Access the full text.
Sign up today, get DeepDyve free for 14 days.
Alexa Weingarden, Antonio Gonzalez, Y. Vázquez-Baeza, Sophie Weiss, Gregory Humphry, Donna berg-Lyons, D. Knights, T. Unno, Aleh Bobr, Johnthomas Kang, A. Khoruts, R. Knight, M. Sadowsky (2015)
Dynamic changes in short- and long-term bacterial composition following fecal microbiota transplantation for recurrent Clostridium difficile infectionMicrobiome, 3
P. Belda-Ferre, James Williamson, A. Simon-Soro, A. Artacho, O. Jensen, A. Mira (2015)
The human oral metaproteome reveals potential biomarkers for caries diseasePROTEOMICS, 15
J. White, N. Nagarajan, Mihai Pop (2009)
Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic SamplesPLoS Computational Biology, 5
C. Lozupone, Jesse Stombaugh, Antonio Gonzalez, G. Ackermann, Doug Wendel, Y. Vázquez-Baeza, J. Jansson, J. Gordon, R. Knight (2013)
Meta-analyses of studies of the human microbiotaGenome Research, 23
Manimozhiyan Arumugam, J. Raes, É. Pelletier, D. Paslier, Takuji Yamada, D. Mende, G. Fernandes, J. Tap, T. Bruls, Jean-Michel Batto, Marcelo Bertalan, N. Borruel, F. Casellas, Leyden Fernández, L. Gautier, T. Hansen, M. Hattori, Tetsuya Hayashi, M. Kleerebezem, K. Kurokawa, M. Leclerc, F. Levenez, C. Manichanh, H. Nielsen, T. Nielsen, N. Pons, J. Poulain, J. Qin, Thomas Sicheritz-Pontén, S. Tims, D. Torrents, Edgardo Ugarte, E. Zoetendal, Junwang, F. Guarner, O. Pedersen, W. Vos, S. Brunak, J. Doré, MetaHIT consortium, J. Weissenbach, S. Ehrlich, P. Bork (2011)
Enterotypes of the human gut microbiomeNature, 474
Hermie Harmsen, Marcus Goffau (2016)
The Human Gut Microbiota.Advances in experimental medicine and biology, 902
(2013)
This study provided a mechanism to underpin the high variation between individuals in efficacy of the cardiac drug digoxin
C. Lozupone, R. Knight (2005)
UniFrac: a New Phylogenetic Method for Comparing Microbial CommunitiesApplied and Environmental Microbiology, 71
E. Puertollano, S. Kolida, P. Yaqoob (2014)
Biological significance of short-chain fatty acid metabolism by the intestinal microbiomeCurrent Opinion in Clinical Nutrition and Metabolic Care, 17
This paper provided the first evidence to directly link the gut microbiota to rheumatoid arthritis in people
D. Gevers, S. Kugathasan, L. Denson, Y. Vázquez-Baeza, William Treuren, Boyu Ren, Emma Schwager, D. Knights, Se Song, M. Yassour, X. Morgan, A. Kostic, Chengwei Luo, Antonio Gonzalez, Daniel McDonald, Y. Haberman, T. Walters, S. Baker, J. Rosh, Michael Stephens, M. Heyman, J. Markowitz, R. Baldassano, A. Griffiths, F. Sylvester, D. Mack, Sandra Kim, W. Crandall, J. Hyams, C. Huttenhower, R. Knight, R. Xavier (2014)
The treatment-naive microbiome in new-onset Crohn's disease.Cell host & microbe, 15 3
Justin Kuczynski, Zongzhi Liu, C. Lozupone, Daniel McDonald, N. Fierer, R. Knight (2010)
Microbial community resemblance methods differ in their ability to detect biologically relevant patternsNature methods, 7
This paper demonstrated that the cancer therapeutic drug irinotecan causes severe diarrhoea because of its reactivation and metabolism by bacterial β-glucuronidases
F. Teng, Fang Yang, Shi Huang, C. Bo, Z. Xu, Amnon Amir, R. Knight, J. Ling, Jian Xu (2015)
Prediction of Early Childhood Caries via Spatial-Temporal Variations of Oral Microbiota.Cell host & microbe, 18 3
Zhanshan Ma, Qiong Guan, Chengxi Ye, Chengchen Zhang, J. Foster, L. Forney (2014)
Network analysis suggests a potentially ‘evil' alliance of opportunistic pathogens inhibited by a cooperative network in human milk bacterial communitiesScientific Reports, 5
C. Maurice, Henry Haiser, P. Turnbaugh (2013)
Xenobiotics Shape the Physiology and Gene Expression of the Active Human Gut MicrobiomeCell, 152
J. Biteen, P. Blainey, Z. Cardon, M. Chun, G. Church, P. Dorrestein, S. Fraser, J. Gilbert, J. Jansson, R. Knight, Jeff Miller, Aydogan Ozcan, K. Prather, S. Quake, E. Ruby, P. Silver, S. Taha, G. Engh, P. Weiss, G. Wong, A. Wright, Thomas Young (2015)
Tools for the Microbiome: Nano and Beyond.ACS nano, 10 1
D. Knights, E. Costello, R. Knight (2011)
Supervised classification of human microbiota.FEMS microbiology reviews, 35 2
K. Forslund, F. Hildebrand, T. Nielsen, G. Falony, E. Chatelier, S. Sunagawa, Edi Prifti, S. Vieira-Silva, V. Gudmundsdottir, H. Pedersen, Manimozhiyan Arumugam, K. Kristiansen, A. Voigt, H. Vestergaard, R. Hercog, P. Costea, Jens Kultima, Junhua Li, T. Jørgensen, F. Levenez, J. Doré, H. Nielsen, S. Brunak, J. Raes, T. Hansen, Jun Wang, S. Ehrlich, P. Bork, O. Pedersen (2015)
Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiotaNature, 528
J. Barr, Rita Auro, Mike Furlan, K. Whiteson, M. Erb, J. Pogliano, Aleksandr Stotland, R. Wolkowicz, A. Cutting, K. Doran, P. Salamon, M. Youle, F. Rohwer (2013)
Bacteriophage adhering to mucus provide a non–host-derived immunityProceedings of the National Academy of Sciences, 110
C. Huttenhower, D. Gevers, R. Knight, Sahar Abubucker, J. Badger, A. Chinwalla, H. Creasy, A. Earl, Michael Fitzgerald, R. Fulton, M. Giglio, Kymberlie Hallsworth-Pepin, E. Lobos, R. Madupu, V. Magrini, John Martin, M. Mitreva, D. Muzny, E. Sodergren, J. Versalovic, A. Wollam, K. Worley, J. Wortman, Sarah Young, Qiandong Zeng, K. Aagaard, Olukemi Abolude, E. Allen-Vercoe, E. Alm, Lucia Alvarado, G. Andersen, S. Anderson, Elizabeth Appelbaum, H. Arachchi, G. Armitage, Cesar Arze, T. Ayvaz, Carl Baker, L. Begg, Tsegahiwot Belachew, Veena Bhonagiri, Monika Bihan, M. Blaser, Toby Bloom, Vivien Bonazzi, J. Brooks, G. Buck, C. Buhay, D. Busam, Joseph Campbell, S. Canon, B. Cantarel, P. Chain, I. Chen, Lei Chen, Shaila Chhibba, Ken Chu, Dawn Ciulla, J. Clemente, S. Clifton, S. Conlan, J. Crabtree, M. Cutting, Noam Davidovics, Catherine Davis, T. DeSantis, C. Deal, Kimberley Delehaunty, F. Dewhirst, E. Deych, Yan Ding, D. Dooling, Shannon Dugan, W. Dunne, A. Durkin, Robert Edgar, R. Erlich, Candace Farmer, R. Farrell, Karoline Faust, M. Feldgarden, Victor Felix, Sheila Fisher, A. Fodor, L. Forney, Les Foster, V. Francesco, Jonathan Friedman, Dennis Friedrich, C. Fronick, L. Fulton, Hongyu Gao, Nathalia Garcia, G. Giannoukos, C. Giblin, Maria Giovanni, J. Goldberg, Johannes Goll, Antonio Gonzalez, Allison Griggs, Sharvari Gujja, S. Haake, B. Haas, Holli Hamilton, Emily Harris, Theresa Hepburn, Brandi Herter, D. Hoffmann, M. Holder, Clinton Howarth, Katherine Huang, Susan Huse, J. Izard, J. Jansson, Huaiyang Jiang, Catherine Jordan, Vandita Joshi, J. Katancik, W. Keitel, S. Kelley, C. Kells, N. King, D. Knights, H. Kong, O. Koren, S. Koren, Karthik Kota, C. Kovar, N. Kyrpides, P. Rosa, Sandy Lee, K. Lemon, N. Lennon, Cecil Lewis, L. Lewis, R. Ley, Kelvin Li, K. Liolios, Bo Liu, Yue Liu, C. Lo, C. Lozupone, R. Lunsford, T. Madden, A. Mahurkar, P. Mannon, E. Mardis, V. Markowitz, K. Mavromatis, J. McCorrison, Daniel McDonald, J. Mcewen, A. McGuire, P. Mcinnes, Teena Mehta, K. Mihindukulasuriya, J. Miller, P. Minx, I. Newsham, C. Nusbaum, M. O'Laughlin, Joshua Orvis, I. Pagani, Krishna Palaniappan, Shital Patel, Matthew Pearson, Jane Peterson, M. Podar, C. Pohl, K. Pollard, Mihai Pop, M. Priest, L. Proctor, X. Qin, J. Raes, J. Ravel, J. Reid, Mina Rho, R. Rhodes, Kevin Riehle, M. Rivera, B. Rodriguez-Mueller, Y. Rogers, M. Ross, C. Russ, Ravi Sanka, P. Sankar, J. Sathirapongsasuti, J. Schloss, P. Schloss, T. Schmidt, M. Scholz, L. Schriml, Alyxandria Schubert, N. Segata, J. Segre, W. Shannon, R. Sharp, T. Sharpton, N. Shenoy, N. Sheth, Gina Simone, Indresh Singh, C. Smillie, J. Sobel, Daniel Sommer, P. Spicer, G. Sutton, S. Sykes, D. Tabbaa, M. Thiagarajan, Chad Tomlinson, M. Torralba, T. Treangen, R. Truty, T. Vishnivetskaya, Jason Walker, Lu Wang, Zhengyuan Wang, D. Ward, W. Warren, M. Watson, Christopher Wellington, K. Wetterstrand, J. White, Katarzyna Wilczek-Boney, Yuanqing Wu, K. Wylie, T. Wylie, C. Yandava, Liang Ye, Yuzhen Ye, Shibu Yooseph, Bonnie Youmans, Lan Zhang, Yanjiao Zhou, Yiming Zhu, L. Zoloth, Jeremy Zucker, B. Birren, R. Gibbs, S. Highlander, B. Methé, K. Nelson, J. Petrosino, G. Weinstock, R. Wilson, O. White (2012)
Structure, Function and Diversity of the Healthy Human MicrobiomeNature, 486
N. Huda-Faujan, A. Abdulamir, A. Fatimah, O. Anas, M. Shuhaimi, A. Yazid, Y. Loong (2010)
The Impact of the Level of the Intestinal Short Chain Fatty Acids in Inflammatory Bowel Disease Patients Versus Healthy SubjectsThe Open Biochemistry Journal, 4
H. Li, Wei Jia, Wei Jia (2013)
Cometabolism of Microbes and Host: Implications for Drug Metabolism and Drug‐Induced ToxicityClinical Pharmacology & Therapeutics, 94
R. Sinha, C. Abnet, O. White, R. Knight, C. Huttenhower (2015)
The microbiome quality control project: baseline study design and future directionsGenome Biology, 16
