine dendritic cells and modulates T cell responses . Sci Rep 2016 ; 6 : 18507 . Google Scholar CrossRef Search ADS PubMed Round JL , Mazmanian SK . Inducible Foxp3+ regulatory T-cell development by a commensal bacterium of the intestinal microbiota . Proc Natl Acad Sci USA 2010 ; 107 : 12204 – 9 . Google Scholar CrossRef Search ADS PubMed Russell AB , Wexler AG , Harding BN et al. A type VI secretion-related pathway in Bacteroidetes mediates interbacterial antagonism . Cell Host Microbe 2014 ; 16 : 227 – 36 . Google Scholar CrossRef Search ADS PubMed Rutayisire E , Huang K , Liu Y et al. The mode of delivery affects the diversity and colonization pattern of the gut microbiota during the first year of infants' life: a systematic review . BMC Gastroenterol 2016 ; 16 : 86 . Google Scholar CrossRef Search ADS PubMed Salomon D , Klimko JA , Trudgian DC et al. Type VI secretion system toxins horizontally shared between marine bacteria . PLoS Pathog 2015 ; 11 : e1005128 . Google Scholar CrossRef Search ADS PubMed Salzman NH , Hung K , Haribhai D et al. Enteric defensins are essential regulators of intestinal microbial ecology . Nat Immunol 2010 ; 11 : 76 – 83 . Google Scholar CrossRef Search ADS PubMed Sana TG , Flaugnatti N , Lugo KA et al. Salmonella typhimurium utilizes a T6SS-mediated antibacterial weapon to establish in the host gut . Proc Natl Acad Sci USA 2016 ; 113 : E5044 – 51 . Google Scholar CrossRef Search ADS PubMed Sansonetti PJ . War and peace at mucosal surfaces . Nat Rev Immunol 2004 ; 4 : 953 – 64 . Google Scholar CrossRef Search ADS PubMed Sassone-Corsi M , Chairatana P , Zheng T et al. Siderophore-based immunization strategy to inhibit growth of enteric pathogens . Proc Natl Acad Sci USA 2016a ; 113 : 13462 – 7 . Google Scholar CrossRef Search ADS Sassone-Corsi M , Nuccio S-P , Liu H et al. Microcins mediate competition among Enterobacteriaceae in the inflamed gut . Nature 2016b ; 540 : 280 – 3 . Google Scholar CrossRef Search ADS Schnupf P , Gaboriau-Routhiau V , Cerf-Bensussan N . Host interactions with segmented filamentous bacteria: an unusual trade-off that drives the post-natal maturation of the gut immune system . Semin Immunol 2013 ; 25 : 342 – 51 . Google Scholar CrossRef Search ADS PubMed Schnupf P , Gaboriau-Routhiau V , Sansonetti PJ et al. Segmented filamentous bacteria, Th17 inducers and helpers in a hostile world . Curr Opin Microbiol 2017 ; 35 : 100 – 9 . Google Scholar CrossRef Search ADS PubMed Schütte A , Ermund A , Becker-Pauly C et al. Microbial-induced meprin β cleavage in MUC2 mucin and a functional CFTR channel are required to release anchored small intestinal mucus . Proc Natl Acad Sci USA 2014 ; 111 : 12396 – 401 . Google Scholar CrossRef Search ADS PubMed Sekirov I , Tam NM , Jogova M et al. Antibiotic-induced perturbations of the intestinal microbiota alter host susceptibility to enteric infection . Infect Immun 2008 ; 76 : 4726 – 36 . Google Scholar CrossRef Search ADS PubMed Shannon B , Gajer P , Yi TJ et al. Distinct effects of the cervicovaginal microbiota and herpes simplex type 2 infection on female genital tract immunology . J Infect Dis 2017a ; 215 : 1366 – 75 . Google Scholar CrossRef Search ADS Shannon B , Yi TJ , Perusini S et al. Association of HPV infection and clearance with cervicovaginal immunology and the vaginal microbiota . Mucosal Immunol 2017b ; 6 : 751 . Shimotoyodome A , Meguro S , Hase T et al. Short chain fatty acids but not lactate or succinate stimulate mucus release in the rat colon . Comp Biochem Physiol, Part A Mol Integr Physiol 2000 ; 125 : 525 – 31 . Google Scholar CrossRef Search ADS PubMed Si M , Zhao C , Burkinshaw B et al. Manganese scavenging and oxidative stress response mediated by type VI secretion system in Burkholderia thailandensis . Proc Natl Acad Sci USA 2017 ; 114 : E2233 – 42 . Google Scholar CrossRef Search ADS PubMed Siegwald L , Audebert C , Even G et al. Targeted metagenomic sequencing data of human gut microbiota associated with Blastocystis colonization . Sci Data 2017 ; 4 : 170081 . Google Scholar CrossRef Search ADS PubMed Slack E , Balmer ML , Fritz JH et al. Functional flexibility of intestinal IgA—broadening the fine line . Front Immunol 2012 ; 3 : 100 . Google Scholar CrossRef Search ADS PubMed Slack E , Hapfelmeier S , Stecher B et al. Innate and adaptive immunity cooperate flexibly to maintain host-microbiota mutualism . Science 2009 ; 325 : 617 – 20 . Google Scholar CrossRef Search ADS PubMed Smith MI , Yatsunenko T , Manary MJ et al. Gut microbiomes of Malawian twin pairs discordant for kwashiorkor . Science 2013 ; 339 : 548 – 54 . Google Scholar CrossRef Search ADS PubMed Sommer F , Adam N , Johansson MEV et al. Altered mucus glycosylation in core 1 O-glycan-deficient mice affects microbiota composition and intestinal architecture . PLoS One 2014 ; 9 : e85254 . Google Scholar CrossRef Search ADS PubMed Spasova DS , Surh CD . Blowing on embers: commensal microbiota and our immune system . Front Immunol 2014 ; 5 : 318 . Google Scholar CrossRef Search ADS PubMed Spees AM , Wangdi T , Lopez CA et al. Streptomycin-induced inflammation enhances Escherichia coli gut colonization through nitrate respiration . MBio 2013 ; 4 : e00430 – 13 . Google Scholar CrossRef Search ADS PubMed Spiga L , Winter MG , Furtado de Carvalho T et al. An oxidative central metabolism enables salmonella to utilize microbiota-derived succinate . Cell Host Microbe 2017 ; 22 : 291 – 6 . Google Scholar CrossRef Search ADS PubMed Stecher B , Chaffron S , Käppeli R et al. Like will to like: abundances of closely related species can predict susceptibility to intestinal colonization by pathogenic and commensal bacteria . PLoS Pathog 2010 ; 6 : e1000711 . Google Scholar CrossRef Search ADS PubMed Stecher B , Denzler R , Maier L et al. Gut inflammation can boost horizontal gene transfer between pathogenic and commensal Enterobacteriaceae . Proc Natl Acad Sci USA 2012 ; 109 : 1269 – 74 . Google Scholar CrossRef Search ADS PubMed Stecher B , Hardt W-D . Mechanisms controlling pathogen colonization of the gut . Curr Opin Microbiol 2011 ; 14 : 82 – 91 . Google Scholar CrossRef Search ADS PubMed Stelter C , Käppeli R , König C et al. Salmonella-induced mucosal lectin RegIIIβ kills competing gut microbiota . PLoS One 2011 ; 6 : e20749 . Google Scholar CrossRef Search ADS PubMed Stokholm J , Thorsen J , Chawes BL et al. Cesarean section changes neonatal gut colonization . J Allergy Clin Immunol 2016 ; 138 : 881 – 2 . Google Scholar CrossRef Search ADS PubMed Studer N , Desharnais L , Beutler M et al. Functional intestinal bile acid 7α-dehydroxylation by Clostridium scindens associated with protection from Clostridium difficile infection in a gnotobiotic mouse model . Front Cell Infect Microbiol 2016 ; 6 : 191 . Google Scholar CrossRef Search ADS PubMed Subramanian S , Huq S , Yatsunenko T et al. Persistent gut microbiota immaturity in malnourished Bangladeshi children . Nature 2014 ; 510 : 417 – 21 . Google Scholar CrossRef Search ADS PubMed Suzuki K , Meek B , Doi Y et al. Aberrant expansion of segmented filamentous bacteria in IgA-deficient gut . Proc Natl Acad Sci USA 2004 ; 101 : 1981 – 6 . Google Scholar CrossRef Search ADS PubMed Tailford LE , Crost EH , Kavanaugh D et al. Mucin glycan foraging in the human gut microbiome . Front Genet 2015a ; 6 : 81 . Google Scholar CrossRef Search ADS Tailford LE , Owen CD , Walshaw J et al. Discovery of intramolecular trans-sialidases in human gut microbiota suggests novel mechanisms of mucosal adaptation . Nat Commun 2015b ; 6 : 7624 . Google Scholar CrossRef Search ADS Thiennimitr P , Winter SE , Winter MG et al. Intestinal inflammation allows Salmonella to use ethanolamine to compete with the microbiota . Proc Natl Acad Sci USA 2011 ; 108 : 17480 – 5 . Google Scholar CrossRef Search ADS PubMed Tian Y , Zhao Y , Shi L et al. Type VI secretion systems of Erwinia amylovora contribute to bacterial competition, virulence, and exopolysaccharide production . Phytopathology 2017 ; 107 : 654 – 61 . Google Scholar CrossRef Search ADS PubMed Tomas J , Mulet C , Saffarian A et al. High-fat diet modifies the PPAR-γ pathway leading to disruption of microbial and physiological ecosystem in murine small intestine . Proc Natl Acad Sci USA 2016 ; 113 : E5934 – 43 . Google Scholar CrossRef Search ADS PubMed Torow N , Hornef MW . The neonatal window of opportunity: setting the stage for life-long host-microbial interaction and immune homeostasis . J Immunol 2017 ; 198 : 557 – 63 . Google Scholar CrossRef Search ADS PubMed Turfkruyer M , Verhasselt V . Breast milk and its impact on maturation of the neonatal immune system . Curr Opin Infect Dis 2015 ; 28 : 199 – 206 . Google Scholar CrossRef Search ADS PubMed Turnbaugh PJ , Ley RE , Mahowald MA et al. An obesity-associated gut microbiome with increased capacity for energy harvest . Nature 2006 ; 444 : 1027 – 31 . Google Scholar CrossRef Search ADS PubMed Uebanso T , Ohnishi A , Kitayama R et al. Effects of low-dose non-caloric sweetener consumption on gut microbiota in mice . Nutrients 2017 ; 9 : 560 . Google Scholar CrossRef Search ADS Unterweger D , Miyata ST , Bachmann V et al. The Vibrio cholerae type VI secretion system employs diverse effector modules for intraspecific competition . Nat Commun 2014 ; 5 : 3549 . Google Scholar CrossRef Search ADS PubMed Ursell LK , Metcalf JL , Parfrey LW et al. Defining the human microbiome . Nutr Rev 2012 ; 70 ( Suppl 1 ): S38 – 44 . Google Scholar CrossRef Search ADS PubMed Vaishnava S , Yamamoto M , Severson KM et al. The antibacterial lectin RegIIIgamma promotes the spatial segregation of microbiota and host in the intestine . Science 2011 ; 334 : 255 – 8 . Google Scholar CrossRef Search ADS PubMed Valeri M , Rossi Paccani S , Kasendra M et al. Pathogenic E. coli exploits SslE mucinase activity to translocate through the mucosal barrier and get access to host cells . PLoS One 2015 ; 10 : e0117486 . Google Scholar CrossRef Search ADS PubMed Van den Bossche L , Hindryckx P , Devisscher L et al. Ursodeoxycholic acid and its taurine- or glycine-conjugated species reduce colitogenic dysbiosis and equally suppress experimental colitis in mice . Appl Environ Microbiol 2017 ; 83 : e02766 – 16 . Google Scholar CrossRef Search ADS PubMed van der Post S , Subramani DB , Bäckström M et al. Site-specific O-glycosylation on the MUC2 mucin protein inhibits cleavage by the Porphyromonas gingivalis secreted cysteine protease (RgpB) . J Biol Chem 2013 ; 288 : 14636 – 46 . Google Scholar CrossRef Search ADS PubMed Van der Waaij D , Berghuis-de Vries JM , Lekkerkerk-van der Wees JEC . Colonization resistance of the digestive tract in conventional and antibiotic-treated mice . J Hyg 2009 ; 69 : 405 – 11 . Google Scholar CrossRef Search ADS Vazquez-Gutierrez P , de Wouters T , Werder J et al. High iron-sequestrating bifidobacteria inhibit enteropathogen growth and adhesion to intestinal epithelial cells in vitro . Front Microbiol 2016 ; 7 : 1480 . Google Scholar CrossRef Search ADS PubMed Velasquez-Manoff M . Gut microbiome: the peacekeepers . Nature 2015 ; 518 : S3 – 11 . Google Scholar CrossRef Search ADS PubMed Wagner VE , Dey N , Guruge J et al. Effects of a gut pathobiont in a gnotobiotic mouse model of childhood undernutrition . Sci Transl Med 2016 ; 8 : 366ra164 – 4 . Google Scholar CrossRef Search ADS PubMed Wahlström A , Sayin SI , Marschall H-U et al. Intestinal crosstalk between bile acids and microbiota and its impact on host metabolism . Cell Metab 2016 ; 24 : 41 – 50 . Google Scholar CrossRef Search ADS PubMed Walk ST , Blum AM , Ewing SA-S et al. Alteration of the murine gut microbiota during infection with the parasitic helminth Heligmosomoides polygyrus . Inflamm Bowel Dis 2010 ; 16 : 1841 – 9 . Google Scholar CrossRef Search ADS PubMed Walsh KP , Brady MT , Finlay CM et al. Infection with a helminth parasite attenuates autoimmunity through TGF-beta-mediated suppression of Th17 and Th1 responses . J Immunol 2009 ; 183 : 1577 – 86 . Google Scholar CrossRef Search ADS PubMed Wan B , Zhang Q , Ni J et al. Type VI secretion system contributes to Enterohemorrhagic Escherichia coli virulence by secreting catalase against host reactive oxygen species (ROS) . PLoS Pathog 2017 ; 13 : e1006246 . Google Scholar CrossRef Search ADS PubMed Wang T , Si M , Song Y et al. Type VI secretion system transports Zn2+ to combat multiple stresses and host immunity . PLoS Pathog 2015 ; 11 : e1005020 . Google Scholar CrossRef Search ADS PubMed Willemsen LEM , Koetsier MA , van Deventer SJH et al. Short chain fatty acids stimulate epithelial mucin 2 expression through differential effects on prostaglandin E(1) and E(2) production by intestinal myofibroblasts . Gut 2003 ; 52 : 1442 – 7 . Google Scholar CrossRef Search ADS PubMed Winston JA , Theriot CM . Impact of microbial derived secondary bile acids on colonization resistance against Clostridium difficile in the gastrointestinal tract . Anaerobe 2016 ; 41 : 44 – 50 . Google Scholar CrossRef Search ADS PubMed Winter SE , Bäumler AJ . Why related bacterial species bloom simultaneously in the gut: principles underlying the “Like will to like” concept . Cell Microbiol 2014a ; 16 : 179 – 84 . Google Scholar CrossRef Search ADS Winter SE , Bäumler AJ . Dysbiosis in the inflamed intestine: chance favors the prepared microbe . Gut Microbes 2014b ; 5 : 71 – 3 . Google Scholar CrossRef Search ADS Winter SE , Keestra AM , Tsolis RM et al. The blessings and curses of intestinal inflammation . Cell Host Microbe 2010a ; 8 : 36 – 43 . Google Scholar CrossRef Search ADS Winter SE , Lopez CA , Bäumler AJ . The dynamics of gut-associated microbial communities during inflammation . EMBO Rep 2013a ; 14 : 319 – 27 . Google Scholar CrossRef Search ADS Winter SE , Thiennimitr P , Winter MG et al. Gut inflammation provides a respiratory electron acceptor for salmonella . Nature 2010b ; 467 : 426 – 9 . Google Scholar CrossRef Search ADS Winter SE , Winter MG , Xavier MN et al. Host-derived nitrate boosts growth of E. coli in the inflamed gut . Science 2013b ; 339 : 708 – 11 . Google Scholar CrossRef Search ADS Wrzosek L , Miquel S , Noordine M-L et al. Bacteroides thetaiotaomicron and Faecalibacterium prausnitzii influence the production of mucus glycans and the development of goblet cells in the colonic epithelium of a gnotobiotic model rodent . BMC Biol 2013 ; 11 : 61 . Google Scholar CrossRef Search ADS PubMed Yang M , Liu Z , Hughes C et al. Bile salt-induced intermolecular disulfide bond formation activates Vibrio cholerae virulence . Proc Natl Acad Sci USA 2013 ; 110 : 2348 – 53 . Google Scholar CrossRef Search ADS PubMed Yatsunenko T , Rey FE , Manary MJ et al. Human gut microbiome viewed across age and geography . Nature 2012 ; 486 : 222 – 7 . Google Scholar CrossRef Search ADS PubMed Zaiss MM , Rapin A , Lebon L et al. The intestinal microbiota contributes to the ability of helminths to modulate allergic inflammation . Immunity 2015 ; 43 : 998 – 1010 . Google Scholar CrossRef Search ADS PubMed © FEMS 2018. This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/about_us/legal/notices) http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png FEMS Microbiology Reviews Oxford University Press

Pathogens, microbiome and the host: emergence of the ecological Koch's postulates

FEMS Microbiology Reviews , Volume Advance Article (3) – Jan 9, 2018

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Oxford University Press
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© FEMS 2018.
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0168-6445
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1574-6976
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10.1093/femsre/fuy003
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Abstract

Abstract Even though tremendous progress has been made in the last decades to elucidate the mechanisms of intestinal homeostasis, dysbiosis and disease, we are only at the beginning of understanding the complexity of the gut ecosystem and the underlying interaction networks. We are also only starting to unravel the mechanisms that pathogens have evolved to overcome the barriers imposed by the microbiota and host to exploit the system to their own benefit. Recent work in these domains clearly indicates that the ‘traditional Koch's postulates’, which state that a given pathogen leads to a distinct disease, are not valid for all ‘infectious’ diseases, but that a more complete and complex interpretation of Koch's postulates is needed in order to understand and explain them. This review summarises the current understanding of what defines a healthy gut ecosystem and highlights recent progress in uncovering the interplay between the host, its microbiota and invading intestinal pathogens. Based on these recent findings, we propose a new interpretation of Koch's postulates that we term ‘ecological Koch's postulates’. microbiota, Koch's postulates, pathogen, host INTRODUCTION Traditionally, pathogens have been viewed as armed warriors, fighting against the host (Sansonetti 2004). However, it is well established that not everyone that has ingested a typical infectious dose of a given pathogen, for example Salmonella typhimurium, Helicobacter pylori or Campylobacter jejuni, will develop disease. There also is increasing evidence for asymptomatic carriage of enteric pathogens (Kotloff et al.2013; Breurec et al.2016; Randremanana et al.2016). In addition, it is also known that antibiotic use leads to an increased susceptibility to infection by enteropathogens (Bohnhoff, Drake and Miller 1954; Miller, Bohnhoff and Drake 1954; Barthel et al.2003; Sekirov et al.2008; Van der Waaij, Berghuis-de Vries and Lekkerkerk-van der Wees 2009). These observations led to an extended concept that acknowledged the role of the microbiota in protecting the host against pathogens, referred to first as ‘microbial barrier’ and later as ‘colonisation resistance’. Bacteria can have an inhibitory effect on phylogenetically unrelated species/groups of bacteria (interspecies barrier effect). This was demonstrated as early as the late 1970s through work showing that the pre-colonisation of axenic mice with Escherichia coli could inhibit the colonisation of Shigella flexneri (Ducluzeau et al.1977). Furthermore, bacteria from the same species/group can have an inhibitory effect on the installation of their peers (intra-species barrier effect). This concept was shown in the 1980s in studies using closely related Clostridium species (Corthier and Muller 1988). Several studies have also assessed the role of the prokaryotic microbiota on the susceptibility to viral infections. Indeed, susceptibility to rota- and norovirus seems to depend, at least in part, on the composition of a host's prokaryotic microbiota (Rodríguez-Díaz et al.2017), as do sexually transmitted diseases, such as for example Human Immunodeficiency Virus (Nunn et al.2015), Cervical Human Papillomavirus (Shannon et al.2017b) or Herpes Simplex Virus (Shannon et al.2017a), in the context of a changed vaginal microbiota. For many years, the exact mechanisms underlying the phenomenon of colonisation resistance remained unclear. However, work over the last decades has demonstrated that the microbiota forms a complex ecosystem and interacts with the host and invading pathogens in a dynamic manner. The intestinal microbiota is composed of trillions of organisms belonging to hundreds of different species (Eckburg et al.2005; Yatsunenko et al.2012), reviewed in (Cho and Blaser 2012). While the majority belongs to the prokaryota (bacteria and archae), it also comprises viruses (including phages) and different eukaryotes, especially yeasts and protists (Parfrey, Walters and Knight 2011; Clemente et al.2012; Ursell et al.2012; Parfrey et al.2014; Hamad, Raoult and Bittar 2016). Members of the gram-negative Bacteroidetes and the gram-positive Firmicutes dominate the bacterial community residing in the gut. Less abundant groups include members of the Proteobacteria, the Verrucomicrobia, the Tenericutes, the Defferibacteres and the Fusobacteria (Eckburg et al.2005; Yatsunenko et al.2012). In areas of the world without developed water supplies, the intestinal microbiota can also include multicellular organisms, for example helminths (Giacomin, Agha and Loukas 2016). Several different ecosystems formed by microbial communities in and on the body (e.g. the skin microbiota, the gastric microbiota and the vaginal microbiota) engage in a constant crosstalk with the human host (Costello et al.2009). The microbes belonging to each of these communities are often specific and adapted to living in their particular environment (e.g. anaerobic bacteria in the gut). This review will focus on the interactions found in the intestine, relying mainly on data gathered in laboratory mice. Even though similar mechanisms are at work in all ecosystems found in and on the human host, a complete description would go beyond the scope of this review. In this review, we will summarise the current understanding of what defines a healthy gut ecosystem and highlight recent progress in uncovering the interplay between the hosts, its microbiota and invading intestinal pathogens. THE GUT ECOSYSTEM- SPECIES ABUNDANCE, CHANCE AND THE ENVIRONMENT It has been hypothesised that at least some of the gut microbes have co-evolved and/or co-speciated with mammals (Groussin et al.2017). However, co-occurrence of microbes and their host, even if they affect each others’ fitness, does not necessarily mean a shared evolutionary history but can also be forged by numerous other mechanisms, including unidirectional selection (Moran and Sloan 2015). Regardless of their evolutionary origin, most mammals have a distinct assembly of microorganisms organised into a complex social network, which is remarkably robust and resilient to aggressions from, for example, allogenic/pathogenic intruders. Two major competing ecological theories have been proposed to explain how microbial communities are organised and maintained, i.e. how communities are assembled. The first, termed niche theory (Chase and Leibold 2004), is based on deterministic processes and assumes that each species occupies a given realised niche (i.e. a particular position in the abiotic and biotic space) due to its species-specific properties that define its fundamental niche. The grounding of this theory for microbes lies in the work of Martinus Willem Beijerinck (1851–1931) and in the famous statement: ‘Everything is everywhere, but the environment selects’ (O’Malley 2007). On the other hand, the ‘neutral theory’ is based only on stochastic processes and was proposed at the beginning of the century by Hubbell (2001) (The Unified Neutral Theory of Biodiversity and Biogeography, Princeton University Press, Princeton, NJ, USA.). The theory suggests that local communities are assembled independently of species fitness differences, hence assuming that all individual have the same fitness. Furthermore, the neutral theory claims that the fitness differences between species are not larger than the fitness differences within a given species. Competition is therefore not the driving factor of the observed community structure (all species are equivalent; they have the same chance of immigration, extinction and speciation). Of course, these two theories are not mutually exclusive and can act in parallel to drive microbial community assembly at (i) different spatial scales (e.g. at different locations in the intestine) or (ii) in different environments e.g. in different location on or in our body. Testing the fit of both theories on intestinal microbial communities has been hampered by the inability to culture many of the present species and hence define the composition of the microbial communities. With the rise of advanced sequencing methodologies and the decreasing associated costs, large datasets have been put together that now allow testing of these theories on highly complex communities, for example the intestinal microbiota. In studies conducted in the past few years, evidence is emerging that the intestine is not only an ecosystem based on Hubbell's ‘neutral theory’ where each member has the same fitness (Costello et al.2012). Indeed the Human Microbiome Project, which screened several hundred stool samples from individuals residing in the United States, revealed that the microbiota of only one individual showed a composition structure consistent primarily with the ‘neutral theory’ (Li and Ma 2016). Instead, modelling confirmed that the microbiota is governed mainly by deterministic processes, including environmental factors (Li and Ma 2016). This, however, does not exclude that both processes are shaping the communities at the same time, and clearly more work is needed to elucidate these questions. The microbiome is shaped by different deterministic forces, including maternal transmission at birth (Dogra et al.2015; Frese and Mills 2015; Rutayisire et al.2016; Stokholm et al.2016; Edwards 2017), nutrition (Turnbaugh et al.2006; De Filippo et al.2010; Muegge et al.2011; David et al.2014; Donovan and Comstock 2016; Kashtanova et al.2016; Araújo et al.2017; Donovan 2017; Edwards 2017), host genetics (Leamy et al.2014; Camarinha-Silva et al.2017), the use of different food additives or drugs (Dethlefsen et al.2008; Modi, Collins and Relman 2014; Chassaing et al.2015, 2017; Namasivayam et al.2017; Pourabedin et al.2017; Uebanso et al.2017) and infection (Hoffmann et al.2009; Hill et al.2010; Braun et al.2017). The immune system's dynamic IgA host response to the microbiota (Suzuki et al.2004; Peterson et al.2007; Macpherson, Geuking and Slack 2012; Slack et al.2012; Pabst, Cerovic and Hornef 2016; Moor et al.2017) and its action to hamper bacteria from interacting with the gut tissue (immune exclusion) and to grow (enchained growth; Moor et al.2017), as well as other innate and adaptive immune mechanisms, also have an important role in controlling the microbiota and shaping the community structure (Ivanov et al.2009; Slack et al.2009; Macpherson, Geuking and McCoy 2012; Schnupf, Gaboriau-Routhiau and Cerf-Bensussan 2013; Goto et al.2014; Kato et al.2014; Rescigno 2014; Spasova and Surh 2014; Atarashi et al.2015; Dowds, Blumberg and Zeissig 2015; Furusawa, Obata and Hase 2015; Ivanov 2017). The different environments that individuals and their gut ecosystem experience therefore select for a particular set of strains within the microbiota. However, a core bacterial genetic pool can be defined that is common to all individuals (Ley et al.2006; Qin et al.2010). Scarce resources such as nutrients and access to a given niche are limiting factors for growth in this confined ecosystem (reviewed in Stecher and Hardt 2011). These thoughts were already, in part, formulated earlier in the ‘nutrient niche theory’, a refined niche theory established by Freter et al. (1983a, 1983b, 1983c). The ‘nutrient niche theory’ or ‘niche co-existence theory’ stresses that ecological niches are defined by the available nutrients. Furthermore, Freter asserted that a given species can only establish itself if it is using at least one of the limiting nutrients in the most efficient way. He also hypothesised that only a few nutrients are responsible for shaping the whole community as they limit the growth potential of the whole ecological niche (Freter et al.1983a, 1983b, 1983c). Although Freter's classic ‘nutrient niche theory’ is useful to understand some of the mechanisms occurring in the gut ecosystem, it is not reflective of the entire complexity observed. Indeed, several cases of mixed-substrate utilisation and metabolic flexibility have been described. For example, E. coli and Salmonella spp., can thrive on tetrathionate, nitrate, succinate, 1,2-propanediol, or ethanolamines among others, and therefore rapidly adapt to a changing environment in the intestine during inflammation (Thiennimitr et al.2011; Winter et al. 2013b; Rivera-Chávez et al.2016a; Faber et al.2017; Spiga et al.2017). There are also a few examples of nutritional cooperation between gut microbes described (Rakoff-Nahoum, Foster and Comstock 2016). To date, the complexity of the gut ecosystem and the underlying interaction networks are only beginning to be understood. We are also only starting to unravel the mechanisms that pathogens have evolved to overcome the barriers imposed by the microbiota and host to exploit the system to their own benefit. HALLMARKS OF HOMEOSTASIS Intestinal pathogens are mainly ingested through the consumption of contaminated food or water. During their travel to their preferred ‘niche’, they encounter several obstacles and barriers imposed by the members of the ecosystem, which impede colonisation and invasion by intruders. Most pathogens must replicate in the gut lumen in order to elicit disease (Ackermann et al.2008). Below, we discuss the primary mechanisms in a healthy host that hamper pathogens from overcoming these obstacles and cause disease (see Fig. 1). Figure 1. View largeDownload slide Homeostatic gut environment (A) versus a dysbiotic gut environment (B). Scheme of an intestine in homeostasis (left) and in dysbiosis upon invasion of a pathogen (depicted in red). Upon dysbiosis, the mucus layer is thinner, larger amounts of antimicrobial peptides are secreted (e.g. C-type lectins as Reg3γ) to prevent bacteria breach the barrier and get access to the underlying tissue. This leads to villous blunting, influx of inflammatory cells into the lamina propria and depletion of members of the microbiota, leading to a changed composition and lower diversity of the resident microbiota. Figure 1. View largeDownload slide Homeostatic gut environment (A) versus a dysbiotic gut environment (B). Scheme of an intestine in homeostasis (left) and in dysbiosis upon invasion of a pathogen (depicted in red). Upon dysbiosis, the mucus layer is thinner, larger amounts of antimicrobial peptides are secreted (e.g. C-type lectins as Reg3γ) to prevent bacteria breach the barrier and get access to the underlying tissue. This leads to villous blunting, influx of inflammatory cells into the lamina propria and depletion of members of the microbiota, leading to a changed composition and lower diversity of the resident microbiota. Stomach acidity and bile acids After ingestion and resisting salivary enzymes, the first major barrier to infection is the low pH environment of the stomach. Indeed, pharmacological perturbation of stomach acidity through the use of proton-pump inhibitors leads to an increased pH and greater susceptibility to enteric infections (reviewed in Eusebi et al.2017). After surviving the stomach, the pathogen then enters the duodenum, where it is exposed to the massive influx of bile acids that are produced by the liver and released by the gall bladder. The primary bile acids are involved in lipid absorption from food. They also show toxicity towards given groups of bacteria. For example, in rats treated with cholic acid, phylum-level alterations in the composition of the gut microbiota were observed with an increase in Firmicutes and a concomitant decrease in Bacteroidetes. Cholic acid feeding also led to a less complex composition of the microbiota with overrepresentation of members of the classes Clostridia and Erysipelotrichi (Islam et al.2011). Therefore, bile acids shape the resident bacterial community by promoting the growth of bile acid-metabolising bacteria and by inhibiting in turn, the growth of bile-sensitive bacteria. Several studies in patients suffering from biliary obstruction, who display blocked bile flow into the small intestine, have shown an association with bacterial overgrowth and translocation of bacteria in the small intestine (Clements et al.1996). It was also shown that this phenotype can be reversed by the administration of bile acids (Lorenzo-Zúñiga et al.2003). Bile acids thus play an important role in regulating the microbiota in the small intestine. Over the length of the intestinal tract, these primary bile acids are metabolised by the microbiota to over 50 different secondary bile acids. One of the possible transformations is the deconjugation of bile acids through extracellular bile salt hydrolases (BSHs). BSHs are encoded by different members of the microbiota, especially in members of the Firmicutes, Bacteroidetes and some Actinobacteria. The deconjugated secondary bile acids show less toxicity towards the microbiota than the primary bile acids. Bile acids can also be oxidised and epimerised (transformation in between two stereoisomers) at specific hydroxyl-groups through transformation by 3-α, 7-α, or 12-α hydroxysteroid dehydrogenases. The secondary bile acids have an important role in gut homeostasis by inhibiting inflammation (reviewed in Ridlon et al.2014; Wahlström et al.2016; Winston and Theriot 2016). A recent study has shown that disuccinimidyl suberate (DSS)-mediated colitis was ameliorated in the presence of ursodeoxycholic acid or its taurine- or glycine-conjugated derivatives. Even though daily administration of these bile acids did not restore the full diversity of the microbiota to pre-DSS levels, specific species, such as Akkermansia muciniphila and the Clostridium cluster XIVa, were less depleted upon DSS treatment and the ratio of Firmicutes to Bacteroidetes remained normal (Van den Bossche et al.2017). Secondary bile acids have also been implicated in colony resistance, for example resistance against infection by Clostridium difficile (Winston and Theriot 2016; Van den Bossche et al.2017). Reducing the pool of secondary bile acids through antibiotic treatment relieves colonisation resistance towards C. difficile and enhances spore germination. A later study demonstrated that the colonisation resistance was mediated by a close relative, Clostridium scindens, through the production of the 7-α- dehydroxylated bile acids lithocholic acid and deoxycholic acid (Studer et al.2016). Box 1. Colonisation resistance. Colonisation resistance describes a phenomenon, observed in the human gut as well as in many other ecosystems that invading pathogens (and other organisms) face resistance against establishing themselves in this densely populated space. This ‘colonisation resistance’ is due to several factors, namely competition for nutrients or direct inhibition by chemical compounds or ‘molecular weapons’, for example Type 6 secretion systems and translocated toxins or other toxins. Colonisation resistance can be breached by interfering with the equilibrium of the ecosystem, for example by the administration of antibiotics or by infection. Short-chain fatty acids and other mechanisms of colony resistance through direct inhibition In the colon, complex carbohydrates present in the food or eaten in the form of prebiotics are metabolised by the resident microbiota into short chain fatty acids (SCFA), the three most abundant being acetate, propionate and butyrate. Acetate and propionate are produced mainly by members of the Lactobacilli and Bifidobacteriae. Butyrate is produced by bacteria of the phylum Firmicutes, for example Roseburia spp. and Faecalibacterium prausnitzii, or different members of the genus Clostridium (Ramirez-Farias