D. Zeevi, Tal Korem, N. Zmora, D. Israeli, Daphna Rothschild, A. Weinberger, Orly Ben-Yacov, Dar Lador, T. Avnit-Sagi, M. Lotan-Pompan, Jotham Suez, Jemal Mahdi, Elad Matot, Gal Malka, Noa Kosower, Michal Rein, Gili Zilberman-Schapira, L. Dohnalová, M. Pevsner-Fischer, Rony Bikovsky, Z. Halpern, E. Elinav, E. Segal (2015)
Personalized Nutrition by Prediction of Glycemic ResponsesCell, 163
Dezhi Kang, Baochen Shi, Marie Erfe, N. Craft, Huiying Li (2015)
Vitamin B12 modulates the transcriptome of the skin microbiota in acne pathogenesisScience Translational Medicine, 7
This study linked the microbiota to IBD and also demonstrated that various forms of the condition have distinct signatures of microbiota
E. Franzosa, Katherine Huang, James Meadow, D. Gevers, K. Lemon, B. Bohannan, C. Huttenhower (2015)
Identifying personal microbiomes using metagenomic codesProceedings of the National Academy of Sciences, 112
J. Gilbert, Chris Henry (2015)
Predicting ecosystem emergent properties at multiple scales.Environmental microbiology reports, 7 1
E. Hsiao, S. Mcbride, S. Hsien, G. Sharon, Embriette Hyde, Tyler McCue, Julian Codelli, J. Chow, S. Reisman, J. Petrosino, P. Patterson, S. Mazmanian (2013)
Microbiota Modulate Behavioral and Physiological Abnormalities Associated with Neurodevelopmental DisordersCell, 155
M. Goyal, Siddarth Venkatesh, J. Milbrandt, J. Gordon, M. Raichle (2015)
Feeding the brain and nurturing the mind: Linking nutrition and the gut microbiota to brain developmentProceedings of the National Academy of Sciences, 112
Cecilia Noecker, A. Eng, S. Srinivasan, C. Theriot, V. Young, J. Jansson, D. Fredricks, Elhanan Borenstein (2016)
Metabolic Model-Based Integration of Microbiome Taxonomic and Metabolomic Profiles Elucidates Mechanistic Links between Ecological and Metabolic VariationmSystems, 1
N. Fierer, C. Lauber, N. Zhou, Daniel McDonald, E. Costello, R. Knight (2010)
Forensic identification using skin bacterial communitiesProceedings of the National Academy of Sciences, 107
J. Allegretti, Sean Kearney, Ning Li, Elijah Bogart, K. Bullock, G. Gerber, L. Bry, C. Clish, E. Alm, J. Korzenik (2016)
Recurrent Clostridium difficile infection associates with distinct bile acid and microbiome profilesAlimentary Pharmacology & Therapeutics, 43
W. Tang, Zeneng Wang, D. Kennedy, Yuping Wu, J. Buffa, Brendan Agatisa-Boyle, Xinmin Li, B. Levison, S. Hazen (2015)
Gut Microbiota-Dependent Trimethylamine N-Oxide (TMAO) Pathway Contributes to Both Development of Renal Insufficiency and Mortality Risk in Chronic Kidney DiseaseCirculation Research, 116
P. Turnbaugh, M. Hamady, Tanya Yatsunenko, B. Cantarel, A. Duncan, R. Ley, M. Sogin, W. Jones, B. Roe, J. Affourtit, M. Egholm, B. Henrissat, A. Heath, R. Knight, J. Gordon (2008)
A core gut microbiome in obese and lean twinsNature, 457
T. Clayton, Dave Baker, J. Lindon, J. Everett, J. Nicholson (2009)
Pharmacometabonomic identification of a significant host-microbiome metabolic interaction affecting human drug metabolismProceedings of the National Academy of Sciences, 106
Julia Goodrich, Jillian Waters, Angela Poole, Jessica Sutter, O. Koren, R. Blekhman, M. Beaumont, W. Treuren, R. Knight, J. Bell, T. Spector, A. Clark, R. Ley (2014)
Human Genetics Shape the Gut MicrobiomeCell, 159
L. Allen, D. Dockrell, T. Pattery, Daniel Lee, P. Cornelis, P. Hellewell, M. Whyte (2005)
Pyocyanin Production by Pseudomonas aeruginosa Induces Neutrophil Apoptosis and Impairs Neutrophil-Mediated Host Defenses In Vivo1The Journal of Immunology, 174
J. Nicholson, J. Lindon, E. Holmes (1999)
'Metabonomics': understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biological NMR spectroscopic data.Xenobiotica; the fate of foreign compounds in biological systems, 29 11
S. Gibbons, Tara Schwartz, Jennifer Fouquier, Michelle Mitchell, Naseer Sangwan, J. Gilbert, S. Kelley (2014)
Ecological Succession and Viability of Human-Associated Microbiota on Restroom SurfacesApplied and Environmental Microbiology, 81
R. Ley, F. Bäckhed, P. Turnbaugh, C. Lozupone, R. Knight, J. Gordon (2005)
Obesity alters gut microbial ecology.Proceedings of the National Academy of Sciences of the United States of America, 102 31
M. ElRakaiby, B. Dutilh, Mariam Rizkallah, A. Boleij, J. Cole, R. Aziz (2014)
Pharmacomicrobiomics: the impact of human microbiome variations on systems pharmacology and personalized therapeutics.Omics : a journal of integrative biology, 18 7