et al.2009; Rivière et al.2016). Acetate triggers anti-inflammatory and anti-apoptotic responses in host epithelial cells, which leads to protection in the gut against colonisation with pathogenic bacteria like Enterobacteriaceae and Clostridiae (Fukuda et al.2011). Recently, butyrate production by Clostridia species has been implicated in colonisation resistance against S. typhimurium (Rivera-Chávez et al.2016b). The authors show that either through antibiotic treatment or, to a lesser extent, through Salmonella infection and the action of the Salmonella type three secretion system (T3SS) and associated virulence factors a depletion of butyrate-producing Clostridia species occurs in the intestine of affected mice. This then leads to an increased epithelial oxygenation and subsequently aerobic expansion of S. typhimurium. The colonisation resistance against Salmonella, alongside an anaerobic epithelial environment, could be restored through gavage of the mice with tributyrin, a butyrate metabolic precursor, clearly demonstrating the inhibitory role of butyrate on Salmonella invasion. Colonisation resistance and maintenance of the ecosystem through competition and cooperation In addition to direct inhibition, invading bacteria must also contend with limited available nutrient resources. Nutrient availability in the gut varies with food intake and time of day. Therefore, the microbiota faces a constantly changing environment. In a healthy, fully established intestine, all nutrient niches are occupied and incoming species must utilise methods to displace resident species from their established niches in order to create their own niche. A recent study analysing the gene expression of co-occurring human gut microbes showed that for 41% of all co-occurring species the presence of one of the organisms was associated with an altered transcriptional profile in the other, the most affected genes being involved in nutrient uptake and anaerobic respiration (Plichta et al.2016). This suggests that nutrient niche partitioning is prevalent within the gut ecosystem. Furthermore, early in development or after a destabilisation of the equilibrium, e.g. by an infection or antibiotic treatment, the microbiota has to re-establish itself. In this context, the so-called priority effect is observed, whereby the first re-colonising species establish a large colony that hampers the subsequent re-establishment of otherwise fully adapted species to the other's niche (Fukami and Nakajima 2011) (reviewed in Pereira and Berry 2017). This leads to fierce competition for nutrients within the microbiota and by invading pathogens. It also suggests that most of the interactions in the gut are based on competition. To date, cooperation is a type of interaction only very rarely described and does not seem to be as successful as competition in a crowded and competitive environment such as the intestine (Foster and Bell 2012). In one study of cooperation within the gut microbiota, Bacteroides ovatus was shown to produce two outer surface glycoside hydrolases, which digest complex carbohydrates, for example inulin. However, these two hydrolases are not necessary for B. ovatus to grow on inulin. Rather, other members of the microbiota, such as Bacteroides vulgatus, grow on the inulin breakdown products produced by B. ovatus. Bacteroides ovatus then uses products produced by B. vulgatus and both species flourish (Rakoff-Nahoum, Foster and Comstock 2016). Despite the rare documented cases of cooperation, most microbial interactions in the intestine are indeed competitive. The metabolic landscape is shaped by a few so-called keystone species or keystone taxa, which have a large impact on the rest of the community by degrading initial substrates and making these accessible to many other species. Keystone species may only be detectable in very low relative abundance; however their outsized effect on the global microbial composition makes them a ‘keystone’ of the microbiota (reviewed in Pereira and Berry 2017). One example of ‘keystone species’ is Akkermansia muciniphila, which degrades secreted host mucus into products that are then accessible to other bacteria, such as B. vulgatus (Png et al.2010). Hydrogen and sulphate/sulphite consuming species represent an example of a ‘keystone taxa’ due to their regulatory effect on the fermentative activity of other species (Carbonero et al.2012; Rey et al.2013). Yet, some of these taxa, for example Ruminococcus, have evolved to degrade mucin without giving other species access to the degradation products. The intramolecular transsialidase produced by R. gnavus releases 2,7-anhydro- Neu5Ac instead of sialic acid from mucin and other glycoproteins, a product that cannot be utilised by other species (Tailford et al.2015b; reviewed in Tailford et al.2015a). This nutritional limitation represents a strong barrier for the niche establishment of invading species. Box 2. The concept of the nutritional/dietary niche. A nutritional niche describes the nutrient sources which are available to, and usable by, a given set of organisms at a given time and space. The nutritional niche therefore defines if an organism is capable of establishing itself in a given place or not. The concept of the nutritional niche is a sub-definition of the ecological niche concept. The concept has been first proposed by Rolf Freter (Freter's nutritional niche theory) and has subsequently been adapted to take into account the instable flux of nutrients in given ecosystems, for example the intestine, and to take into account the co-existence of other microorganisms utilising the same nutrients either at different geographic locations in the intestine or at different time points. The theory also has been expanded to take into account the metabolic flexibility and mixed-substrate utilisation that most microorganisms exhibit. The process by which a given organism changes its ecological niche is known as ‘niche construction’. (See Pereira and Berry 2017, for an extended review of the topic.) Mucus layer The mucus layer forms a physical barrier to the microbiota, preventing direct interaction with the epithelium (reviewed in McGuckin et al.2011; Pelaseyed et al.2014). In the gut, the goblet cells are responsible for the secretion of the mucin MUC2, which forms a disulphide cross-linked network. This network is comprised of an inner layer, which is tightly attached to the epithelium and mainly impenetrable to bacteria, as well as a looser, outer layer. This outer layer harbours a specific community of bacteria, feeding on the mucus (Li et al.2015) and attaching to its o-glycosylated side-chains (Johansson, Larsson and Hansson 2011). Mucus production is dynamic and depends on the presence of bacterial stimuli, especially lipopolysaccharide and peptidoglycan as reported in an elegant study using germ-free mice (Petersson et al.2011). It has also been known for a long time that SCFAs are involved in mucus secretion from goblet cells into the gut lumen (Shimotoyodome et al.2000; Willemsen et al.2003). Homeostasis of mucus production is regulated by two complementary bacteria, Bacteroides thetaiotaomicron (stimulating mucus production through increased goblet cell differentiation) and F. prausnitzii (inhibiting goblet cell proliferation and mucus glycosylation; Wrzosek et al.2013). A preponderance of evidence shows that mucus composition and structure directly depends on the interplay between resident microbiota and epithelial tissues (Jakobsson et al.2015). Several studies have also linked reduced or aberrant O-glycosylation of mucin to the development of intestinal inflammation (Fu et al.2011; Larsson et al.2011; Sommer et al.2014). Other studies have shown the penetration of commensal bacteria into the inner mucus layer in the context of colitis (Johansson et al.2014). The mucus layer thickness is also related to nutrition, especially dietary intake, as it has been shown recently that low-fibre diets increase mucus-eroding bacteria communities, leading to greater access for pathogens at the epithelial surface and subsequently increased susceptibility to infection (Desai et al.2016). Furthermore, the attachment of the mucus layer to the epithelium is dependent on the microbiota. Meprin β, a host-derived zinc-dependent metalloprotease induced by the microbiota, is needed to detach the mucus in the small intestine and to subsequently release it into the intestinal lumen (Schütte et al.2014). A healthy mucus layer is therefore essential to protect the underlying epithelium from the dense bacterial population and to physically separate this population from immune cells in the underlying tissue in order to prevent exaggerated immune activation. Mucosal immune system Prokaryotic microbiota and the immune system It is now well established that the immune system relies on the microbiota for proper maturation (reviewed in Schnupf, Gaboriau-Routhiau and Cerf-Bensussan 2013; Spasova and Surh 2014; Turfkruyer and Verhasselt 2015; Donovan and Comstock 2016; Torow and Hornef 2017). Different bacterial species guide the development of specific cell subsets; for example, segmented filamentous bacteria induce the development of TH17 cells (Gaboriau-Routhiau et al.2009; Ivanov et al.2009; Goto et al.2014; reviewed in Ivanov 2017; Schnupf et al.2017), and Bacteroides fragilis has been shown to induce Treg proliferation and to act on the T(H)1/T(H)2 balance (Mazmanian et al.2005; Round and Mazmanian 2010). Faecalibacterium prausnitzii increases antigen-specific T cells and decreases the number of IFN-γ(+) T cells (Rossi et al.2016) and other Clostridia species induce different Treg subsets (Atarashi et al.2011). Additionally, short chained fatty acids derived from bacteria regulate Treg numbers in the intestine (Geuking et al.2011; Smith et al.2013; Furusawa, Obata and Hase 2015) and have a direct impact on overall IgA levels (Kim et al.2016; reviewed in Velasquez-Manoff 2015). Mucosal IgA plays a crucial role in gut homeostasis (Macpherson and Slack 2007; Peterson et al.2007; Pabst, Cerovic and Hornef 2016). It is known to protect the gut mucosa from the access of bacteria (immune exclusion) and to inhibit bacterial replication in the gut lumen (enchained growth; Moor et al.2017). Through these mechanisms, IgA regulates the composition and dynamics of the gut microbiota. IgA and the microbiota therefore regulate each other, leading to a delicate homeostatic balance between stimulation and control (reviewed in Macpherson and Slack 2007; Peterson et al.2007; Macpherson, Geuking and Slack 2012; Slack et al.2012; Pabst, Cerovic and Hornef 2016). The microbiota's effect on the mucosal immune system is not limited to regulatory T cells and IgA secretion. It also plays a major role in inducing production of antimicrobial peptides (AMPs), which concentrate at the interphase between the thick, tightly formed, mucus layer and the more dispersed outer layer (reviewed in Lehrer, Lichtenstein and Ganz 1993; Salzman et al.2010)(Meyer-Hoffert et al.2008; Vaishnava et al.2011). AMPs include the defensins, the Reg-protein family and several other proteins, which act directly on the bacteria by targeting the bacterial cell wall. In addition, other host factors with antimicrobial activity include lipocalin2/NGAL, which chelates bacterial siderophores involved in iron acquisition, as well as calprotectin, which leads to the chelation of two other essential trace elements, zinc and manganese. Eukaryotic microbiota and the immune system The intestinal microbiota is not only composed of bacteria, but also harbours a whole array of archae, viruses and eukaryotes. It has been shown that the presence of helminths, through their effect on the host immune system (Walsh et al.2009; Finlay, Walsh and Mills 2014; Finlay et al.2016; Ramanan et al.2016), can have profound effects on the microbiota composition in the intestine (Walk et al.2010; Broadhurst et al.2012; Giacomin et al.2015; McKenney et al.2015; Li et al.2016; Ramanan et al.2016; Guernier et al.2017; reviewed in Gause and Maizels 2016) as well as on disease susceptibility within the intestine (Reynolds et al.2017) and at distant sites, e.g. the respiratory system (McFarlane et al.2017). However, alterations in the microbiota composition due to the presence of helminths are not generalisable, as changes were observed in a first study of 51 persons infected with Trichuris trichiuria in Malaysia (Lee et al.2014), but no changes were found in a second study in 97 children from Ecuador (Cooper et al.2013) nor in 8 persons living in Australia infected experimentally by Necator americanus (Cantacessi et al.2014). Helminths have also been shown to attenuate the effect of intestinal bowel disease by restoring the number of goblet cells and preventing outgrowth of B. vulgatus in the context of Nod2−/− mice and associated intestinal inflammation (Ramanan et al.2016). For some of the observed immune changes, the helminth-induced changes seem to be mediated through the prokaryotic microbiota (Zaiss et al.2015). For other effects, they seem to be independent from the microbiota (Osborne et al.2014), highlighting the complex interplay found within the gut ecosystem. Very recently, a member of the eukaryome, Tritrichomonas musculis, was shown to activate the epithelial inflammasome and to induce protection against bacterial mucosal infection (Chudnovskiy et al.2016). Other protists, such as Giardia (Barash et al.2017) and possibly Blastocystis (Audebert et al.2016; Siegwald et al.2017), have also been shown to change the resident prokaryotic microbiota. However, data remain conflicting, pointing towards the fact that shifts in the microbiota through given eukaryotes might be strain specific. Due to incomplete databases, it is currently difficult to determine the exact strain of a eukaryotic organism by comparison against the database. More work in curating these databases is therefore needed to better appreciate the influence that specific eukaryotes might have on the prokaryotic microbiota. More work is also needed to unravel the triad of eukaryotes, prokaryotes and the immune system to better understand the mutual interactions that take place. Taken together, the microbiota and the development and proper function of the mucosal immune system are exquisitely intertwined. Thus, perturbations on either side of this ecosystem can deregulate the balance and leave the host open to infection or inflammatory diseases (Clarke 2014). FRIEND OR FOE: PATHOGENS FACING THE MICROBIOTA AND THE HOST As discussed, the host and its microbiota have set up a tightly regulated network of mutual control. Invading pathogens therefore have several barriers to overcome in order to establish themselves and cause disease (see Fig. 2). Figure 2. View largeDownload slide Mechanisms evolved by pathogen to combat the resident microbiota and the host. Pathogens have evolved several mechanisms to overcome the barrier imposed by the resident microbiota and the host. These include direct (bacteriocins, microcins, T6SS) and indirect (nutrient restriction) inhibition of members of the microbiota, the use of alternative energy sources as well as different mechanisms to overcome the barriers imposed by the hosts (mucinases, T3SS and other virulence factors acting on the host). Figure 2. View largeDownload slide Mechanisms evolved by pathogen to combat the resident microbiota and the host. Pathogens have evolved several mechanisms to overcome the barrier imposed by the resident microbiota and the host. These include direct (bacteriocins, microcins, T6SS) and indirect (nutrient restriction) inhibition of members of the microbiota, the use of alternative energy sources as well as different mechanisms to overcome the barriers imposed by the hosts (mucinases, T3SS and other virulence factors acting on the host). Within the last decade, much progress has been made in understanding the ‘ménage à trois’ of the microbiota, the host and pathogens. In this section, we will discuss the mechanisms that have evolved in pathogens to overcome the protective environment arising from homeostasis and summarise the complex interactions that take place between pathogens, the microbrobiota and their host. Combatting the resident microbiota by direct killing or by inhibition Small antibacterial toxins A number of small, mainly plasmid-encoded, antibacterial peptides, termed bacteriocins or microcins, are produced and secreted by a broad range of bacteria, including the Bifidobacteria (reviewed in Martinez et al.2013; Alvarez-Sieiro et al.2016), Lactobacilli (Collins et al.2017), Enterococci (Kommineni et al.2015) and many more. It has been demonstrated that bacteriocin production leads to a niche advantage for the bacteria expressing them (Riley and Wertz 2002; Kommineni et al.2015). Some of the bacteriocins and microcins have been shown to act against pathogenic strains (Kommineni et al.2015; Sassone-Corsi et al.2016b), thereby augmenting colonisation resistance and mediating resistance to invading pathogens. One bacteriocin subclass produced by Enterobacteriaceae and termed colicins are encoded by several pathogenic strains including S. typhimurium (Nedialkova et al.2014) and Shigella sonnei (Anderson et al.2017; Calcuttawala et al.2017). It has been shown recently that S. typhimurium expresses colicin Ib (ColIB), giving it a fitness advantage over the closely related E. coli, which blooms simultaneously in the gut upon Salmonella-induced intestinal inflammation. ColIb is regulated through the SOS-response and iron-limitation and upregulated in the context of inflammation (Nedialkova et al.2014). Therefore, the carriage and induced upregulation of colicins seems to be an evolutionary adaption of enteropathogens in order to have a selective advantage in the ecological niche they share with commensal E. coli in the inflamed gut. Type 6 secretion system (T6SS) T6SS are encoded by a substantial number of gram-negative pathogens, as diverse as Helicobacter hepaticus (Chow and Mazmanian 2010), S. typhimurium (Sana et al.2016), S. sonnei (Anderson et al.2017), Pseudomonas aeruginosa (Mougous et al.2006), enteroaggregative E. coli (Dudley et al.2006), Vibrio cholera (Pukatzki et al.2006) and B. fragilis (Chatzidaki-Livanis, Geva-Zatorsky and Comstock 2016; Hecht et al.2016) to name a few. Indeed, T6SS homologous have been described in up to 25% of all sequenced gram-negative genomes. While some bacteria use their T6SS to interfere with host processes (Brodmann et al.2017), alter the immune response upon infection (Chow and Mazmanian 2010; Aubert et al.2016; Hachani, Wood and Filloux 2016; Chen et al.2017), or modulate virulence (Bladergroen, Badelt and Spaink 2003; Parsons and Heffron 2005; Pukatzki et al.2006), growing evidence suggests that T6SS are also used to attack the resident microbiota and to confer the bacteria expressing them with a competitive advantage (Russell et al.2014; Unterweger et al.2014; Chatzidaki-Livanis, Geva-Zatorsky and Comstock 2016; Sana et al.2016; Anderson et al.2017; Bernal et al.2017; Kim et al.2017; Tian et al.2017). Indeed, Shigella, which encodes a T6SS had a selective advantage in colonisation of the mouse gut compared to S. flexneri or E. coli, a phenomenon which was shown to be largely due to the T6SS (Anderson et al.2017). In B. fragilis, this could also be observed at the strain level, where symbiotic, non-toxic B. fragilis was shown to outcompete a pathogenic strain in a T6SS-dependent manner (Chatzidaki-Livanis, Geva-Zatorsky and Comstock 2016; Hecht et al.2016). The T6SS is also implicated in other important tasks that confer the bacterium harbouring it a selective advantage over the resident microbiota. These include iron acquisition (Lin et al.2017) as well as different mechanisms to handle oxidative stress induced by the host (Wang et al.2015; Si et al.2017; Wan et al.2017). It has been shown recently in marine bacteria that T6SS are horizontally shared between different species (Salomon et al.2015). Furthermore, in V. cholera, the T6SS was shown to be able to foster horizontal gene transfer (Borgeaud et al.2015). Clearly, the last few years have seen strong advancements in the understanding of T6SS contributions to microbial life cycles (Filloux 2013), while more work is needed in order to fully understand the full scope of T6SS functions. Exploiting nutrients to gain a selective advantage over the resident microbiota The most limiting nutrients in the gut are micronutrients, especially iron, as well as general energy sources, such as carbohydrates. Bacterial pathogens have evolved a number of strategies to selectively acquire nutrients over the resident microbiota in the race for these resources. Iron scavenging and use of specific siderophores The host has evolved sophisticated strategies termed ‘nutritional immunity’ to limit the amount of available iron that the microbiota has access to (reviewed in Cassat and Skaar 2013; Kortman et al.2014). Bacteria have responded by maximising their ability to uptake iron through the secretion of iron-scavenging molecules, termed siderophores, which give them a selective advantage over strains lacking the scavenging capability (Niehus et al.2017). Lipocalin2 (NGAL in humans) is a potent antimicrobial factor secreted by the host whose function is to sequester iron bound siderophores (Flo et al.2004). Bacteria do not only have to compete with the host for iron, but also with the resident members of the microbiota. Indeed, many microbes encode species-specific siderophores that require specific re-uptake machinery to bind and import the iron-siderophore complex (reviewed in Miethke and Marahiel 2007). Many enteropathogens have also evolved specific strategies to more efficiently scavenge any available iron. Salmonella typhimurium for example secretes Salmochelin, which is not recognised by lipocalin2/NGAL (Raffatellu et al.2009). Using Salmochelin, S. typhimurium is able to obtain enough iron to overcome iron-restriction, leading to a selective growth advantage over neighbouring bacteria. This proves especially important in the context of the inflamed intestine where Salmonella thrives amidst large quantities of Lipocalin2 secreted mainly by recruited neutrophils. Use of alternative energy sources Salmonella typhimurium is a useful model pathogen to illustrate the basic mechanisms that pathogens employ to bypass the metabolic environment established by the microbiota. Initial replication of Salmonella in the yet undisturbed gut depends on hydrogen gas, an important intermediate in microbiota metabolism (Maier et al.2013). Once Salmonella has invaded the gut mucosa and induced inflammation, other energy sources become available and are exploited by the pathogen. One of these is the aerobic and anaerobic respiration of 1, 2-propanediol generated by the resident microbiota (demonstrated in mono-associated mice using B. fragilis and B. thetaiotaomicron) through fermentation of fucose or rhamnose in the inflamed intestine (Faber et al.2017). Salmonella can also thrive by oxidative respiration on succinate, which is released by the resident microbiota (Spiga et al.2017). As an alternative energy source, Salmonella is also capable of using galactarate and glucarate, generated by the microbiota after antibiotic treatment. This metabolic versatility, especially in an oxidative environment as is found in the inflamed intestine, is likely the basis of the long known condition of antibiotic-mediated Salmonella expansion (Faber et al.2016). Another nutrient source is siacylic acid, liberated from the breakdown of sialyated mucins by B. thetaiotaomicron and other microbiota members. Bacteroides thetaiotaomicron secretes a sialidase but lacks the ability to use the freed siacylic acid itself. In turn, this acid is metabolised by C. difficile and S. typhimurium as an alternative nutrient source giving them a selective nutritional advantage over neighbouring bacteria (Ng et al.2013; Huang et al.2015). Differential energy utilisation has also been recently shown in some E. coli species, which use microbiota-derived formate as an alternative energy source to increase their advantage over other resident species (Hughes et al.2017). Several enteropathogens, including Citrobacter rodentium, C. jejuni and S. typhimurium, induce acute intestinal inflammation through their virulence factors (reviewed in Winter et al.2010a). The inflammation provides these pathogens with an advantage over the resident microbiota by transforming the intestine into an aerobic environment. Niche creation can be exemplified by the widely studied enteropathogen S. typhimurium (reviewed in Winter, Lopez and Bäumler 2013a; Winter and Bäumler 2014a). It is likely that similar mechanisms that have evolved in Salmonella have also evolved in other enteropathogens, for example E. coli and Shigella spp. and together contribute to the ‘enterobacterial bloom’ that is observed in the inflamed gut (Lupp et al.2007; Stecher et al.2010; reviewed in Winter and Bäumler 2014a). Inflammation leads to the production of respiratory electron acceptors, for example nitrogen species and reactive oxygen species. These products are converted in the intestine to nitrate. Nitrate can be used by Salmonella spp., E. coli and potentially other facultative anaerobe members of the Enterobacteriaceae as an alternative electron acceptor, giving them a selective advantage over other resident bacteria, which rely mainly on anaerobic fermentation of carbohydrates (Lopez et al.2012; Spees et al.2013; Winter et al. 2013a). Salmonella has also been shown to use other electron acceptors, for example S-oxides, ethanolamine or tetrathionate, which are present in larger amounts in the inflamed intestine (Winter et al.2010b; Thiennimitr et al.2011). In a recent study, it could be shown that Salmonella T3SS activation leads to a depletion of Clostridium species, which in turn leads to a decrease in butyrate levels. Butyrate is the most important energy source of colonocytes and butyrate oxidation to carbon dioxide leads to the consumption of local oxygen and the generation of an anaerobic environment. The lack of butyrate therefore increases tissue oxygenation, generating a favourable niche for Salmonella's aerobic expansion in the gut lumen (Rivera-Chávez et al.2016b). Under physiological conditions, the microbiota induces expression of PPARγ, resulting in an increase in β-oxidation of the colonocytes and hence an anoxic environment. In the context of antibiotic treatment, PPARγ-induction is inhibited and the colonocytes switch to anaerobic glucose oxidation. This then leads to increased availability of nitrate and allows for aerobic expansion of Enterobacteriaceae (Byndloss et al.2017). Inflammation also leads to the outgrowth of other bacterial species, for example B. vulgatus (Huang et al.2015). Through its sialidase activity, B. vulgatus releases sialic acid from the intestinal tissue, supporting the growth of E. coli. Bacteroides vulgatus thereby contributes to the occurrence of the ‘enterobacterial blooms’ observed during inflammation. Conversely, enterobacterial blooms during infection are abrogated when sialidase inhibitors are administered (Huang et al.2015). Gut inflammation can also boost horizontal gene transfer, either between pathogenic and commensal enteropathogens or between dense populations of enteropathogens in the context of the so-called enterobacterial booms (see text above). This has been shown for the transfer of a colicin-carrying plasmid p2 (Stecher et al.2012) as well as of temperate phages (Diard et al.2017). Enterobacterial blooms can therefore contribute to pathogen evolution of some species. Virulence genes Once in contact with the host, pathogens have developed different strategies to influence the host and exploit it to their own benefit. This is mainly achieved through the so-called virulence factors. First and foremost, pathogens express ‘classical’ virulence factors, for example toxins and the T3SS and their associated effector proteins. The function and specific role of these virulence factors have been discussed in detail elsewhere (Puhar and Sansonetti 2014; Qiu and Luo 2017; and many others for specific pathogens). The expression of these virulence factors can be constitutive. However, with the immense fitness cost virulence gene expression imparts on the pathogen, virulence gene expression is often regulated by environmental cues. This means that the bacterium only expresses the virulence genes once it is in close contact with the host and at the right location along the gastrointestinal tract. Induction of pathogen virulence genes by cues from the host Different host cues allow invading pathogens to pinpoint their position within their host and to regulate virulence genes only once the appropriate location has been reached. Host cues for virulence regulation include bile acids (Antunes et al.2012; Brotcke Zumsteg et al.2014; Eade et al.2016), pH (Behari, Stagon and Calderwood 2001), temperature (Elhadad et al.2015; Nuss et al.2015; Fraser and Brown 2017), nutrient availability (reviewed in Porcheron, Schouler and Dozois 2016), and oxygen levels (Marteyn et al.2010; Fraser and Brown 2017; reviewed in Marteyn et al.2011; Marteyn, Gazi and Sansonetti 2012). Oxygen levels are dynamic within the intestine and even within the anoxic colon an oxygen tension gradient is present in close proximity to the epithelial surface. Shigella flexneri has adapted to this gradient by repressing its T3SS in response to reduced oxygen levels encountered in the lumen of the intestine. The key outcome is to conserve metabolic resources in this energy and nutrient depleted environment. This regulation has the added benefit of more closely aligning the expression of virulence factors to the site of infection at the epithelial layer, where they are actually used. The suppression of the T3SS system is mediated by the oxygen sensitive regulator gene fnr. When oxygen pressure increases near the epithelium, the anaerobic block on the master regulators of the T3SS, spa32 and spa33 is released and the genes of the T3SS can be expressed (Marteyn et al.2010). Another example of regulated virulence is the bile salt-mediated activation of virulence in V. cholerae. It was recently shown through a series of elegant in vitro experiments in a tissue model of infection that virulence genes of V. cholerae are induced by the bile salt taurocholate, glyocholate and cholate, but not the deconjugated deoxycholate or chenodeoxycholate. This virulence activation is mediated through the dimerisation of the transcription factor TcpP by disulphide bond formation. Consequently, a V. cholerae strain mutated in the respective cysteine is unable to respond to the bile salts, leading to a competitive disadvantage compared to the wild-type strain in an infant mouse model of colonisation. This colonisation difference was abolished when a bile-salt sequestering resine, cholestyramine, was co-administered, confirming the crucial role of bile acids in the observed colonisation defect (Yang et al.2013). A third example is the regulation of virulence genes in Enterotoxigenic E. coli (ETEC) and its close relative, the mouse pathogen C. rodentium in the intestine. A recent study has shown that the two neurotransmitters epinephrine and norepinephrine that are produced by the endocrine cells localised in the intestine are needed for the full expression of virulence/colonisation genes (Moreira et al.2016). Together, these observations show that pathogens have evolved varied and complex mechanisms to tightly regulate their virulence attributes. This helps pathogens avoid unnecessary energetic costs that may lead to a loss of fitness in the highly competitive gut environment (see Diard and Hardt 2017, for a recent review on the evolution of bacterial virulence). Induction of pathogens's virulence genes by members of the microbiota We previously discussed the cues from the host that lead to the induction of virulence genes expression in the invading pathogens. Beside this host-mediated induction, some virulence genes are also controlled by sensing metabolites derived from the microbiota, for example SCFAs (butyrate, actetate, lactate and propionate). A recent study has shown that microbiota-derived SCFAs modulate the expression of virulence genes in C. jejuni. The authors discovered that the gradient of SCFAs butyrate, acetate, and lactate along the intestinal tract guide expression of genes involved in virulence and commensalism of C. jejuni. Lactate, which is abundant in the upper intestinal tract, suppresses production of C. jejuni virulence genes, while acetate and butyrate, two SCFAs that are mostly produced in the lower intestinal tract, activate virulence pathways (Luethy et al.2017). Expression of the Salmonella pathogenicity island 1 (SPI-1) is inhibited in the presence of propionate, an SCFA that is produced mainly by Lactobacilli and Bifidobacteria and is more abundant in the upper gastrointestinal tract. Propionate acts through posttranslational modification on HilD, the master regulator of the Salmonella SPI-1 (Hung et al.2013). This inhibition ensures that the coordinated expression of SPI-1 genes starts only in the distal small intestine, the main site of Salmonella infection. Another example of microbiota-mediated virulence gene expression is the enhancement of enterohemorraghic E. coli (EHEC) T3SS by B. thetaiotaomicron. Bacteroides thetaiotaomicron is an abundant member of the gut microbiota metabolising complex polysaccharides into monosaccharides that can be further processed by a number of other bacteria. The presence of B. thetaiotaomicron leads to a local increase in the levels of succinate, which is sensed by the transcription factor Cra of EHEC. Cra activation leads to an increase in the expression of the genes encoding EHECs T3SS while leaving the general growth of the pathogen unaffected (Curtis et al.2014). Induction of AMP's by pathogens to inhibit microbiota competition Some pathogens have evolved mechanisms to exploit the host's own antibacterial defences. By developing countermeasures against host AMPs, pathogens can rely on the host response to combat the resident microbiota and gain a selective advantage. Salmonella typhimurium for example uses an alternative siderophore (Salmochelin, described above), which is resistant to chelation by Lipocalin2. Salmonella has also evolved strategies to resist against calprotectin-induced sequestration of zinc and manganese (Liu et al.2012), giving Salmonella a selective advantage over the majority of microbiota members that do not have the necessary tools to survive in the inflamed gut. Salmonella infection induces the cytokine IL-22, which in turn activates AMPs (Behnsen et al.2014). One of the proteins induced is the AMP Reg3beta. Previously, Stelter et al. (2011) and Miki, Holst and Hardt 2012 showed that the induction of this AMP inhibits the competing microbiota, while having no effect on the resistant S. typhimurium. In a new study, Miki and collaborators could show that Reg3beta extends gut colonisation by S. typhimurium through the prolonged induction of a pro-inflammatory environment and changes to the microbiota, especially an inhibition of Bacteroides species. The alteration of the microbiota also leads to profound changes in the metabolic landscape with metabolites of Vitamin B6 being the most affected. The authors could show that the re-insertion of Bacteroides species or supplementation of Vitamin B6 alone was able to accelerate clearance of Salmonella from infected mice (Miki et al.2017). A recent study in Ixodes scacpularis ticks showed a similar mechanism whereby Anaplasma phagocytophilum infection induced Ixodes anti-freeze glycoprotein (Iafgp), which alters biofilm formation in the Ixodes gut to destabilise the resident microbiota and facilitate niche construction of A. phagocytophilum. It is likely that many pathogens have evolved similar mechanisms to take the advantage of host defence mechanisms to facilitate niche construction and induce a host-derived selective advantage over the resident microbiota. Evolutionary adaptions of pathogens to overcome homeostasis: penetrating the mucus layer As described previously, the mucus layer constitutes a thick, protective layer between the gut lumen and the epithelium. To get access to the epithelium, pathogens have evolved strategies to penetrate the mucus layer and enter the underlying epithelium. Porphyromonas gingivalis, a pathogen found mostly in the oral cavity, secretes a cysteine protease (RgpB), which leads to Muc2 cleavage (van der Post et al.2013). Mucinases also play an important role in the colonisation and fitness of pathogenic E. coli (Valeri et al.2015), an E. coli strain associated with Crohn's disease (Gibold et al.2016), and also eukaryotic pathogens such as Candida albicans (Colina et al.1996) or Entamoeba histolytica (Lidell et al.2006). It is likely that other enteropathogens also express mucinases to gain access to the underlying epithelium although more research is needed to fully address the scope of mucinase secretion and usage by pathogens. Mechanisms established by the microbiota to clear off invading pathogen after infection The microbiota not only plays an important role in preventing the colonisation of pathogens, but also in the pathogen clearing from the gut upon resolution of the inflammation. The mechanisms underlying this process differ from those governing colonisation resistance as the mucosa and the microbiota have both been affected and therefore need to return to homeostasis (Endt et al.2010). In the case of S. typhimurium infection it was shown that recovery is mainly mediated by the microbiota and was largely independent of the IgA pool (Endt et al.2010). Mechanistic insights on the underlying causes of clearance were elucidated in a study on V. cholera infection, showing an increase in Ruminococcus obeum upon infection of mice with the pathogen. The same was also observed in a cohort of infected humans from Bangladesh recovering from the disease. In elegant mouse studies, the authors showed that R. obeum, through the expression of the luxS gene (autoinducer-2 synthase), promotes quorum sensing-mediated restriction of virulence gene expression in V. cholerae, leading to a decrease in host symptoms (Hsiao et al.2014). DYSBIOSIS: TOWARDS A NEW INTERPRETATION OF KOCH'S POSTULATES It is now common knowledge that the gut is a complex ecosystem with different interacting entities and that infections must be understood in this context rather than isolated as a pathogen and a host. In consequence, for these complex diseases, neither Koch's postulates (a pathogen, a disease) nor the molecular Koch's postulates as proposed by Stanley Falkow (a virulence gene, a disease; Falkow 1988) are sufficient. In a very recent review by Neville and collaborators, a third interpretation of Koch's postulates, the commensal Koch's postulates, was proposed (a beneficial microbe, an ameliorated disease state). The authors infer a new framework for establishing causation in microbiome studies where they use the commensal Koch's postulates to test if a given microorganism is able to ameliorate a disease state in a reproducible manner (Neville, Forster and Lawley 2017). As in the original Koch's