A. Kostic, D. Gevers, H. Siljander, T. Vatanen, T. Hyötyläinen, A. Hämäläinen, A. Peet, V. Tillmann, Päivi Pöhö, I. Mattila, H. Lähdesmäki, E. Franzosa, O. Vaarala, M. Goffau, H. Harmsen, J. Ilonen, S. Virtanen, C. Clish, M. Orešič, C. Huttenhower, M. Knip, R. Xavier (2015)
The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes.Cell host & microbe, 17 2
J. Lewis, Eric Chen, R. Baldassano, A. Otley, A. Griffiths, Dale Lee, K. Bittinger, Aubrey Bailey, E. Friedman, C. Hoffmann, L. Albenberg, R. Sinha, Charlene Compher, Erin Gilroy, Lisa Nessel, A. Grant, C. Chehoud, Hongzhe Li, Gary Wu, F. Bushman (2015)
Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn's Disease.Cell host & microbe, 18 4
P. Ms, Palmer Va (1965)
THE SPECIALTY OF MEDICAL ADMINISTRATION.The Lancet, 1
Jonathan Friedman, E. Alm (2012)
Inferring Correlation Networks from Genomic Survey DataPLoS Computational Biology, 8
D. Knights, Justin Kuczynski, Emily Charlson, Jesse Zaneveld, M. Mozer, R. Collman, F. Bushman, R. Knight, S. Kelley (2011)
Bayesian community-wide culture-independent microbial source trackingNature Methods, 8
Johannes Putze, C. Hennequin, J. Nougayrède, Wenlan Zhang, Stefan Homburg, H. Karch, M. Bringer, C. Fayolle, É. Carniel, W. Rabsch, T. Oelschlaeger, É. Oswald, C. Forestier, J. Hacker, U. Dobrindt (2009)
Genetic Structure and Distribution of the Colibactin Genomic Island among Members of the Family EnterobacteriaceaeInfection and Immunity, 77
F. Bäckhed, J. Roswall, Yangqing Peng, Q. Feng, Huijue Jia, P. Kovatcheva-Datchary, Yin Li, Yan Xia, Hailiang Xie, Huanzi Zhong, M. Khan, Jianfeng Zhang, Junhua Li, L. Xiao, J. Al-Aama, Dongya Zhang, Ying Lee, D. Kotowska, Camilla Colding, V. Tremaroli, Ye Yin, S. Bergman, Xun Xu, L. Madsen, K. Kristiansen, J. Dahlgren, Jun Wang (2015)
Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life.Cell host & microbe, 17 6
This study provided the first link between the toxicity of a drug (in this case, acetaminophen, a widely used analgesic) and microbial metabolism
Tao Ding, P. Schloss (2014)
Dynamics and associations of microbial community types across the human bodyNature, 509
S. Gill, Mihai Pop, R. Deboy, P. Eckburg, P. Turnbaugh, B. Samuel, J. Gordon, D. Relman, Claire Fraser-Liggett, K. Nelson (2006)
Metagenomic Analysis of the Human Distal Gut MicrobiomeScience, 312
GE Flores (2014)
Temporal variability is a personalized feature of the human microbiomeGenome Biol., 15
R. Quinn, Vanessa Phelan, K. Whiteson, Neha Garg, Barbara Bailey, Y. Lim, D. Conrad, P. Dorrestein, F. Rohwer (2015)
Microbial, host and xenobiotic diversity in the cystic fibrosis sputum metabolomeThe ISME Journal, 10
O. Koren, Julia Goodrich, Tyler Cullender, A. Spor, K. Laitinen, Helene Bäckhed, Antonio Gonzalez, J. Werner, L. Angenent, R. Knight, F. Bäckhed, E. Isolauri, S. Salminen, R. Ley (2012)
Host Remodeling of the Gut Microbiome and Metabolic Changes during PregnancyCell, 150
Rong Xu, QuanQiu Wang, Li Li (2015)
A genome-wide systems analysis reveals strong link between colorectal cancer and trimethylamine N-oxide (TMAO), a gut microbial metabolite of dietary meat and fatBMC Genomics, 16
O. Koren, A. Spor, Jenny Felin, F. Fåk, Jesse Stombaugh, V. Tremaroli, C. Behre, R. Knight, B. Fagerberg, R. Ley, F. Bäckhed (2010)
Human oral, gut, and plaque microbiota in patients with atherosclerosisProceedings of the National Academy of Sciences, 108
Zongzhi Liu, T. DeSantis, G. Andersen, R. Knight (2008)
Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencersNucleic Acids Research, 36
Xuan Zhang, Dongya Zhang, Huijue Jia, Q. Feng, Donghui Wang, Di Liang, Xiang-ni Wu, Junhua Li, Longqing Tang, Yin Li, Zhou Lan, Bing Chen, Yanling Li, Huanzi Zhong, Hailiang Xie, Zhuye Jie, Weineng Chen, Shanmei Tang, Xiaoqiang Xu, Xiaokai Wang, Xianghang Cai, Sheng Liu, Yan Xia, Jiyang Li, X. Qiao, J. Al-Aama, Hua Chen, Li Wang, Qing-jun Wu, Fengchun Zhang, Wenjie Zheng, Yongzhe Li, Mingrong Zhang, Guangwen Luo, Wenbin Xue, L. Xiao, Jun Li, Wanting Chen, Xun Xu, Ye Yin, Huanming Yang, Jian Wang, K. Kristiansen, Liang Liu, Ting Li, Qingchun Huang, Yingrui Li, Jun Wang (2015)
The oral and gut microbiomes are perturbed in rheumatoid arthritis and partly normalized after treatmentNature Medicine, 21
W. Walters, Zech Xu, R. Knight (2014)
Meta‐analyses of human gut microbes associated with obesity and IBDFEBS Letters, 588
V. Ridaura, J. Faith, F. Rey, Jiye Cheng, A. Duncan, A. Kau, Nicholas Griffin, V. Lombard, B. Henrissat, J. Bain, M. Muehlbauer, O. Ilkayeva, C. Semenkovich, K. Funai, David Hayashi, B. Lyle, M. Martini, L. Ursell, J. Clemente, William Treuren, W. Walters, R. Knight, C. Newgard, A. Heath, J. Gordon (2013)
Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in MiceScience, 341
J. Koenig, A. Spor, Nicholas Scalfone, A. Fricker, Jesse Stombaugh, R. Knight, L. Angenent, R. Ley (2010)
Succession of microbial consortia in the developing infant gut microbiomeProceedings of the National Academy of Sciences, 108
David Lovell, V. Pawlowsky-Glahn, J. Egozcue, S. Marguerat, J. Bähler (2014)
Proportionality: A Valid Alternative to Correlation for Relative DataPLoS Computational Biology, 11
CG Buffie (2015)
Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficileNature, 517
M. Dominguez-Bello, Kassandra Jesús-Laboy, N. Shen, Laura Cox, Amnon Amir, Antonio Gonzalez, Nicholas Bokulich, Se Song, Marina Hoashi, J. Rivera-Viñas, Keimari Méndez, R. Knight, J. Clemente (2016)
Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transferNature medicine, 22
This paper introduced animation techniques that revealed the transformation of the whole microbiota during faecal microbiota transplantation for C. difficile infection
Jason Ridlon, Daejoong Kang, P. Hylemon, J. Bajaj (2014)
Bile acids and the gut microbiomeCurrent Opinion in Gastroenterology, 30
H. Sokol, B. Pigneur, Laurie Watterlot, O. Lakhdari, L. Bermúdez-Humarán, J. Gratadoux, S. Blugeon, C. Bridonneau, J. Furet, G. Corthier, C. Grangette, Nadia Vasquez, P. Pochart, G. Trugnan, G. Thomas, H. Blottière, J. Doré, P. Marteau, P. Seksik, P. Langella (2008)
Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patientsProceedings of the National Academy of Sciences, 105
G. Flores, J. Caporaso, Jessica Henley, J. Rideout, Daniel Domogala, John Chase, J. Leff, Y. Vázquez-Baeza, Antonio Gonzalez, R. Knight, R. Dunn, N. Fierer (2010)
Additional file 7
S. Mani, U. Boelsterli, M. Redinbo (2014)
Understanding and modulating mammalian-microbial communication for improved human health.Annual review of pharmacology and toxicology, 54
J. Scher, C. Ubeda, Michele Equinda, R. Khanin, Y. Buischi, A. Viale, Lauren Lipuma, M. Attur, M. Pillinger, G. Weissmann, D. Littman, E. Pamer, W. Bretz, S. Abramson (2012)
Periodontal disease and the oral microbiota in new-onset rheumatoid arthritis.Arthritis and rheumatism, 64 10
M. Langille, Jesse Zaneveld, J. Caporaso, Daniel McDonald, D. Knights, Joshua Reyes, J. Clemente, D. Burkepile, Rebecca Thurber, R. Knight, R. Beiko, C. Huttenhower (2013)
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequencesNature biotechnology, 31
Zeneng Wang, W. Tang, J. Buffa, Xiaoming Fu, Earl Britt, Robert Koeth, B. Levison, Yiying Fan, Yuping Wu, S. Hazen (2014)
Prognostic value of choline and betaine depends on intestinal microbiota-generated metabolite trimethylamine-N-oxide.European heart journal, 35 14
W. Wikoff, A. Anfora, Jun Liu, P. Schultz, S. Lesley, E. Peters, G. Siuzdak (2009)
Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolitesProceedings of the National Academy of Sciences, 106
J. Stockman (2012)
Metabolic Syndrome and Altered Gut Microbiota in Mice Lacking Toll-Like Receptor 5Yearbook of Pediatrics, 2012
戴俭, 李鑫, 钱威, 常丽红 (2014)
The systematic application of non-destructive testing techniques for ancient wood buildingsNature
M. Donia, M. Fischbach (2015)
Small molecules from the human microbiotaScience, 349
J. Nougayrède, Stefan Homburg, F. Taieb, M. Boury, E. Brzuszkiewicz, G. Gottschalk, C. Buchrieser, J. Hacker, U. Dobrindt, É. Oswald (2006)
Escherichia coli Induces DNA Double-Strand Breaks in Eukaryotic CellsScience, 313
Jia Yin, Shuo-Xi Liao, Yan He, Shan Wang, Genghong Xia, Fei Liu, Jiajia Zhu, Chao You, Qiong Chen, Liang Zhou, S. Pan, Hong-Wei Zhou (2015)
Dysbiosis of Gut Microbiota With Reduced Trimethylamine‐N‐Oxide Level in Patients With Large‐Artery Atherosclerotic Stroke or Transient Ischemic AttackJournal of the American Heart Association: Cardiovascular and Cerebrovascular Disease, 4
D. Wishart (2016)
Emerging applications of metabolomics in drug discovery and precision medicineNature Reviews Drug Discovery, 15