postulates, they propose that for inferring causation, the ‘beneficial’ commensals need to be isolated in pure cultures before they are re-introduced and tested in a host for their capacity to mitigate disease. We propose yet another interpretation of Koch’ postulates, which we have termed ‘ecological Koch's postulates (a gut ecosystem state, a disease). Underlying these postulates is the fact that the gut harbours a full ecosystem, rather than an isolated bacterium or pathogen. This means that rather than an isolated microorganism or group of microorganisms, a whole ecosystem, including the microbiota, the genetic make-up of the host as well as nutrition, age, etc., form an entity, which can ultimately lead to disease (see Fig. 3 and Box 3). Figure 3. View largeDownload slide The evolution of Koch's postulates. In recent years, the original Koch's postulates (‘a pathogen, a disease’) have been extended to the molecular Koch's postulates (Stanley Falkow, ‘a virulence genes, a disease’) and here to the ecological Koch's postulates (‘a dysbiosis, a disease’). Figure 3. View largeDownload slide The evolution of Koch's postulates. In recent years, the original Koch's postulates (‘a pathogen, a disease’) have been extended to the molecular Koch's postulates (Stanley Falkow, ‘a virulence genes, a disease’) and here to the ecological Koch's postulates (‘a dysbiosis, a disease’). Box 3. Postulates for defining a disease-promoting ecosystem (dysbiosis). Ecological Koch's postulates The dysbiotic microbiota is found in similar composition/with similar characteristics in all affected individuals. The dysbiotic microbiota can be retrieved from the affected host. Gavaging of germ-free hosts with this retrieved microbiota leads, in combination with a similar environment (ex. genetic make-up of the host, nutrition, age), to similar symptoms as in the affected individual. The dysbiotic microbiota composition remains fairly stable in the newly affected host. Original Koch's postulates The microorganism must be present in all diseased individuals. The microorganism must be isolated from the diseased host and be grown in a pure culture. The re-inoculation of a naïve host with this pure culture must lead to the same disease as in the original host. The microorganism must be recovered from the newly diseased host. The ecological Koch's postulates are based on two major observations, both pointing towards the fact that the clear distinction between a pathogen and a commensal are probably too simple of a model to explain complex disease states. Not every person infected with a ‘pathogen’ will manifest disease. Therefore, host susceptibility not only from a genetic point of view, but also from the resident microbiota, the nutrition, earlier infections, or other insults to the microbiota, plays as much of a role in the manifestation of disease as does the presence of given virulence factors in an aggressing pathogen. The pathogens not only need to be present and harbour the virulence genes, but they also need to express these genes and be able to establish a niche for themselves within the competitive environment of the already established microbial community in order to replicate and then cause disease. In the last years, several gastrointestinal diseases have emerged, which are not associated with an overt pathogen, but where the microbial community as a whole seems to mediate the disease. Examples are intestinal bowel disease, colorectal cancer, obesity, and different states of malnutrition. Indeed, depending on the microbial community pathogens find themselves in, bacteria, which normally do behave as commensals may become invasive and cause disease. For all of these diseases, a decrease in the composition complexity of the microbiota leads to dysbiosis and an oxidation of the gut environment as well as an increase in aeortolerant species such as Enterobacteriaceae (Rivera-Chávez, Lopez and Bäumler 2017). These disturbances in the ecosystem lead to a lowered resilience and increased susceptibility to pathogens and other, normally commensal, bacteria with potential harmful properties (often called pathobionts). Indeed, these diseases are characterised by the fact that the wrong bacteria are in wrong proportions, in wrong ‘company’ (Huang et al.2015) or in the wrong ‘place’ (Brown et al.2015; Tomas et al.2016). The presence of commensal bacteria near the epithelial surface has been put in relation with the breakdown of gut homeostasis and emergence of pathological states in the context of environmental enteropathy (Brown et al.2015) or in a pre-diabetic state (Tomas et al.2016). In the ecological Koch's postulates, a dysbiotic community, including or not ‘classical pathogens’ or pathobionts therefore represents a disease. The entity of transmission is the complete dysbiotic microbiota rather than a pathogen (Koch's postulates), a virulence gene (molecular Koch's postulates) or a commensal (commensal Koch's postulates). In accordance to the other Koch's postulates, the ecological Koch's postulates are proven through the fact that a given entity (here the dysbiotic microbiota) from a diseased individual can provoke disease in a formerly healthy individual. To prove this hypothesis, one hence has to transmit the microbiota from a diseased individual into a germfree individual/mouse and this transplanted individual subsequently has to develop the signs of the disease. This transfer can either be performed in (I) ‘standard’ conditions, using a ‘wild-type, normally fed’ germ-free host (showing a direct effect of the microbiota on disease), or, else, in (II) a ‘pre-fragilised’ host, as an example in a mouse exhibiting a mutation in a given gene or eating a specific chow. In syndromes, which do need a pre-fragilised host, the dysbiotic microbiota contributes to disease, without however being the only cause for it. As stated earlier, several inflammatory, gastrointestinal diseases can be explained through the ecological Koch's postulates, including obesity. Indeed, if a microbiota from obese mice is transplanted into lean mice, the transplanted mice showed increased fat deposition (Turnbaugh et al.2006; Ridaura et al.2013). The same could also be proven for kwashiorkor, the oedematous form of acute undernutrition (Smith et al.2013) as well as for environmental enteropathy (Brown et al.2015). On the other hand, it is well known that mutations in nod2 facilitate and support the onset of IBD (Cho 2001). Therefore, to prove the contribution of the microbiota in IBD, a susceptible host, mutated for nod2, should be transplanted with the dysbiotic microbiota and this transplanted microbiota should worsen the disease state. An instructive example of a ‘pathological dysbiosis’ and hence a disease following the ecological Koch's postulates is chronic and acute malnutrition coupled to associated environmental enteropathy. Several reports have shown evidence that children suffering from one of these two syndromes have an altered colonic microbiota (Smith et al.2013; Subramanian et al.2014; Gough et al.2015; Blanton et al.2016a, 2016b) and increased abundance of asymptomatic pathogen carriage, including enteroaggregative E. coli (Havt et al.2017), Campylobacter spp. and Giardia spp. (Platts-Mills et al.2017). Furthermore, a recent study sequencing cultured microbes from two Bangladeshi children suffering or not of undernutrition showed that the B. fragilis strain found in the undernourished child is enterotoxic, while the strains found within the normally nourished child were not. When transplanting the native community into germfree mice and infecting with the enterotoxigenic B. fragilis strain, the authors could show that the enterotoxigenic strain causally led to malnutrition and associated pathophysiological disturbances only in its native community, but not when administered to mice harbouring the microbiota of the healthy child (Wagner et al.2016). These observations put forward the hypotheses that (I) even subclinical infections with enteropathogens can have negative effects on gut health and that (II) pathogens or pathobionts, depending on the community they dwell in, might have negative effects on host homeostasis or not. This indeed supports the concept of the ‘ecological Koch's postulates’, stating that the whole ecosystem, rather than an isolated element contributes to morbidity. Overall, we are only beginning to understand the complex relationships and interactions within the gut ecosystem and more research is needed in order to elucidate the origin and pathophysiological effect of the different dysbiotic communities and to understand the crosstalk they have between each other as well as with the host. CONCLUSION Infection biology has been moving in the last decades from the original Koch's postulates looking at pathogens, to molecular Koch's postulates looking at virulence factors, to the newly proposed ecological Koch's postulates looking at dysbiosis. Indeed, infection biology has shifted towards an integrated approach of systems biology, ecology and evolution. This increasing complexity makes it more and more difficult to untangle the causative effects of disease states and asks for imaginative and sophisticated designs of experiments to explain the underlying pathophysiological mechanisms. Particularly, experiments need to take into account the physiological and pathophysiological state of the infected host, for example the microbiota and the exact nutrition the model animals are receiving. In recent years, several initiatives have been launched to standardise the microbiota of model animals (Brugiroux et al.2016) or at least to meticulously report, not only the exact strain of pathogen used and the genetics of the mouse model, but also the microbiota composition, as well as the food composition of the animal models used (Ma et al.2012; Macpherson and McCoy 2015). This will prove indispensable in the future in order to compare different studies and explain the pathophysiological mechanisms underlying the complex interplay between pathogens, the microbiota, and their host. To date, we are only at the beginning of understanding the interactions within these ecosystems, the perturbations, which can be induced, and their effect on pathogen susceptibility and disease. The widely available techniques of sequencing, especially of metagenomics, metatranscriptomics and metabolomics, will prove essential in this endeavour. Special attention should also be paid to not forget that the microbiota harbours other organisms than prokaryotes, first and foremost viruses (including phages and prophages), and eukaryotes. Only an integrated view of the gut ecosystem, including the host, the pro- and eukaryome and virome as well as the pathogens will allow us to move forward in our understanding of which mechanisms are governing infection. The scientific community is on the verge of experiencing another revolution in understanding the complex network of gut interactions. This will surely open the way for more targeted and personalised interventions to infectious diseases based on interference or corrections to the misbalances in the gut ecosystem and restoration of gut homeostasis. This could include siderophore-based immunisation strategies (Mike et al.2016; Sassone-Corsi et al.2016a), probiotic bacteria (e.g. E. coli strain Nissle) using similar iron-scavenging mechanisms than the invading pathogen (Deriu et al.2013), probiotic strains consuming H2 and hence restricting the use of this energy source for invading pathogens (Maier et al.2013), the development of probiotic strains expressing bacteriocins or microcins targeting the pathogen (Kommineni et al.2015; Hegarty et al.2016; Sassone-Corsi et al.2016b), expressing iron-sequestering mechanisms to inhibit invading pathogens (Vazquez-Gutierrez et al.2016), siacylidase inhibitors (Huang et al.2015) or inhibitors of anaerobic respiration (Winter and Bäumler 2014b) (see Table 1). There are certainly many other possible intervention strategies yet to be discovered. The generated knowledge will therefore prove very important in paving the way to propose other intervention strategies, which do not rely on antibiotics. In a world where antibiotic resistance is on a constant rise this aspect will be of utmost importance. Table 1. Possible new intervention strategies intervening with the gut ecosystem to target diseases related to dysbioses-induced enteropathogenic blooms. Intervention strategy Evidence for intervention References Siderophore-based immunisation strategies Mice immunised mice with siderophores conjugated to an immunogenic carrier protein were able to elicit a potent immune response and to protect against urinary tract infections. Mike et al. (2016) and Sassone-Corsi et al. (2016a) Mice immunised with a cholera toxin β-siderophore conjugate show a potent immune response and are able to protect against infection with Salmonella typhimurium. Probiotic strains with similar or more efficient iron-sequestering mechanisms inhibiting invading pathogens Oral gavage with Escherichia coli strain Nissle 1917 reduces S. typhimurium colonisation in mouse models of acute colitis or chronic persistent infection. The observed probiotic activity depends on the iron-sequestering mechanisms of E. coli Nissle, which is highly similar to the one found in Salmonella typhimurium. Deriu et al. (2013) and Vazquez-Gutierrez et al. (2016) The two bifidobacterial strains Bifidobacterium pseudolongum PV8-2 (Bp PV8-2) and Bifidobacterium kashiwanohense PV20-2 (Bk PV20-2) are able to inhibit growth of S. typhimurium and E. coli O157:H45 (EHEC) in in vitro co-culture experiments and are able to displace the pathogens on mucus-producing HT29-MTX cell lines. Probiotic strains consuming H2 to prevent initial ecosystem invasion In a non-inflamed intestine, S. typhimurium relies on H2 metabolisms for invasion. Introducing H2-consuming bacteria into the microbiota reduces hyb-dependent S. typhimurium growth. Maier et al. (2013) Probiotic strains producing butyrate Oral gavage of mice with tributyrin reduces growth of S. typhimurium in the inflamed intestine. Rivera-Chávez et al. (2016b) Probiotic strains expressing bacteriocins or microcins targeting the pathogen Colonisation of mice with a bacteriocin-carrying E. faecalis strain defective for conjugation leads to clearance of vancomycin resistant enterococci. Kommineni et al. (2015), Hegarty et al. (2016) and Sassone-Corsi et al. (2016b) Microcin-producing E. coli Nissle is able to limit the growth of commensal E. coli, adherent–invasive E. coli and Salmonella enterica in the inflamed intestine. Siacylidase inhibitors Oral administration of sialidase inhibitors decreases outgrowth of E. coli as well as the severity of colitis in a mouse model. (Huang et al. (2015) Inhibitors of aerobic respiration Aerobic respiration is used by Salmonella spp and other Enterobacteriaceae to thrive in the inflamed intestine. Winter and Bäumler (2014b) Sustaining PPAR-γ signalling PPAR-γ signalling in the homeostatic intestine leads to β-oxidation in the colonocytes and hence an anoxic environment limiting nitrate availability and outgrowth of Enterobacteriaceae Byndloss et al. (2017) Intervention strategy Evidence for intervention References Siderophore-based immunisation strategies Mice immunised mice with siderophores conjugated to an immunogenic carrier protein were able to elicit a potent immune response and to protect against urinary tract infections. Mike et al. (2016) and Sassone-Corsi et al. (2016a) Mice immunised with a cholera toxin β-siderophore conjugate show a potent immune response and are able to protect against infection with Salmonella typhimurium. Probiotic strains with similar or more efficient iron-sequestering mechanisms inhibiting invading pathogens Oral gavage with Escherichia coli strain Nissle 1917 reduces S. typhimurium colonisation in mouse models of acute colitis or chronic persistent infection. The observed probiotic activity depends on the iron-sequestering mechanisms of E. coli Nissle, which is highly similar to the one found in Salmonella typhimurium. Deriu et al. (2013) and Vazquez-Gutierrez et al. (2016) The two bifidobacterial strains Bifidobacterium pseudolongum PV8-2 (Bp PV8-2) and Bifidobacterium kashiwanohense PV20-2 (Bk PV20-2) are able to inhibit growth of S. typhimurium and E. coli O157:H45 (EHEC) in in vitro co-culture experiments and are able to displace the pathogens on mucus-producing HT29-MTX cell lines. Probiotic strains consuming H2 to prevent initial ecosystem invasion In a non-inflamed intestine, S. typhimurium relies on H2 metabolisms for invasion. Introducing H2-consuming bacteria into the microbiota reduces hyb-dependent S. typhimurium growth. Maier et al. (2013) Probiotic strains producing butyrate Oral gavage of mice with tributyrin reduces growth of S. typhimurium in the inflamed intestine. Rivera-Chávez et al. (2016b) Probiotic strains expressing bacteriocins or microcins targeting the pathogen Colonisation of mice with a bacteriocin-carrying E. faecalis strain defective for conjugation leads to clearance of vancomycin resistant enterococci. Kommineni et al. (2015), Hegarty et al. (2016) and Sassone-Corsi et al. (2016b) Microcin-producing E. coli Nissle is able to limit the growth of commensal E. coli, adherent–invasive E. coli and Salmonella enterica in the inflamed intestine. Siacylidase inhibitors Oral administration of sialidase inhibitors decreases outgrowth of E. coli as well as the severity of colitis in a mouse model. (Huang et al. (2015) Inhibitors of aerobic respiration Aerobic respiration is used by Salmonella spp and other Enterobacteriaceae to thrive in the inflamed intestine. Winter and Bäumler (2014b) Sustaining PPAR-γ signalling PPAR-γ signalling in the homeostatic intestine leads to β-oxidation in the colonocytes and hence an anoxic environment limiting nitrate availability and outgrowth of Enterobacteriaceae Byndloss et al. (2017) View Large Table 1. Possible new intervention strategies intervening with the gut ecosystem to target diseases related to dysbioses-induced enteropathogenic blooms. Intervention strategy Evidence for intervention References Siderophore-based immunisation strategies Mice immunised mice with siderophores conjugated to an immunogenic carrier protein were able to elicit a potent immune response and to protect against urinary tract infections. Mike et al. (2016) and Sassone-Corsi et al. (2016a) Mice immunised with a cholera toxin β-siderophore conjugate show a potent immune response and are able to protect against infection with Salmonella typhimurium. Probiotic strains with similar or more efficient iron-sequestering mechanisms inhibiting invading pathogens Oral gavage with Escherichia coli strain Nissle 1917 reduces S. typhimurium colonisation in mouse models of acute colitis or chronic persistent infection. The observed probiotic activity depends on the iron-sequestering mechanisms of E. coli Nissle, which is highly similar to the one found in Salmonella typhimurium. Deriu et al. (2013) and Vazquez-Gutierrez et al. (2016) The two bifidobacterial strains Bifidobacterium pseudolongum PV8-2 (Bp PV8-2) and Bifidobacterium kashiwanohense PV20-2 (Bk PV20-2) are able to inhibit growth of S. typhimurium and E. coli O157:H45 (EHEC) in in vitro co-culture experiments and are able to displace the pathogens on mucus-producing HT29-MTX cell lines. Probiotic strains consuming H2 to prevent initial ecosystem invasion In a non-inflamed intestine, S. typhimurium relies on H2 metabolisms for invasion. Introducing H2-consuming bacteria into the microbiota reduces hyb-dependent S. typhimurium growth. Maier et