J. Qin, Ruiqiang Li, J. Raes, Manimozhiyan Arumugam, K. Burgdorf, C. Manichanh, T. Nielsen, N. Pons, F. Levenez, Takuji Yamada, D. Mende, Junhua Li, Junming Xu, Shaochuan Li, Dongfang Li, Jianjun Cao, Bo Wang, Huiqing Liang, Huisong Zheng, Yinlong Xie, J. Tap, P. Lepage, Marcelo Bertalan, Jean-Michel Batto, T. Hansen, D. Paslier, A. Linneberg, H. Nielsen, É. Pelletier, P. Renault, Thomas Sicheritz-Pontén, Keith Turner, Hong-mei Zhu, Chang Yu, Shengting Li, Min Jian, Yan Zhou, Yingrui Li, Xiuqing Zhang, Songgang Li, Nan Qin, Huanming Yang, Jian Wang, S. Brunak, J. Doré, F. Guarner, K. Kristiansen, O. Pedersen, J. Parkhill, J. Weissenbach, P. Bork, S. Ehrlich, Jun Wang (2010)
A human gut microbial gene catalogue established by metagenomic sequencingNature, 464
Daniel DiGiulio, B. Callahan, Paul McMurdie, E. Costello, D. Lyell, Anna Robaczewska, Christine Sun, D. Goltsman, R. Wong, G. Shaw, D. Stevenson, S. Holmes, D. Relman (2015)
Temporal and spatial variation of the human microbiota during pregnancyProceedings of the National Academy of Sciences, 112
J. Gilbert, Folker Meyer, D. Antonopoulos, P. Balaji, C. Brown, Christopher Brown, N. Desai, J. Eisen, D. Evers, D. Field, Wu Feng, D. Huson, J. Jansson, R. Knight, James Knight, E. Kolker, Kostas Konstantindis, J. Kostka, N. Kyrpides, R. Mackelprang, A. Mchardy, C. Quince, J. Raes, A. Sczyrba, A. Shade, Rick Stevens (2010)
Meeting Report: The Terabase Metagenomics Workshop and the Vision of an Earth Microbiome ProjectStandards in Genomic Sciences, 3
R. Ley, P. Turnbaugh, S. Klein, J. Gordon (2006)
Microbial ecology: Human gut microbes associated with obesityNature, 444
A. Butte, Null Null (2014)
The Integrative Human Microbiome Project: Dynamic Analysis of Microbiome-Host Omics Profiles during Periods of Human Health and DiseaseCell host & microbe, 16
This study of treatment-naive children who had been freshly diagnosed with Crohn's disease enabled the effects of treatment to be separated from those of the condition
G. Lima-Mendez, Karoline Faust, N. Henry, J. Decelle, S. Colin, Fabrizio Carcillo, Samuel Chaffron, J. Ignacio-Espinosa, S. Roux, Flora Vincent, L. Bittner, Youssef Darzi, Jun Wang, S. Audic, L. Berline, Gianluca Bontempi, A. Cabello, L. Coppola, Francisco Cornejo-Castillo, F. d’Ovidio, L. Meester, I. Ferrera, Marie-José Garet-Delmas, L. Guidi, Elena Lara, S. Pesant, M. Royo-Llonch, Guillem Salazar, P. Sánchez, M. Sebastián, Caroline Souffreau, Céline Dimier, M. Picheral, S. Searson, S. Kandels-Lewis, G. Gorsky, F. Not, H. Ogata, S. Speich, L. Stemmann, J. Weissenbach, P. Wincker, S. Acinas, S. Sunagawa, P. Bork, M. Sullivan, E. Karsenti, C. Bowler, C. Vargas, J. Raes (2015)
Determinants of community structure in the global plankton interactomeScience, 348
J. Scher, A. Sczesnak, R. Longman, N. Segata, C. Ubeda, C. Bielski, T. Rostron, V. Cerundolo, E. Pamer, S. Abramson, C. Huttenhower, D. Littman (2013)
Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritiseLife, 2
I. Wilson (2009)
Drugs, bugs, and personalized medicine: Pharmacometabonomics enters the ringProceedings of the National Academy of Sciences, 106
P. Turnbaugh, R. Ley, M. Hamady, Claire Fraser-Liggett, R. Knight, J. Gordon (2007)
The Human Microbiome ProjectNature, 449
W. Tang, Zeneng Wang, B. Levison, Robert Koeth, Earl Britt, Xiaoming Fu, Yuping Wu, S. Hazen (2013)
Intestinal microbial metabolism of phosphatidylcholine and cardiovascular risk.The New England journal of medicine, 368 17
A. Kostic, D. Gevers, C. Pedamallu, M. Michaud, F. Duke, A. Earl, A. Ojesina, Joonil Jung, A. Bass, J. Tabernero, J. Baselga, Chen Liu, R. Shivdasani, S. Ogino, B. Birren, C. Huttenhower, W. Garrett, M. Meyerson (2012)
Genomic analysis identifies association of Fusobacterium with colorectal carcinoma.Genome research, 22 2
J. Jansson, B. Willing, M. Lucio, Ages Fekete, J. Dicksved, J. Halfvarson, C. Tysk, P. Schmitt‐Kopplin (2009)
Metabolomics Reveals Metabolic Biomarkers of Crohn's DiseasePLoS ONE, 4
Y. Vázquez-Baeza, M. Pirrung, Antonio Gonzalez, R. Knight (2013)
EMPeror: a tool for visualizing high-throughput microbial community dataGigaScience, 2
Brian Parks, Elizabeth Nam, E. Org, Emrah Kostem, F. Norheim, S. Hui, Calvin Pan, M. Civelek, Christoph Rau, Brian Bennett, M. Mehrabian, L. Ursell, Aiqing He, L. Castellani, B. Zinker, M. Kirby, T. Drake, C. Drevon, R. Knight, Peter Gargalovic, T. Kirchgessner, E. Eskin, A. Lusis (2013)
Genetic control of obesity and gut microbiota composition in response to high-fat, high-sucrose diet in mice.Cell metabolism, 17 1