al. (2013) Probiotic strains producing butyrate Oral gavage of mice with tributyrin reduces growth of S. typhimurium in the inflamed intestine. Rivera-Chávez et al. (2016b) Probiotic strains expressing bacteriocins or microcins targeting the pathogen Colonisation of mice with a bacteriocin-carrying E. faecalis strain defective for conjugation leads to clearance of vancomycin resistant enterococci. Kommineni et al. (2015), Hegarty et al. (2016) and Sassone-Corsi et al. (2016b) Microcin-producing E. coli Nissle is able to limit the growth of commensal E. coli, adherent–invasive E. coli and Salmonella enterica in the inflamed intestine. Siacylidase inhibitors Oral administration of sialidase inhibitors decreases outgrowth of E. coli as well as the severity of colitis in a mouse model. (Huang et al. (2015) Inhibitors of aerobic respiration Aerobic respiration is used by Salmonella spp and other Enterobacteriaceae to thrive in the inflamed intestine. Winter and Bäumler (2014b) Sustaining PPAR-γ signalling PPAR-γ signalling in the homeostatic intestine leads to β-oxidation in the colonocytes and hence an anoxic environment limiting nitrate availability and outgrowth of Enterobacteriaceae Byndloss et al. (2017) Intervention strategy Evidence for intervention References Siderophore-based immunisation strategies Mice immunised mice with siderophores conjugated to an immunogenic carrier protein were able to elicit a potent immune response and to protect against urinary tract infections. Mike et al. (2016) and Sassone-Corsi et al. (2016a) Mice immunised with a cholera toxin β-siderophore conjugate show a potent immune response and are able to protect against infection with Salmonella typhimurium. Probiotic strains with similar or more efficient iron-sequestering mechanisms inhibiting invading pathogens Oral gavage with Escherichia coli strain Nissle 1917 reduces S. typhimurium colonisation in mouse models of acute colitis or chronic persistent infection. The observed probiotic activity depends on the iron-sequestering mechanisms of E. coli Nissle, which is highly similar to the one found in Salmonella typhimurium. Deriu et al. (2013) and Vazquez-Gutierrez et al. (2016) The two bifidobacterial strains Bifidobacterium pseudolongum PV8-2 (Bp PV8-2) and Bifidobacterium kashiwanohense PV20-2 (Bk PV20-2) are able to inhibit growth of S. typhimurium and E. coli O157:H45 (EHEC) in in vitro co-culture experiments and are able to displace the pathogens on mucus-producing HT29-MTX cell lines. Probiotic strains consuming H2 to prevent initial ecosystem invasion In a non-inflamed intestine, S. typhimurium relies on H2 metabolisms for invasion. Introducing H2-consuming bacteria into the microbiota reduces hyb-dependent S. typhimurium growth. Maier et al. (2013) Probiotic strains producing butyrate Oral gavage of mice with tributyrin reduces growth of S. typhimurium in the inflamed intestine. Rivera-Chávez et al. (2016b) Probiotic strains expressing bacteriocins or microcins targeting the pathogen Colonisation of mice with a bacteriocin-carrying E. faecalis strain defective for conjugation leads to clearance of vancomycin resistant enterococci. Kommineni et al. (2015), Hegarty et al. (2016) and Sassone-Corsi et al. (2016b) Microcin-producing E. coli Nissle is able to limit the growth of commensal E. coli, adherent–invasive E. coli and Salmonella enterica in the inflamed intestine. Siacylidase inhibitors Oral administration of sialidase inhibitors decreases outgrowth of E. coli as well as the severity of colitis in a mouse model. (Huang et al. (2015) Inhibitors of aerobic respiration Aerobic respiration is used by Salmonella spp and other Enterobacteriaceae to thrive in the inflamed intestine. Winter and Bäumler (2014b) Sustaining PPAR-γ signalling PPAR-γ signalling in the homeostatic intestine leads to β-oxidation in the colonocytes and hence an anoxic environment limiting nitrate availability and outgrowth of Enterobacteriaceae Byndloss et al. (2017) View Large Acknowledgements We would like to thank Pamela Schnupf, Kelsey Huus and Florent Mazel for fruitful discussions and critical reading of the manuscript. PV was supported by an Early.PostdocMobility Fellowship form the Swiss National Science Foundation, a Roux-Cantarini Postdoctoral Fellowship as well as a L'Oréal-UNESCO for Women in Science France Fellowship. PJS is an HHMI Senior Foreign Scholar and CIFAR scholar in the human microbiome consortium. FUNDING Work in PJS's group is supported by European Research Council (ERC) Grant No. 339579 (DECRYPT) . Conflict of interest. None declared. REFERENCES Ackermann M , Stecher B , Freed NE et al. Self-destructive cooperation mediated by phenotypic noise . Nature 2008 ; 454 : 987 – 90 . Google Scholar CrossRef Search ADS PubMed Alvarez-Sieiro P , Montalbán-López M , Mu D et al. Bacteriocins of lactic acid bacteria: extending the family . Appl Microbiol Biotechnol 2016 ; 100 : 2939 – 51 . Google Scholar CrossRef Search ADS PubMed Anderson MC , Vonaesch P , Saffarian A et al. Shigella sonnei encodes a functional T6SS used for interbacterial competition and niche occupancy . Cell Host Microbe 2017 ; 21 : 769 – 76 . e3 . Google Scholar CrossRef Search ADS PubMed Antunes LCM , Wang M , Andersen SK et al. Repression of Salmonella enterica phoP expression by small molecules from physiological bile. J Bacteriol . American Society for Microbiology ; 2012 ; 194 : 2286 – 96 . Araújo JR , Tomas J , Brenner C et al. Impact of high-fat diet on the intestinal microbiota and small intestinal physiology before and after the onset of obesity . Biochimie . 2017 ; 141 : 97 – 106 . Google Scholar CrossRef Search ADS PubMed Atarashi K , Tanoue T , Ando M et al. Th17 cell induction by adhesion of microbes to intestinal epithelial cells . Cell 2015 ; 163 : 367 – 80 . Google Scholar CrossRef Search ADS PubMed Atarashi K , Tanoue T , Shima T et al. Induction of colonic regulatory T cells by indigenous Clostridium species . Science 2011 ; 331 : 337 – 41 . Google Scholar CrossRef Search ADS PubMed Aubert DF , Xu H , Yang J et al. A Burkholderia type VI effector deamidates Rho GTPases to activate the pyrin inflammasome and trigger inflammation . Cell Host Microbe 2016 ; 19 : 664 – 74 . Google Scholar CrossRef Search ADS PubMed Audebert C , Even G , Cian A et al. Colonization with the enteric protozoa Blastocystis is associated with increased diversity of human gut bacterial microbiota . Sci Rep 2016 ; 6 : 25255 . Google Scholar CrossRef Search ADS PubMed Barash NR , Maloney JG , Singer SM et al. Giardia alters commensal microbial diversity throughout the murine gut . Infect Immun 2017 ; 85 : e00948 – 16 . Google Scholar CrossRef Search ADS PubMed Barthel M , Hapfelmeier S , Quintanilla-Martínez L et al. Pretreatment of mice with streptomycin provides a Salmonella enterica serovar Typhimurium colitis model that allows analysis of both pathogen and host . Infect Immun 2003 ; 71 : 2839 – 58 . Google Scholar CrossRef Search ADS PubMed Behari J , Stagon L , Calderwood SB . pepA, a gene mediating pH regulation of virulence genes in Vibrio cholerae. J Bacteriol . American Society for Microbiology ; 2001 ; 183 : 178 – 88 . Behnsen J , Jellbauer S , Wong CP et al. The cytokine IL-22 promotes pathogen colonization by suppressing related commensal bacteria . Immunity 2014 ; 40 : 262 – 73 . Google Scholar CrossRef Search ADS PubMed Bernal P , Allsopp LP , Filloux A et al. The Pseudomonas putida T6SS is a plant warden against phytopathogens . ISME J 2017 ; 11 : 972 – 87 . Google Scholar CrossRef Search ADS PubMed Bladergroen MR , Badelt K , Spaink HP . Infection-blocking genes of a symbiotic Rhizobium leguminosarum strain that are involved in temperature-dependent protein secretion . Mol Plant Microbe Interact 2003 ; 16 : 53 – 64 . Google Scholar CrossRef Search ADS PubMed Blanton LV , Barratt MJ , Charbonneau MR et al. Childhood undernutrition, the gut microbiota, and microbiota-directed therapeutics . Science 2016a ; 352 : 1533 – 3 . Google Scholar CrossRef Search ADS Blanton LV , Charbonneau MR , Salih T et al. Gut bacteria that prevent growth impairments transmitted by microbiota from malnourished children . Science 2016b ; 351 , DOI: https://doi.org/10.1126/science.aad3311 . Bohnhoff M , Drake BL , Miller CP . Effect of streptomycin on susceptibility of intestinal tract to experimental Salmonella infection . Proc Soc Exp Biol Med 1954 ; 86 : 132 – 7 . Google Scholar CrossRef Search ADS PubMed Borgeaud S , Metzger LC , Scrignari T et al. The type VI secretion system of Vibrio cholerae fosters horizontal gene transfer . Science 2015 ; 347 : 63 – 7 . Google Scholar CrossRef Search ADS PubMed Braun T , Di Segni A , BenShoshan M et al. Fecal microbial characterization of hospitalized patients with suspected infectious diarrhea shows significant dysbiosis . Sci Rep 2017 ; 7 : 1088 . Google Scholar CrossRef Search ADS PubMed Breurec S , Vanel N , Bata P et al. Etiology and epidemiology of diarrhea in hospitalized children from low income country: a matched case-control study in central african republic . PLoS Negl Trop Dis 2016 ; 10 : e0004283 . Google Scholar CrossRef Search ADS PubMed Broadhurst MJ , Ardeshir A , Kanwar B et al. Therapeutic helminth infection of macaques with idiopathic chronic diarrhea alters the inflammatory signature and mucosal microbiota of the colon . PLoS Pathog 2012 ; 8 : e1003000 . Google Scholar CrossRef Search ADS PubMed Brodmann M , Dreier RF , Broz P et al. Francisella requires dynamic type VI secretion system and ClpB to deliver effectors for phagosomal escape . Nat Commun 2017 ; 8 : 15853 . Google Scholar CrossRef Search ADS PubMed Brotcke Zumsteg A , Goosmann C , Brinkmann V et al. IcsA is a Shigella flexneri adhesin regulated by the type III secretion system and required for pathogenesis . Cell Host & Microbe . 2014 ; 15 : 435 – 45 . Google Scholar CrossRef Search ADS PubMed Brown EM , Wlodarska M , Willing BP et al. Diet and specific microbial exposure trigger features of environmental enteropathy in a novel murine model . Nat Commun 2015 ; 6 : 7806 . Google Scholar CrossRef Search ADS PubMed Brugiroux S , Beutler M , Pfann C et al. Genome-guided design of a defined mouse microbiota that confers colonization resistance against Salmonella enterica serovar Typhimurium . Nat Microbiol 2016 ; 2 : 16215 . Google Scholar CrossRef Search ADS PubMed Byndloss MX , Olsan EE , Rivera-Chávez F et al. Microbiota-activated PPAR-γ signaling inhibits dysbiotic Enterobacteriaceae expansion . Science 2017 ; 357 : 570 – 5 . Google Scholar CrossRef Search ADS PubMed Calcuttawala F , Hariharan C , Pazhani GP et al. Characterization of E-type colicinogenic plasmids from Shigella sonnei . FEMS Microbiol Lett 2017 ; 364 , DOI: https://doi.org/10.1093/femsle/fnx060 . Camarinha-Silva A , Maushammer M , Wellmann R et al. Host genome influence on gut microbial composition and microbial prediction of complex traits in pigs . Genetics 2017 ; 206 : 1637 – 44 . Google Scholar CrossRef Search ADS PubMed Cantacessi C , Giacomin P , Croese J et al. Impact of experimental hookworm infection on the human gut microbiota . J Infect Dis 2014 ; 210 : 1431 – 4 . Google Scholar CrossRef Search ADS PubMed Carbonero F , Benefiel AC , Alizadeh-Ghamsari AH et al. Microbial pathways in colonic sulfur metabolism and links with health and disease . Front Physiol 2012 ; 3 : 448 . Google Scholar CrossRef Search ADS PubMed Cassat JE , Skaar EP . Iron in infection and immunity . Cell Host Microbe 2013 ; 13 : 509 – 19 . Google Scholar CrossRef Search ADS PubMed Chase JM , Leibold MA . Ecological niches: linking classical and contemporary approaches . Biodivers Conserv 2004 ; 13 : 1791 – 3 . Google Scholar CrossRef Search ADS Chassaing B , Koren O , Goodrich JK et al. Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome . Nature 2015 ; 519 : 92 – 6 . Google Scholar CrossRef Search ADS PubMed Chassaing B , Van de Wiele T , De Bodt J et al. Dietary emulsifiers directly alter human microbiota composition and gene expression ex vivo potentiating intestinal inflammation . Gut 2017 ; 66 : 1414 – 27 . Google Scholar CrossRef Search ADS PubMed Chatzidaki-Livanis M , Geva-Zatorsky N , Comstock LE . Bacteroides fragilis type VI secretion systems use novel effector and immunity proteins to antagonize human gut Bacteroidales species . Proc Natl Acad Sci USA 2016 ; 113 : 3627 – 32 . Google Scholar CrossRef Search ADS PubMed Chen H , Yang D , Han F et al. The bacterial T6SS effector EvpP prevents NLRP3 inflammasome activation by inhibiting the Ca(2+)-dependent MAPK-Jnk pathway . Cell Host Microbe 2017 ; 21 : 47 – 58 . Google Scholar CrossRef Search ADS PubMed Cho I , Blaser MJ . The human microbiome: at the interface of health and disease . Nat Rev Genet 2012 ; 13 : 260 – 70 . Google Scholar CrossRef Search ADS PubMed Cho JH. Update on the genetics of inflammatory bowel disease . Curr Gastroenterol Rep 2001 ; 3 : 458 – 63 . Google Scholar CrossRef Search ADS PubMed Chow J , Mazmanian SK . A pathobiont of the microbiota balances host colonization and intestinal inflammation . Cell Host Microbe 2010 ; 7 : 265 – 76 . Google Scholar CrossRef Search ADS PubMed Chudnovskiy A , Mortha A , Kana V et al. Host-protozoan interactions protect from mucosal infections through activation of the inflammasome . Cell 2016 ; 167 : 444 – 56 . e14 . Google Scholar CrossRef Search ADS PubMed Clarke TB. Microbial programming of systemic innate immunity and resistance to infection . PLoS Pathog 2014 ; 10 : e1004506 . Google Scholar CrossRef Search ADS PubMed Clemente JC , Ursell LK , Parfrey LW et al. The impact of the gut microbiota on human health: an integrative view . Cell 2012 ; 148 : 1258 – 70 . Google Scholar CrossRef Search ADS PubMed Clements WD , Parks R , Erwin P et al. Role of the gut in the pathophysiology of extrahepatic biliary obstruction . Gut 1996 ; 39 : 587 – 93 . Google Scholar CrossRef Search ADS PubMed Colina AR , Aumont F , Deslauriers N et al. Evidence for degradation of gastrointestinal mucin by Candida albicans secretory aspartyl proteinase . Infect Immun 1996 ; 64 : 4514 – 9 . Google Scholar PubMed Collins FWJ , O’Connor PM , O'Sullivan O et al. Bacteriocin gene-trait matching across the complete Lactobacillus pan-genome . Sci Rep 2017 ; 7 : 3481 . Google Scholar CrossRef Search ADS PubMed Cooper P , Walker AW , Reyes J et al. Patent human infections with the whipworm, Trichuris trichiura, are not associated with alterations in the faecal microbiota . PLoS ONE 2013 ; 8 : e76573 . Google Scholar CrossRef Search ADS PubMed Corthier G , Muller MC . Emergence in gnotobiotic mice of nontoxinogenic clones of Clostridium difficile from a toxinogenic one . Infect Immun 1988 ; 56 : 1500 – 4 . Google Scholar PubMed Costello EK , Lauber CL , Hamady M et al. Bacterial community variation in human body habitats across space and time . Science 2009 ; 326 : 1694 – 7 . Google Scholar CrossRef Search ADS PubMed Costello EK , Stagaman K , Dethlefsen L et al. The application of ecological theory toward an understanding of the human microbiome . Science 2012 ; 336 : 1255 – 62 . Google Scholar CrossRef Search ADS PubMed Curtis MM , Hu Z , Klimko C et al. The gut commensal Bacteroides thetaiotaomicron exacerbates enteric infection through modification of the metabolic landscape . Cell Host Microbe 2014 ; 16 : 759 – 69 . Google Scholar CrossRef Search ADS PubMed David LA , Maurice CF , Carmody RN et al. Diet rapidly and reproducibly alters the human gut microbiome . Nature 2014 ; 505 : 559 – 63 . Google Scholar CrossRef Search ADS PubMed De Filippo C , Cavalieri D , Di Paola M et al. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa . Proc Natl Acad Sci USA 2010 ; 107 : 14691 – 6 . Google Scholar CrossRef Search ADS PubMed Deriu E , Liu JZ , Pezeshki M et al. Probiotic bacteria reduce Salmonella typhimurium intestinal colonization by competing for iron . Cell Host Microbe 2013 ; 14 : 26 – 37 . Google Scholar CrossRef Search ADS PubMed Desai MS , Seekatz AM , Koropatkin NM et al. A dietary fiber-deprived gut microbiota degrades the colonic mucus barrier and enhances pathogen susceptibility . Cell 2016 ; 167 : 1339 – 53 . e21 . Google Scholar CrossRef Search ADS PubMed Dethlefsen L , Huse S , Sogin ML et al. The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing . PLoS Biol 2008 ; 6 : e280 . Google Scholar CrossRef Search ADS PubMed Diard M , Bakkeren E , Cornuault JK et al. Inflammation boosts bacteriophage transfer between Salmonella spp . Science 2017 ; 355 : 1211 – 5 . Google Scholar CrossRef Search ADS PubMed Diard M , Hardt W-D . Evolution of bacterial virulence . FEMS Microbiol Rev 2017 ; 41 : 679 – 97 . Google Scholar CrossRef Search ADS PubMed Dogra S , Sakwinska O , Soh S-E et al. Dynamics of infant gut microbiota are influenced by delivery mode and gestational duration and are associated with subsequent adiposity . MBio 2015 ; 6 : e02419 – 14 . Google Scholar CrossRef Search ADS PubMed Donovan SM , Comstock SS . Human milk oligosaccharides influence neonatal mucosal and systemic immunity . Ann Nutr Metab 2016 ; 69 Suppl 2 : 42 – 51 . Google Scholar CrossRef Search ADS PubMed Donovan SM. Introduction to the special focus issue on the impact of diet on gut microbiota composition and function and future opportunities for nutritional modulation of the gut microbiome to improve human health . Gut Microbes 2017 ; 8 : 75 – 81 . Google Scholar CrossRef Search ADS PubMed Dowds CM , Blumberg RS , Zeissig S . Control of intestinal homeostasis through crosstalk between natural killer T cells and the intestinal microbiota . Clin Immunol 2015 ; 159 : 128 – 33 . Google Scholar CrossRef Search ADS PubMed Ducluzeau R , Ladire M , Callut C et al. Antagonistic effect of extremely oxygen-sensitive clostridia from the microflora of conventional mice and of Escherichia coli against Shigella flexneri in the digestive tract of gnotobiotic mice . Infect Immun 1977 ; 17 : 415 – 24 . Google Scholar PubMed Dudley EG , Thomson NR , Parkhill J et al. Proteomic and microarray characterization of the AggR regulon identifies a pheU pathogenicity island in enteroaggregative Escherichia coli . Mol Microbiol 2006 ; 61 : 1267 – 82 . Google Scholar CrossRef Search ADS PubMed Eade CR , Hung C-C , Bullard B et al. Bile Acids Function Synergistically To Repress Invasion Gene Expression in Salmonella by Destabilizing the Invasion Regulator HilD. Payne SM, editor. Infect Immun . American Society for Microbiology ; 2016 ; 84 : 2198 – 208 . Eckburg PB , Bik EM , Bernstein CN et al. Diversity of the human intestinal microbial flora . Science 2005 ; 308 : 1635 – 8 . Google Scholar CrossRef Search ADS PubMed Edwards CA . Determinants and duration of impact of early gut bacterial colonization . Ann Nutr Metab 2017 ; 70 : 246 – 50 . Google Scholar CrossRef Search ADS PubMed Elhadad D , McClelland M , Rahav G et al. Feverlike Temperature is a Virulence Regulatory Cue Controlling the Motility and Host Cell Entry of Typhoidal Salmonella . J INFECT DIS . 2015 ; 212 : 147 – 56 . Google Scholar CrossRef Search ADS PubMed Endt K , Stecher B , Chaffron S et al. The microbiota mediates pathogen clearance from the gut lumen after non-typhoidal Salmonella diarrhea . PLoS Pathog 2010 ; 6 : e1001097 . Google Scholar CrossRef Search ADS PubMed Eusebi LH , Rabitti S , Artesiani ML et al. Proton pump inhibitors: risks of long-term use . J Gastroenterol Hepatol 2017 ; 32 : 1295 – 302 . Google Scholar CrossRef Search ADS PubMed Faber F , Thiennimitr P , Spiga L et al. Respiration of microbiota-derived 1,2-propanediol drives Salmonella expansion during colitis . PLoS Pathog 2017 ; 13 : e1006129 . Google Scholar CrossRef Search ADS PubMed Faber F , Tran L , Byndloss MX et al. Host-mediated sugar oxidation promotes post-antibiotic pathogen expansion . Nature 2016 ; 534 : 697 – 9 . Google Scholar CrossRef Search ADS PubMed Falkow S. Molecular Koch's postulates applied to microbial pathogenicity . Rev Infect Dis 1988 ; 10 Suppl 2 : S274 – 6 . Google Scholar CrossRef Search ADS PubMed Filloux A. The rise of the type VI secretion system . F1000Prime Rep 2013 ; 5 : 52 . Google Scholar CrossRef Search ADS PubMed Finlay CM , Stefanska AM , Walsh KP et al. Helminth products protect against autoimmunity via innate type 2 cytokines IL-5 and IL-33, which promote eosinophilia . J Immunol 2016 ; 196 : 703 – 14 . Google Scholar CrossRef Search ADS PubMed Finlay CM , Walsh KP , Mills KHG . Induction of regulatory cells by helminth parasites: exploitation for the treatment of inflammatory diseases . Immunol Rev 2014 ; 259 : 206 – 30 . Google Scholar CrossRef Search ADS PubMed Flo TH , Smith KD , Sato S et al. Lipocalin 2 mediates an innate immune response to bacterial infection by sequestrating iron . Nature 2004 ; 432 : 917 – 21 . Google Scholar CrossRef Search ADS PubMed Foster KR , Bell T . Competition, not cooperation, dominates interactions among culturable microbial species . Curr Biol 2012 ; 22 : 1845 – 50 . Google Scholar CrossRef Search ADS PubMed Fraser T , Brown PD . Temperature and Oxidative Stress as Triggers for Virulence Gene Expression in Pathogenic Leptospira spp . Front Microbiol . 2017 ; 8 : 783 . Google Scholar CrossRef Search ADS PubMed Frese SA , Mills DA . Birth of the infant gut microbiome: moms deliver twice! Cell Host Microbe 2015 ; 17 : 543 – 4 . Google Scholar CrossRef Search ADS PubMed Freter R , Brickner H , Botney M et al. Mechanisms that control bacterial populations in continuous-flow culture models of mouse large intestinal flora . Infect Immun 1983a ; 39 : 676 – 85 . Freter R , Brickner H , Fekete J et al. Survival and implantation of Escherichia coli in the intestinal tract . Infect Immun 1983b ; 39 : 686 – 703 . Freter R , Stauffer E , Cleven D et al. Continuous-flow cultures as in vitro models of the ecology of large intestinal flora . Infect Immun 1983c ; 39 : 666 – 75 . Fu J , Wei B , Wen T et al. Loss of intestinal core 1-derived O-glycans causes spontaneous colitis in mice . J Clin Invest 2011 ; 121 : 1657 – 66 . Google Scholar CrossRef Search ADS PubMed Fukami T , Nakajima M . Community assembly: alternative stable states or alternative transient states? Ecol Lett 2011 ; 14 : 973 – 84 . Google Scholar CrossRef Search ADS PubMed Fukuda S , Toh H , Hase K et al. Bifidobacteria can protect from enteropathogenic infection through production of acetate . Nature 2011 ; 469 : 543 – 7 . Google Scholar CrossRef Search ADS PubMed Furusawa Y , Obata Y , Hase K . Commensal microbiota regulates T cell fate decision in the gut . Semin Immunopathol 2015 ; 37 : 17 – 25 . Google Scholar CrossRef Search ADS PubMed Gaboriau-Routhiau V , Rakotobe S , Lécuyer E et al. The key role of segmented filamentous bacteria in the coordinated maturation of gut helper T cell responses . Immunity 2009 ; 31 : 677 – 89 . Google Scholar CrossRef Search ADS PubMed Gause WC , Maizels RM . Macrobiota - helminths as active participants and partners of the microbiota in host intestinal homeostasis . Curr Opin Microbiol 2016 ; 32 : 14 – 8 . Google Scholar CrossRef Search ADS PubMed Geuking MB , Cahenzli J , Lawson MAE et al. Intestinal bacterial colonization induces mutualistic regulatory T cell responses . Immunity 2011 ; 34 : 794 – 806 . Google Scholar CrossRef Search ADS PubMed Giacomin P , Agha Z , Loukas A . Helminths and intestinal flora team up to improve gut health . Trends Parasitol 2016 ; 32 : 664 – 6 . Google Scholar CrossRef Search ADS PubMed Giacomin P , Zakrzewski M , Croese J et al. Experimental hookworm infection and escalating gluten challenges are associated with increased microbial richness in celiac subjects . Sci Rep 2015 ; 5 : 13797 . Google Scholar CrossRef Search ADS PubMed Gibold L , Garenaux E , Dalmasso G et al. The Vat-AIEC protease promotes crossing of the intestinal mucus layer by Crohn's disease-associated Escherichia coli . Cell Microbiol 2016 ; 18 : 617 – 31 . Google Scholar CrossRef Search ADS PubMed Goto Y , Panea C , Nakato G et al. Segmented filamentous bacteria antigens presented by intestinal dendritic cells drive mucosal Th17 cell differentiation . Immunity 2014 ; 40 : 594 – 607 . Google Scholar CrossRef Search ADS PubMed Gough EK , Stephens DA , Moodie EEM et al. Linear growth faltering in infants is associated with Acidaminococcus sp. and community-level changes in the gut microbiota . Microbiome 2015 ; 3 : 24 . Google Scholar CrossRef Search ADS PubMed Groussin M , Mazel F , Sanders JG et al. Unraveling the processes shaping mammalian gut microbiomes over evolutionary time . Nat Commun 2017 ; 8 : 14319 . Google Scholar CrossRef Search ADS PubMed Guernier V , Brennan B , Yakob L et al. Gut microbiota disturbance during helminth infection: can it affect cognition and behaviour of children? BMC Infect Dis 2017 ; 17 : 58 . Google Scholar CrossRef Search ADS PubMed Hachani A , Wood TE , Filloux A . Type VI secretion and anti-host effectors . Curr Opin Microbiol 2016 ; 29 : 81 – 93 . Google Scholar CrossRef Search ADS PubMed Hamad I , Raoult D , Bittar F . Repertory of eukaryotes (eukaryome) in the human gastrointestinal tract: taxonomy and detection methods . Parasite Immunol 2016 ; 38 : 12 – 36 . Google Scholar CrossRef Search ADS PubMed Havt A , Lima IF , Medeiros PH et al. Prevalence and virulence gene profiling of enteroaggregative Escherichia coli in malnourished and nourished Brazilian children . Diagn Microbiol Infect Dis 2017 ; 89 : 98 – 105 . Google Scholar CrossRef Search ADS PubMed Hecht AL , Casterline BW , Earley ZM et al. Strain competition restricts colonization of an enteric pathogen and prevents colitis . EMBO Rep 2016 ; 17 : 1281 – 91 . Google Scholar CrossRef Search ADS PubMed Hegarty JW , Guinane CM , Ross RP et al. Bacteriocin production: a relatively unharnessed probiotic trait? F1000Res 2016 ; 5 : 2587 . Google Scholar CrossRef Search ADS PubMed Hill DA , Hoffmann C , Abt MC et al. Metagenomic analyses reveal antibiotic-induced temporal and spatial changes in intestinal microbiota with associated alterations in immune cell homeostasis . Mucosal Immunol 2010 ; 3 : 148 – 58 . Google Scholar CrossRef Search ADS PubMed Hoffmann C , Hill DA , Minkah N et al. Community-wide response of the gut microbiota to enteropathogenic Citrobacter rodentium infection revealed by deep sequencing . Infect Immun 2009 ; 77 : 4668 – 78 . Google Scholar CrossRef Search ADS PubMed Hsiao A , Ahmed AMS , Subramanian S et al. Members of the human gut microbiota involved in recovery from Vibrio cholerae infection . Nature 2014 ; 515 : 423 – 6 . Google Scholar CrossRef Search ADS PubMed Huang Y-L , Chassard C , Hausmann M et al. Sialic acid catabolism drives intestinal inflammation and microbial dysbiosis in mice . Nat Commun 2015 ; 6 : 8141 . Google Scholar CrossRef Search ADS PubMed Hughes ER , Winter MG , Duerkop BA et al. Microbial respiration and formate oxidation as metabolic signatures of inflammation-associated dysbiosis . Cell Host Microbe 2017 ; 21 : 208 – 19 . Google Scholar CrossRef Search ADS PubMed Hung C-C , Garner CD , Slauch JM et al. The intestinal fatty acid propionate inhibits Salmonella invasion through the post-translational control of HilD . Mol Microbiol 2013 ; 87 : 1045 – 60 . Google Scholar CrossRef Search ADS PubMed Islam KBMS , Fukiya S , Hagio M et al. Bile acid is a host factor that regulates the composition of the cecal microbiota in rats . Gastroenterology 2011 ; 141 : 1773 – 81 . Google Scholar CrossRef Search ADS PubMed Ivanov II , Atarashi K , Manel N et al. Induction of intestinal Th17 cells by segmented filamentous bacteria . Cell 2009 ; 139 : 485 – 98 . Google Scholar CrossRef Search ADS PubMed Ivanov II . Microbe hunting hits home . Cell Host Microbe 2017 ; 21 : 282 – 5 . Google Scholar CrossRef Search ADS PubMed Jakobsson HE , Rodríguez-Piñeiro AM , Schütte A et al. The composition of the gut microbiota shapes the colon mucus barrier . EMBO Rep 2015 ; 16 : 164 – 77 . Google Scholar CrossRef Search ADS PubMed Johansson MEV , Gustafsson JK , Holmén-Larsson J et al. Bacteria penetrate the normally impenetrable inner colon mucus layer in both murine colitis models and patients with ulcerative colitis . Gut 2014 ; 63 : 281 – 91 . Google Scholar CrossRef Search ADS PubMed Johansson MEV , Larsson JMH , Hansson GC . The two mucus layers of colon are organized by the MUC2 mucin, whereas the outer layer is a legislator of host-microbial interactions . Proc Natl Acad Sci USA 2011 ; 108 Suppl 1 : 4659 – 65 . Google Scholar CrossRef Search ADS PubMed Kashtanova DA , Popenko AS , Tkacheva ON et al. Association between the gut microbiota and diet: fetal life, early childhood, and further life . Nutrition 2016 ; 32 : 620 – 7 . Google Scholar CrossRef Search ADS PubMed Kato LM , Kawamoto S , Maruya M et al. The role of the adaptive immune system in regulation of gut microbiota . Immunol Rev 2014 ; 260 : 67 – 75 . Google Scholar CrossRef Search ADS PubMed Kim J , Lee J-Y , Lee H et al. Microbiological features and clinical impact of the type VI secretion system (T6SS) in Acinetobacter baumannii isolates causing bacteremia . Virulence 2017 ; 8 : 1378 – 89 . Google Scholar CrossRef Search ADS PubMed Kim M , Qie Y , Park J et al. Gut microbial metabolites fuel host antibody responses . Cell Host Microbe 2016 ; 20 : 202 – 14 . Google Scholar CrossRef Search ADS PubMed Kommineni S , Bretl DJ , Lam V et al. Bacteriocin production augments niche competition by enterococci in the mammalian gastrointestinal tract . Nature 2015 ; 526 : 719 – 22 . Google Scholar CrossRef Search ADS PubMed Kortman GAM , Raffatellu M , Swinkels DW et al. Nutritional iron turned inside out: intestinal stress from a gut microbial perspective . FEMS Microbiol Rev 2014 ; 38 : 1202 – 34 . Google Scholar CrossRef Search ADS PubMed Kotloff KL , Nataro JP , Blackwelder WC et al. Burden and aetiology of diarrhoeal disease in infants and young children in developing countries (the Global Enteric Multicenter Study, GEMS): a prospective, case-control study . Lancet 2013 ; 382 : 209 – 22 . Google Scholar CrossRef Search ADS PubMed Larsson JMH , Karlsson H , Crespo JG et al. Altered O-glycosylation profile of MUC2 mucin occurs in active ulcerative colitis and is associated with increased inflammation . Inflamm Bowel Dis 2011 ; 17 : 2299 – 307 . Google Scholar CrossRef Search ADS PubMed Leamy LJ , Kelly SA , Nietfeldt J et al. Host genetics and diet, but not immunoglobulin A expression, converge to shape compositional features of the gut microbiome in an advanced intercross population of mice . Genome Biol 2014 ; 15 : 552 . Google Scholar CrossRef Search ADS PubMed Lee SC , Tang MS , Lim YAL et al. Helminth colonization is associated with increased diversity of the gut microbiota . PLoS Negl Trop Dis 2014 ; 8 : e2880 . Google Scholar CrossRef Search ADS PubMed Lehrer RI , Lichtenstein AK , Ganz T . Defensins: antimicrobial and cytotoxic peptides of mammalian cells . Annu Rev Immunol 1993 ; 11 : 105 – 28 . Google Scholar CrossRef Search ADS PubMed Ley RE , Turnbaugh PJ , Klein S et al. Microbial ecology: human gut microbes associated with obesity . Nature 2006 ; 444 : 1022 – 3 . Google Scholar CrossRef Search ADS PubMed Li H , Limenitakis JP , Fuhrer T et al. The outer mucus layer hosts a distinct intestinal microbial niche . Nat Commun 2015 ; 6 : 8292 . Google Scholar CrossRef Search ADS PubMed Li L , Ma ZS . Testing the neutral theory of biodiversity with human microbiome datasets . Sci Rep 2016 ; 6 : 31448 . Google Scholar CrossRef Search ADS PubMed Li RW , Li W , Sun J et al. The effect of helminth infection on the microbial composition and structure of the caprine abomasal microbiome . Sci Rep 2016 ; 6 : 20606 . Google Scholar CrossRef Search ADS PubMed Lidell ME , Moncada DM , Chadee K et al. Entamoeba histolytica cysteine proteases cleave the MUC2 mucin in its C-terminal domain and dissolve the protective colonic mucus gel . Proc Natl Acad Sci USA 2006 ; 103 : 9298 – 303 . Google Scholar CrossRef Search ADS PubMed Lin J , Zhang W , Cheng J et al. A pseudomonas T6SS effector recruits PQS-containing outer membrane vesicles for iron acquisition . Nat Commun 2017 ; 8 : 14888 . Google Scholar CrossRef Search ADS PubMed Liu JZ , Jellbauer S , Poe AJ et al. Zinc sequestration by the neutrophil protein calprotectin enhances Salmonella growth in the inflamed gut . Cell Host Microbe 2012 ; 11 : 227 – 39 . Google Scholar CrossRef Search ADS PubMed Lopez CA , Winter SE , Rivera-Chávez F et al. Phage-mediated acquisition of a type III secreted effector protein boosts growth of Salmonella by nitrate respiration . MBio 2012 ; 3 : e00143 – 12 . Google Scholar CrossRef Search ADS PubMed Lorenzo-Zúñiga V , Bartolí R , Planas R et al. Oral bile acids reduce bacterial overgrowth, bacterial translocation, and endotoxemia in cirrhotic rats . Hepatology 2003 ; 37 : 551 – 7 . Google Scholar CrossRef Search ADS PubMed Luethy PM , Huynh S , Ribardo DA et al. Microbiota-derived short-chain fatty acids modulate expression of Campylobacter jejuni determinants required for commensalism and virulence . MBio 2017 ; 8 : e00407 – 17 . Google Scholar CrossRef Search ADS PubMed Lupp C , Robertson ML , Wickham ME et al. Host-mediated inflammation disrupts the intestinal microbiota and promotes the overgrowth of Enterobacteriaceae . Cell Host Microbe 2007 ; 2 : 204 . Google Scholar CrossRef Search ADS PubMed Ma BW , Bokulich NA , Castillo PA et al. Routine habitat change: a source of unrecognized transient alteration of intestinal microbiota in laboratory mice . PLoS One 2012 ; 7 : e47416 . Google Scholar CrossRef Search ADS PubMed Macpherson AJ , Geuking MB , McCoy KD . Innate and adaptive immunity in host-microbiota mutualism . Front Biosci (Schol Ed) 2012 ; 4 : 685 – 98 . Google Scholar PubMed Macpherson AJ , Geuking MB , Slack E et al. The habitat, double life, citizenship, and forgetfulness of IgA . Immunol Rev 2012 ; 245 : 132 – 46 . Google Scholar CrossRef Search ADS PubMed Macpherson AJ , McCoy KD . Standardised animal models of host microbial mutualism . Mucosal Immunol 2015 ; 8 : 476 – 86 . Google Scholar CrossRef Search ADS PubMed Macpherson AJ , Slack E . The functional interactions of commensal bacteria with intestinal secretory IgA . Curr Opin Gastroenterol 2007 ; 23 : 673 – 8 . Google Scholar CrossRef Search ADS PubMed Maier L , Vyas R , Cordova CD et al. Microbiota-derived hydrogen fuels Salmonella typhimurium invasion of the gut ecosystem . Cell Host Microbe 2013 ; 14 : 641 – 51 . Google Scholar CrossRef Search ADS PubMed Marteyn B , Gazi A , Sansonetti P . Shigella: a model of virulence regulation in vivo . Gut Microbes . Taylor & Francis ; 2012 ; 3 : 104 – 20 . Marteyn B , Scorza FB , Sansonetti PJ et al. Breathing life into pathogens: the influence of oxygen on bacterial virulence and host responses in the gastrointestinal tract . Cell Microbiol . Blackwell Publishing Ltd ; 2011 ; 13 : 171 – 6 . Google Scholar CrossRef Search ADS PubMed Marteyn B , West NP , Browning DF et al. Modulation of Shigella virulence in response to available oxygen in vivo . Nature ; 2010 ; 465 : 355 – 8 . Google Scholar CrossRef Search ADS PubMed Martinez FAC , Balciunas EM , Converti A et al. Bacteriocin production by Bifidobacterium spp. A review . Biotechnol Adv 2013 ; 31 : 482 – 8 . Google Scholar CrossRef Search ADS PubMed Mazmanian SK , Liu CH , Tzianabos AO et al. An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system . Cell 2005 ; 122 : 107 – 18 . Google Scholar CrossRef Search ADS PubMed McFarlane AJ , McSorley HJ , Davidson DJ et al. Enteric helminth-induced type I interferon signaling protects against pulmonary virus infection through interaction with the microbiota . J Allergy Clin Immunol . 2017 ; 140 : 1068 – 1078.e6 . Google Scholar CrossRef Search ADS PubMed McGuckin MA , Lindén SK , Sutton P et al. Mucin dynamics and enteric pathogens . Nat Rev Microbiol 2011 ; 9 : 265 – 78 . Google Scholar CrossRef Search ADS PubMed McKenney EA , Williamson L , Yoder AD et al. Alteration of the rat cecal microbiome during colonization with the helminth Hymenolepis diminuta . Gut Microbes 2015 ; 6 : 182 – 93 . Google Scholar CrossRef Search ADS PubMed Meyer-Hoffert U , Hornef MW , Henriques-Normark B et al. Secreted enteric antimicrobial activity localises to the mucus surface layer . Gut 2008 ; 57 : 764 – 71 . Google Scholar CrossRef Search ADS PubMed Miethke M , Marahiel MA . Siderophore-based iron acquisition and pathogen control . Microbiol Mol Biol Rev 2007 ; 71 : 413 – 51 . Google Scholar CrossRef Search ADS PubMed Mike LA , Smith SN , Sumner CA et al. Siderophore vaccine conjugates protect against uropathogenic Escherichia coli urinary tract infection . Proc Natl Acad Sci USA 2016 ; 113 : 13468 – 73 . Google Scholar CrossRef Search ADS PubMed Miki T , Goto R , Fujimoto M et al. The bactericidal lectin RegIIIβ prolongs gut colonization and enteropathy in the streptomycin mouse model for Salmonella diarrhea . Cell Host Microbe 2017 ; 21 : 195 – 207 . Google Scholar CrossRef Search ADS PubMed Miki T , Holst O , Hardt W-D . The bactericidal activity of the C-type lectin RegIIIβ against gram-negative bacteria involves binding to lipid A . J Biol Chem 2012 ; 287 : 34844 – 55 . Google Scholar CrossRef Search ADS PubMed Miller CP , Bohnhoff M , Drake BL . The effect of antibiotic therapy on susceptibility to an experimental enteric infection . Trans Assoc Am Physicians 1954 ; 67 : 156 – 61 . Google Scholar PubMed Modi SR , Collins JJ , Relman DA . Antibiotics and the gut microbiota . J Clin Invest 2014 ; 124 : 4212 – 8 . Google Scholar CrossRef Search ADS PubMed Moor K , Diard M , Sellin ME et al. High-avidity IgA protects the intestine by enchaining growing bacteria . Nature 2017 ; 544 : 498 – 502 . Google Scholar CrossRef Search ADS PubMed Moran NA , Sloan DB . The hologenome concept: helpful or hollow? PLoS Biol 2015 ; 13 : e1002311 . Google Scholar CrossRef Search ADS PubMed Moreira CG , Russell R , Mishra AA et al. Bacterial adrenergic sensors regulate virulence of enteric pathogens in the gut . MBio 2016 ; 7 : e00826 – 16 . Google Scholar CrossRef Search ADS PubMed Mougous JD , Cuff ME , Raunser S et al. A virulence locus of Pseudomonas aeruginosa encodes a protein secretion apparatus . Science 2006 ; 312 : 1526 – 30 . Google Scholar CrossRef Search ADS PubMed Muegge BD , Kuczynski J , Knights D et al. Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans . Science 2011 ; 332 : 970 – 4 . Google Scholar CrossRef Search ADS PubMed Namasivayam S , Maiga M , Yuan W et al. Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy . Microbiome 2017 ; 5 : 71 . Google Scholar CrossRef Search ADS PubMed Nedialkova LP , Denzler R , Koeppel MB et al. Inflammation fuels colicin Ib-dependent competition of Salmonella Serovar Typhimurium and E. coli in enterobacterial blooms. Galán JE, editor . PLoS Pathog . 