R. Sinha, Jun Chen, Amnon Amir, E. Vogtmann, Jianxin Shi, Kristin Inman, Roberto Flores, J. Sampson, R. Knight, N. Chia (2015)
Collecting Fecal Samples for Microbiome Analyses in Epidemiology StudiesCancer Epidemiology, Biomarkers & Prevention, 25
D. Frank, A. Amand, R. Feldman, E. Boedeker, N. Harpaz, N. Pace (2007)
Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseasesProceedings of the National Academy of Sciences, 104
M. Goffau, Kristiina Luopajärvi, M. Knip, J. Ilonen, T. Ruohtula, T. Härkönen, L. Orivuori, S. Hakala, G. Welling, H. Harmsen, O. Vaarala (2013)
Fecal Microbiota Composition Differs Between Children With β-Cell Autoimmunity and Those WithoutDiabetes, 62
C. Manichanh, A. Eck, E. Varela, J. Roca, J. Clemente, Antonio Gonzalez, D. Knights, R. Knight, Sandra Estrella, Carlos Hernández, D. Guyonnet, A. Accarino, Javier Santos, J. Malagelada, F. Guarner, F. Azpiroz (2013)
Anal gas evacuation and colonic microbiota in patients with flatulence: effect of dietGut, 63
C. Buffie, V. Bucci, R. Stein, Peter McKenney, Lilan Ling, Asia Gobourne, Daniel No, Hui Liu, M. Kinnebrew, A. Viale, E. Littmann, M. Brink, R. Jenq, Y. Taur, C. Sander, J. Cross, Nora Toussaint, J. Xavier, E. Pamer (2014)
Precision microbiome restoration of bile acid-mediated resistance to Clostridium difficileNature, 517
Tanya Yatsunenko, F. Rey, M. Manary, Indi Trehan, M. Dominguez-Bello, M. Contreras, M. Magris, G. Hidalgo, R. Baldassano, A. Anokhin, A. Heath, B. Warner, Jens Reeder, Justin Kuczynski, J. Caporaso, C. Lozupone, C. Lauber, J. Clemente, D. Knights, R. Knight, J. Gordon (2012)
Human gut microbiome viewed across age and geographyNature, 486
This study identified high levels of Fusobacterium nucleatum in tissue from human tumours; the bacterium was later confirmed to cause tumours in experiments in animals
Shi Huang, Rui Li, Xiaowei Zeng, T. He, Helen Zhao, Alice Chang, C. Bo, Jie Chen, Fang Yang, R. Knight, Jiquan Liu, Catherine Davis, Jian Xu (2014)
Predictive modeling of gingivitis severity and susceptibility via oral microbiotaThe ISME Journal, 8
Henry Haiser, D. Gootenberg, K. Chatman, G. Sirasani, E. Balskus, P. Turnbaugh (2013)
Predicting and Manipulating Cardiac Drug Inactivation by the Human Gut Bacterium Eggerthella lentaScience, 341
Aurélie Cotillard, S. Kennedy, L. Kong, Edi Prifti, N. Pons, E. Chatelier, Mathieu Almeida, B. Quinquis, F. Levenez, N. Galleron, S. Gougis, S. Rizkalla, Jean-Michel Batto, P. Renault, J. Dore, Jean-Daniel Zucker, K. Clément, S. Ehrlich (2013)
Dietary intervention impact on gut microbial gene richnessNature, 500
J. Quick, P. Ashton, S. Calus, C. Chatt, S. Gossain, J. Hawker, S. Nair, K. Neal, K. Nye, T. Peters, E. Pinna, E. Robinson, K. Struthers, M. Webber, A. Catto, T. Dallman, P. Hawkey, N. Loman (2015)
Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of SalmonellaGenome Biology, 16
F. Scheperjans, V. Aho, P. Pereira, K. Koskinen, L. Paulin, E. Pekkonen, E. Haapaniemi, S. Kaakkola, J. Eerola‐Rautio, M. Pohja, E. Kinnunen, K. Murros, P. Auvinen (2015)
Gut microbiota are related to Parkinson's disease and clinical phenotypeMovement Disorders, 30
A. Eren, L. Maignien, W. Sul, L. Murphy, Sharon Grim, H. Morrison, M. Sogin, R. Freckleton (2013)
Oligotyping: differentiating between closely related microbial taxa using 16S rRNA gene dataMethods in Ecology and Evolution, 4
R. Quinn, Jose Navas-Molina, Embriette Hyde, Se Song, Y. Vázquez-Baeza, G. Humphrey, James Gaffney, J. Minich, A. Melnik, Jakob Herschend, J. Dereus, Austin Durant, R. Dutton, Mahdieh Khosroheidari, Cliff Green, R. Silva, P. Dorrestein, R. Knight (2016)
From Sample to Multi-Omics Conclusions in under 48 HoursmSystems, 1
M. Donia, Peter Cimermancic, C. Schulze, Laura Brown, John Martin, M. Mitreva, J. Clardy, Roger Linington, M. Fischbach (2014)
A Systematic Analysis of Biosynthetic Gene Clusters in the Human Microbiome Reveals a Common Family of AntibioticsCell, 158
Alison Erickson, B. Cantarel, Regina Lamendella, Youssef Darzi, E. Mongodin, C. Pan, M. Shah, J. Halfvarson, C. Tysk, B. Henrissat, J. Raes, N. Verberkmoes, C. Fraser, R. Hettich, J. Jansson (2012)
Integrated Metagenomics/Metaproteomics Reveals Human Host-Microbiota Signatures of Crohn's DiseasePLoS ONE, 7
R. Silva, P. Dorrestein, R. Quinn (2015)
Illuminating the dark matter in metabolomicsProceedings of the National Academy of Sciences, 112