2014 ; 10 : e1003844 . Google Scholar CrossRef Search ADS PubMed Neville BA , Forster SC , Lawley TD . Commensal Koch's postulates: establishing causation in human microbiota research . Curr Opin Microbiol 2017 ; 42 : 47 – 52 . Google Scholar CrossRef Search ADS PubMed Ng KM , Ferreyra JA , Higginbottom SK et al. Microbiota-liberated host sugars facilitate post-antibiotic expansion of enteric pathogens . Nature 2013 ; 502 : 96 – 9 . Google Scholar CrossRef Search ADS PubMed Niehus R , Picot A , Oliveira NM et al. The evolution of siderophore production as a competitive trait . Evolution 2017 ; 71 : 1443 – 55 . Google Scholar CrossRef Search ADS PubMed Nunn KL , Wang Y-Y , Harit D et al. Enhanced trapping of HIV-1 by human cervicovaginal mucus is associated with Lactobacillus crispatus-dominant microbiota . MBio 2015 ; 6 : e01084 – 15 . Google Scholar CrossRef Search ADS PubMed O’Malley MA. The nineteenth century roots of “everything is everywhere.” Nat Rev Microbiol 2007 ; 5 : 647 – 51 . Google Scholar CrossRef Search ADS PubMed Nuss AM , Heroven AK , Waldmann B et al. Transcriptomic profiling of Yersinia pseudotuberculosis reveals reprogramming of the Crp regulon by temperature and uncovers Crp as a master regulator of small RNAs. Sharma CM, editor. PLoS Genet . Public Library of Science ; 2015 ; 11 : e1005087 . Osborne LC , Monticelli LA , Nice TJ et al. Coinfection. Virus-helminth coinfection reveals a microbiota-independent mechanism of immunomodulation . Science 2014 ; 345 : 578 – 82 . Google Scholar CrossRef Search ADS PubMed Pabst O , Cerovic V , Hornef M . Secretory IgA in the coordination of establishment and maintenance of the microbiota . Trends Immunol 2016 ; 37 : 287 – 96 . Google Scholar CrossRef Search ADS PubMed Parfrey LW , Walters WA , Knight R . Microbial eukaryotes in the human microbiome: ecology, evolution, and future directions . Front Microbiol 2011 ; 2 : 153 . Google Scholar CrossRef Search ADS PubMed Parfrey LW , Walters WA , Lauber CL et al. Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity . Front Microbiol 2014 ; 5 : 298 . Google Scholar CrossRef Search ADS PubMed Parsons DA , Heffron F . sciS, an icmF homolog in Salmonella enterica serovar Typhimurium, limits intracellular replication and decreases virulence . Infect Immun 2005 ; 73 : 4338 – 45 . Google Scholar CrossRef Search ADS PubMed Pelaseyed T , Bergström JH , Gustafsson JK et al. The mucus and mucins of the goblet cells and enterocytes provide the first defense line of the gastrointestinal tract and interact with the immune system . Immunol Rev 2014 ; 260 : 8 – 20 . Google Scholar CrossRef Search ADS PubMed Pereira FC , Berry D . Microbial nutrient niches in the gut . Environ Microbiol 2017 ; 19 : 1366 – 78 . Google Scholar CrossRef Search ADS PubMed Peterson DA , McNulty NP , Guruge JL et al. IgA response to symbiotic bacteria as a mediator of gut homeostasis . Cell Host Microbe 2007 ; 2 : 328 – 39 . Google Scholar CrossRef Search ADS PubMed Petersson J , Schreiber O , Hansson GC et al. Importance and regulation of the colonic mucus barrier in a mouse model of colitis . Am J Physiol Gastrointest Liver Physiol 2011 ; 300 : G327 – 33 . Google Scholar CrossRef Search ADS PubMed Platts-Mills JA , Taniuchi M , Uddin MJ et al. Association between enteropathogens and malnutrition in children aged 6–23 mo in Bangladesh: a case-control study . Am J Clin Nutr 2017 ; 105 : 1132 – 8 . Google Scholar CrossRef Search ADS PubMed Plichta DR , Juncker AS , Bertalan M et al. Transcriptional interactions suggest niche segregation among microorganisms in the human gut . Nat Microbiol 2016 ; 1 : 16152 . Google Scholar CrossRef Search ADS PubMed Png CW , Lindén SK , Gilshenan KS et al. Mucolytic bacteria with increased prevalence in IBD mucosa augment in vitro utilization of mucin by other bacteria . Am J Gastroenterol 2010 ; 105 : 2420 – 8 . Google Scholar CrossRef Search ADS PubMed Porcheron G , Schouler C , Dozois CM . Survival games at the dinner table: regulation of Enterobacterial virulence through nutrient sensing and acquisition . Curr Opin Microbiol . 2016 ; 30 : 98 – 106 . Google Scholar CrossRef Search ADS PubMed Pourabedin M , Chen Q , Yang M et al. Mannan- and xylooligosaccharides modulate caecal microbiota and expression of inflammatory-related cytokines and reduce caecal Salmonella enteritidis colonisation in young chickens . FEMS Microbiol Ecol 2017 ; 93 : fiw226 . Google Scholar CrossRef Search ADS PubMed Puhar A , Sansonetti PJ . Type III secretion system . Curr Biol 2014 ; 24 : R784 – 91 . Google Scholar CrossRef Search ADS PubMed Pukatzki S , Ma AT , Sturtevant D et al. Identification of a conserved bacterial protein secretion system in Vibrio cholerae using the Dictyostelium host model system . Proc Natl Acad Sci USA 2006 ; 103 : 1528 – 33 . Google Scholar CrossRef Search ADS PubMed Qin J , Li R , Raes J et al. A human gut microbial gene catalogue established by metagenomic sequencing . Nature 2010 ; 464 : 59 – 65 . Google Scholar CrossRef Search ADS PubMed Qiu J , Luo Z-Q . Legionella and Coxiella effectors: strength in diversity and activity . Nat Rev Microbiol 2017 ; 23 : 274 . Raffatellu M , George MD , Akiyama Y et al. Lipocalin-2 resistance confers an advantage to Salmonella enterica serotype Typhimurium for growth and survival in the inflamed intestine . Cell Host Microbe 2009 ; 5 : 476 – 86 . Google Scholar CrossRef Search ADS PubMed Rakoff-Nahoum S , Foster KR , Comstock LE . The evolution of cooperation within the gut microbiota . Nature 2016 ; 533 : 255 – 9 . Google Scholar CrossRef Search ADS PubMed Ramanan D , Bowcutt R , Lee SC et al. Helminth infection promotes colonization resistance via type 2 immunity . Science 2016 ; 352 : 608 – 12 . Google Scholar CrossRef Search ADS PubMed Ramirez-Farias C , Slezak K , Fuller Z et al. Effect of inulin on the human gut microbiota: stimulation of Bifidobacterium adolescentis and Faecalibacterium prausnitzii . Br J Nutr 2009 ; 101 : 541 – 50 . Google Scholar CrossRef Search ADS PubMed Randremanana RV , Razafindratsimandresy R , Andriatahina T et al. Etiologies, risk factors and impact of severe diarrhea in the under-fives in Moramanga and Antananarivo, Madagascar . PLoS One 2016 ; 11 : e0158862 . Google Scholar CrossRef Search ADS PubMed Rescigno M. Intestinal microbiota and its effects on the immune system . Cell Microbiol 2014 ; 16 : 1004 – 13 . Google Scholar CrossRef Search ADS PubMed Rey FE , Gonzalez MD , Cheng J et al. Metabolic niche of a prominent sulfate-reducing human gut bacterium . Proc Natl Acad Sci USA 2013 ; 110 : 13582 – 7 . Google Scholar CrossRef Search ADS PubMed Reynolds LA , Redpath SA , Yurist-Doutsch S et al. Enteric helminths promote Salmonella coinfection by altering the intestinal metabolome . J Infect Dis 2017 ; 215 : 1245 – 54 . Google Scholar CrossRef Search ADS PubMed Ridaura VK , Faith JJ , Rey FE et al. Gut microbiota from twins discordant for obesity modulate metabolism in mice . Science 2013 ; 341 : 1241214 – 4 . Google Scholar CrossRef Search ADS PubMed Ridlon JM , Kang DJ , Hylemon PB et al. Bile acids and the gut microbiome . Curr Opin Gastroenterol 2014 ; 30 : 332 – 8 . Google Scholar CrossRef Search ADS PubMed Riley MA , Wertz JE . Bacteriocins: evolution, ecology, and application . Annu Rev Microbiol 2002 ; 56 : 117 – 37 . Google Scholar CrossRef Search ADS PubMed Rivera-Chávez F , Lopez CA , Bäumler AJ . Oxygen as a driver of gut dysbiosis . Free Radic Biol Med 2017 ; 105 : 93 – 101 . Google Scholar CrossRef Search ADS PubMed Rivera-Chávez F , Lopez CA , Zhang LF et al. Energy taxis toward host-derived nitrate supports a Salmonella pathogenicity island 1-independent mechanism of invasion . MBio 2016a ; 7 : e00960 – 16 . Google Scholar CrossRef Search ADS Rivera-Chávez F , Zhang LF , Faber F et al. Depletion of butyrate-producing clostridia from the gut microbiota drives an aerobic luminal expansion of Salmonella . Cell Host Microbe 2016b ; 19 : 443 – 54 . Google Scholar CrossRef Search ADS Rivière A , Selak M , Lantin D et al. Bifidobacteria and butyrate-producing colon bacteria: importance and strategies for their stimulation in the human gut . Front Microbiol 2016 ; 7 : 979 . Google Scholar CrossRef Search ADS PubMed Rodríguez-Díaz J , García-Mantrana I , Vila-Vicent S et al. Relevance of secretor status genotype and microbiota composition in susceptibility to rotavirus and norovirus infections in humans . Sci Rep 2017 ; 7 : 45559 . Google Scholar CrossRef Search ADS PubMed Rossi O , van Berkel LA , Chain F et al. Faecalibacterium prausnitzii A2-165 has a high capacity to induce IL-10 in human and murine dendritic cells and modulates T cell responses . Sci Rep 2016 ; 6 : 18507 . Google Scholar CrossRef Search ADS PubMed Round JL , Mazmanian SK . Inducible Foxp3+ regulatory T-cell development by a commensal bacterium of the intestinal microbiota . Proc Natl Acad Sci USA 2010 ; 107 : 12204 – 9 . Google Scholar CrossRef Search ADS PubMed Russell AB , Wexler AG , Harding BN et al. A type VI secretion-related pathway in Bacteroidetes mediates interbacterial antagonism . Cell Host Microbe 2014 ; 16 : 227 – 36 . Google Scholar CrossRef Search ADS PubMed Rutayisire E , Huang K , Liu Y et al. The mode of delivery affects the diversity and colonization pattern of the gut microbiota during the first year of infants' life: a systematic review . BMC Gastroenterol 2016 ; 16 : 86 . Google Scholar CrossRef Search ADS PubMed Salomon D , Klimko JA , Trudgian DC et al. Type VI secretion system toxins horizontally shared between marine bacteria . PLoS Pathog 2015 ; 11 : e1005128 . Google Scholar CrossRef Search ADS PubMed Salzman NH , Hung K , Haribhai D et al. Enteric defensins are essential regulators of intestinal microbial ecology . Nat Immunol 2010 ; 11 : 76 – 83 . Google Scholar CrossRef Search ADS PubMed Sana TG , Flaugnatti N , Lugo KA et al. Salmonella typhimurium utilizes a T6SS-mediated antibacterial weapon to establish in the host gut . Proc Natl Acad Sci USA 2016 ; 113 : E5044 – 51 . Google Scholar CrossRef Search ADS PubMed Sansonetti PJ . War and peace at mucosal surfaces . Nat Rev Immunol 2004 ; 4 : 953 – 64 . Google Scholar CrossRef Search ADS PubMed Sassone-Corsi M , Chairatana P , Zheng T et al. Siderophore-based immunization strategy to inhibit growth of enteric pathogens . Proc Natl Acad Sci USA 2016a ; 113 : 13462 – 7 . Google Scholar CrossRef Search ADS Sassone-Corsi M , Nuccio S-P , Liu H et al. Microcins mediate competition among Enterobacteriaceae in the inflamed gut . Nature 2016b ; 540 : 280 – 3 . Google Scholar CrossRef Search ADS Schnupf P , Gaboriau-Routhiau V , Cerf-Bensussan N . Host interactions with segmented filamentous bacteria: an unusual trade-off that drives the post-natal maturation of the gut immune system . Semin Immunol 2013 ; 25 : 342 – 51 . Google Scholar CrossRef Search ADS PubMed Schnupf P , Gaboriau-Routhiau V , Sansonetti PJ et al. Segmented filamentous bacteria, Th17 inducers and helpers in a hostile world . Curr Opin Microbiol 2017 ; 35 : 100 – 9 . Google Scholar CrossRef Search ADS PubMed Schütte A , Ermund A , Becker-Pauly C et al. Microbial-induced meprin β cleavage in MUC2 mucin and a functional CFTR channel are required to release anchored small intestinal mucus . Proc Natl Acad Sci USA 2014 ; 111 : 12396 – 401 . Google Scholar CrossRef Search ADS PubMed Sekirov I , Tam NM , Jogova M et al. Antibiotic-induced perturbations of the intestinal microbiota alter host susceptibility to enteric infection . Infect Immun 2008 ; 76 : 4726 – 36 . Google Scholar CrossRef Search ADS PubMed Shannon B , Gajer P , Yi TJ et al. Distinct effects of the cervicovaginal microbiota and herpes simplex type 2 infection on female genital tract immunology . J Infect Dis 2017a ; 215 : 1366 – 75 . Google Scholar CrossRef Search ADS Shannon B , Yi TJ , Perusini S et al. Association of HPV infection and clearance with cervicovaginal immunology and the vaginal microbiota . Mucosal Immunol 2017b ; 6 : 751 . Shimotoyodome A , Meguro S , Hase T et al. Short chain fatty acids but not lactate or succinate stimulate mucus release in the rat colon . Comp Biochem Physiol, Part A Mol Integr Physiol 2000 ; 125 : 525 – 31 . Google Scholar CrossRef Search ADS PubMed Si M , Zhao C , Burkinshaw B et al. Manganese scavenging and oxidative stress response mediated by type VI secretion system in Burkholderia thailandensis . Proc Natl Acad Sci USA 2017 ; 114 : E2233 – 42 . Google Scholar CrossRef Search ADS PubMed Siegwald L , Audebert C , Even G et al. Targeted metagenomic sequencing data of human gut microbiota associated with Blastocystis colonization . Sci Data 2017 ; 4 : 170081 . Google Scholar CrossRef Search ADS PubMed Slack E , Balmer ML , Fritz JH et al. Functional flexibility of intestinal IgA—broadening the fine line . Front Immunol 2012 ; 3 : 100 . Google Scholar CrossRef Search ADS PubMed Slack E , Hapfelmeier S , Stecher B et al. Innate and adaptive immunity cooperate flexibly to maintain host-microbiota mutualism . Science 2009 ; 325 : 617 – 20 . Google Scholar CrossRef Search ADS PubMed Smith MI , Yatsunenko T , Manary MJ et al. Gut microbiomes of Malawian twin pairs discordant for kwashiorkor . Science 2013 ; 339 : 548 – 54 . Google Scholar CrossRef Search ADS PubMed Sommer F , Adam N , Johansson MEV et al. Altered mucus glycosylation in core 1 O-glycan-deficient mice affects microbiota composition and intestinal architecture . PLoS One 2014 ; 9 : e85254 . Google Scholar CrossRef Search ADS PubMed Spasova DS , Surh CD . Blowing on embers: commensal microbiota and our immune system . Front Immunol 2014 ; 5 : 318 . Google Scholar CrossRef Search ADS PubMed Spees AM , Wangdi T , Lopez CA et al. Streptomycin-induced inflammation enhances Escherichia coli gut colonization through nitrate respiration . MBio 2013 ; 4 : e00430 – 13 . Google Scholar CrossRef Search ADS PubMed Spiga L , Winter MG , Furtado de Carvalho T et al. An oxidative central metabolism enables salmonella to utilize microbiota-derived succinate . Cell Host Microbe 2017 ; 22 : 291 – 6 . Google Scholar CrossRef Search ADS PubMed Stecher B , Chaffron S , Käppeli R et al. Like will to like: abundances of closely related species can predict susceptibility to intestinal colonization by pathogenic and commensal bacteria . PLoS Pathog 2010 ; 6 : e1000711 . Google Scholar CrossRef Search ADS PubMed Stecher B , Denzler R , Maier L et al. Gut inflammation can boost horizontal gene transfer between pathogenic and commensal Enterobacteriaceae . Proc Natl Acad Sci USA 2012 ; 109 : 1269 – 74 . Google Scholar CrossRef Search ADS PubMed Stecher B , Hardt W-D . Mechanisms controlling pathogen colonization of the gut . Curr Opin Microbiol 2011 ; 14 : 82 – 91 . Google Scholar CrossRef Search ADS PubMed Stelter C , Käppeli R , König C et al. Salmonella-induced mucosal lectin RegIIIβ kills competing gut microbiota . PLoS One 2011 ; 6 : e20749 . Google Scholar CrossRef Search ADS PubMed Stokholm J , Thorsen J , Chawes BL et al. Cesarean section changes neonatal gut colonization . J Allergy Clin Immunol 2016 ; 138 : 881 – 2 . Google Scholar CrossRef Search ADS PubMed Studer N , Desharnais L , Beutler M et al. Functional intestinal bile acid 7α-dehydroxylation by Clostridium scindens associated with protection from Clostridium difficile infection in a gnotobiotic mouse model . Front Cell Infect Microbiol 2016 ; 6 : 191 . Google Scholar CrossRef Search ADS PubMed Subramanian S , Huq S , Yatsunenko T et al. Persistent gut microbiota immaturity in malnourished Bangladeshi children . Nature 2014 ; 510 : 417 – 21 . Google Scholar CrossRef Search ADS PubMed Suzuki K , Meek B , Doi Y et al. Aberrant expansion of segmented filamentous bacteria in IgA-deficient gut . Proc Natl Acad Sci USA 2004 ; 101 : 1981 – 6 . Google Scholar CrossRef Search ADS PubMed Tailford LE , Crost EH , Kavanaugh D et al. Mucin glycan foraging in the human gut microbiome . Front Genet 2015a ; 6 : 81 . Google Scholar CrossRef Search ADS Tailford LE , Owen CD , Walshaw J et al. Discovery of intramolecular trans-sialidases in human gut microbiota suggests novel mechanisms of mucosal adaptation . Nat Commun 2015b ; 6 : 7624 . Google Scholar CrossRef Search ADS Thiennimitr P , Winter SE , Winter MG et al. Intestinal inflammation allows Salmonella to use ethanolamine to compete with the microbiota . Proc Natl Acad Sci USA 2011 ; 108 : 17480 – 5 . Google Scholar CrossRef Search ADS PubMed Tian Y , Zhao Y , Shi L et al. Type VI secretion systems of Erwinia amylovora contribute to bacterial competition, virulence, and exopolysaccharide production . Phytopathology 2017 ; 107 : 654 – 61 . Google Scholar CrossRef Search ADS PubMed Tomas J , Mulet C , Saffarian A et al. High-fat diet modifies the PPAR-γ pathway leading to disruption of microbial and physiological ecosystem in murine small intestine . Proc Natl Acad Sci USA 2016 ; 113 : E5934 – 43 . Google Scholar CrossRef Search ADS PubMed Torow N , Hornef MW . The neonatal window of opportunity: setting the stage for life-long host-microbial interaction and immune homeostasis . J Immunol 2017 ; 198 : 557 – 63 . Google Scholar CrossRef Search ADS PubMed Turfkruyer M , Verhasselt V . Breast milk and its impact on maturation of the neonatal immune system . Curr Opin Infect Dis 2015 ; 28 : 199 – 206 . Google Scholar CrossRef Search ADS PubMed Turnbaugh PJ , Ley RE , Mahowald MA et al. An obesity-associated gut microbiome with increased capacity for energy harvest . Nature 2006 ; 444 : 1027 – 31 . Google Scholar CrossRef Search ADS PubMed Uebanso T , Ohnishi A , Kitayama R et al. Effects of low-dose non-caloric sweetener consumption on gut microbiota in mice . Nutrients 2017 ; 9 : 560 . Google Scholar CrossRef Search ADS Unterweger D , Miyata ST , Bachmann V et al. The Vibrio cholerae type VI secretion system employs diverse effector modules for intraspecific competition . Nat Commun 2014 ; 5 : 3549 . Google Scholar CrossRef Search ADS PubMed Ursell LK , Metcalf JL , Parfrey LW et al. Defining the human microbiome . Nutr Rev 2012 ; 70 ( Suppl 1 ): S38 – 44 . Google Scholar CrossRef Search ADS PubMed Vaishnava S , Yamamoto M , Severson KM et al. The antibacterial lectin RegIIIgamma promotes the spatial segregation of microbiota and host in the intestine . Science 2011 ; 334 : 255 – 8 . Google Scholar CrossRef Search ADS PubMed Valeri M , Rossi Paccani S , Kasendra M et al. Pathogenic E. coli exploits SslE mucinase activity to translocate through the mucosal barrier and get access to host cells . PLoS One 2015 ; 10 : e0117486 . Google Scholar CrossRef Search ADS PubMed Van den Bossche L , Hindryckx P , Devisscher L et al. Ursodeoxycholic acid and its taurine- or glycine-conjugated species reduce colitogenic dysbiosis and equally suppress experimental colitis in mice . Appl Environ Microbiol 2017 ; 83 : e02766 – 16 . Google Scholar CrossRef Search ADS PubMed van der Post S , Subramani DB , Bäckström M et al. Site-specific O-glycosylation on the MUC2 mucin protein inhibits cleavage by the Porphyromonas gingivalis secreted cysteine protease (RgpB) . J Biol Chem 2013 ; 288 : 14636 – 46 . Google Scholar CrossRef Search ADS PubMed Van der Waaij D , Berghuis-de Vries JM , Lekkerkerk-van der Wees JEC . Colonization resistance of the digestive tract in conventional and antibiotic-treated mice . J Hyg 2009 ; 69 : 405 – 11 . Google Scholar CrossRef Search ADS Vazquez-Gutierrez P , de Wouters T , Werder J et al. High iron-sequestrating bifidobacteria inhibit enteropathogen growth and adhesion to intestinal epithelial cells in vitro . Front Microbiol 2016 ; 7 : 1480 . Google Scholar CrossRef Search ADS PubMed Velasquez-Manoff M . Gut microbiome: the peacekeepers . Nature 2015 ; 518 : S3 – 11 . Google Scholar CrossRef Search ADS PubMed Wagner VE , Dey N , Guruge J et al. Effects of a gut pathobiont in a gnotobiotic mouse model of childhood undernutrition . Sci Transl Med 2016 ; 8 : 366ra164 – 4 . Google Scholar CrossRef Search ADS PubMed Wahlström A , Sayin SI , Marschall H-U et al. Intestinal crosstalk between bile acids and microbiota and its impact on host metabolism . Cell Metab 2016 ; 24 : 41 – 50 . Google Scholar CrossRef Search ADS PubMed Walk ST , Blum AM , Ewing SA-S et al. Alteration of the murine gut microbiota during infection with the parasitic helminth Heligmosomoides