Tal Korem, D. Zeevi, Jotham Suez, A. Weinberger, T. Avnit-Sagi, M. Pompan-Lotan, Elad Matot, G. Jona, A. Harmelin, Nadav Cohen, Alexandra Sirota-Madi, Christoph Thaiss, M. Pevsner-Fischer, R. Sorek, R. Xavier, E. Elinav, E. Segal (2015)
Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samplesScience, 349
E. Hsiao, S. Mcbride, J. Chow, S. Mazmanian, P. Patterson (2012)
Modeling an autism risk factor in mice leads to permanent immune dysregulationProceedings of the National Academy of Sciences, 109
B. Wallace, Hongwei Wang, Kimberly Lane, John Scott, J. Orans, J. Koo, M. Venkatesh, C. Jobin, L. Yeh, S. Mani, M. Redinbo (2010)
Alleviating Cancer Drug Toxicity by Inhibiting a Bacterial EnzymeScience, 330
P. Turnbaugh, R. Ley, M. Mahowald, V. Magrini, E. Mardis, J. Gordon (2006)
An obesity-associated gut microbiome with increased capacity for energy harvestNature, 444
This study provided the first metagenomic gene catalogue of the human gut
J. Cummings (1983)
FERMENTATION IN THE HUMAN LARGE INTESTINE: EVIDENCE AND IMPLICATIONS FOR HEALTHThe Lancet, 321
Dae-Wook Kang, Jin Park, Z. Ilhan, G. Wallstrom, J. LaBaer, J. Adams, R. Krajmalnik-Brown (2013)
Reduced Incidence of Prevotella and Other Fermenters in Intestinal Microflora of Autistic ChildrenPLoS ONE, 8
Mark Koenigsknecht, C. Theriot, I. Bergin, C. Schumacher, P. Schloss, V. Young (2014)
Dynamics and Establishment of Clostridium difficile Infection in the Murine Gastrointestinal TractInfection and Immunity, 83
A. Shade, Stuart Jones, J. Caporaso, J. Handelsman, R. Knight, N. Fierer, J. Gilbert (2014)
Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial DiversitymBio, 5
A. Giongo, K. Gano, David Crabb, Nabanita Mukherjee, L. Novelo, G. Casella, Jennifer Drew, J. Ilonen, M. Knip, H. Hyöty, R. Veijola, T. Simell, O. Simell, J. Neu, C. Wasserfall, D. Schatz, M. Atkinson, E. Triplett (2011)
Toward defining the autoimmune microbiome for type 1 diabetesThe ISME Journal, 5
D. Ríos-Covian, P. Ruas-Madiedo, A. Margolles, M. Gueimonde, C. Reyes-Gavilán, N. Salazar (2016)
Intestinal Short Chain Fatty Acids and their Link with Diet and Human HealthFrontiers in Microbiology, 7
S. Michail, M. Lin, M. Frey, Rob Fanter, O. Paliy, B. Hilbush, N. Reo (2015)
Altered gut microbial energy and metabolism in children with non-alcoholic fatty liver disease.FEMS microbiology ecology, 91 2
Janelle Arthur, E. Peréz-Chanona, Marcus Mühlbauer, Sarah Tomkovich, Joshua Uronis, Ting-Jia Fan, B. Campbell, T. Abujamel, B. Dogan, A. Rogers, J. Rhodes, A. Stintzi, K. Simpson, J. Hansen, T. Keku, A. Fodor, C. Jobin (2012)
Intestinal Inflammation Targets Cancer-Inducing Activity of the MicrobiotaScience, 338
Weifei Zhu, J. Gregory, E. Org, J. Buffa, N. Gupta, Zeneng Wang, Lin Li, Xiaoming Fu, Yuping Wu, M. Mehrabian, R. Sartor, T. McIntyre, R. Silverstein, W. Tang, J. DiDonato, J. Brown, A. Lusis, S. Hazen (2016)
Gut Microbial Metabolite TMAO Enhances Platelet Hyperreactivity and Thrombosis RiskCell, 165
Ali Naseribafrouei, K. Hestad, K. Hestad, E. Avershina, M. Sekelja, A. Linløkken, R. Wilson, K. Rudi, K. Rudi (2014)
Correlation between the human fecal microbiota and depressionNeurogastroenterology & Motility, 26
D. Knights, L. Parfrey, Jesse Zaneveld, C. Lozupone, R. Knight (2011)
Human-associated microbial signatures: examining their predictive value.Cell host & microbe, 10 4
S. Mandal, William Treuren, Richard White, M. Eggesbø, R. Knight, S. Peddada (2015)
Analysis of composition of microbiomes: a novel method for studying microbial compositionMicrobial Ecology in Health and Disease, 26
A. Kostic, Michael Howitt, W. Garrett (2013)
Exploring host-microbiota interactions in animal models and humans.Genes & development, 27 7
Robert Koeth, Zeneng Wang, B. Levison, J. Buffa, E. Org, Brendan Sheehy, Earl Britt, Xiaoming Fu, Yuping Wu, Lin Li, D. Jonathan, Smith, J. DiDonato, Jun Chen, Hongzhe Li, Gary Wu, James Lewis, M. Warrier, J. Brown, R. Krauss, W. Tang, D. Frederic, Bushman, A. Lusis, Stanley Hazen (2013)
Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosisNature medicine, 19
B. Willing, J. Dicksved, J. Halfvarson, Anders Andersson, M. Lucio, Zongli Zheng, G. Järnerot, C. Tysk, J. Jansson, L. Engstrand (2010)
A pyrosequencing study in twins shows that gastrointestinal microbial profiles vary with inflammatory bowel disease phenotypes.Gastroenterology, 139 6
Peter Cimermancic, M. Medema, Jan Claesen, Kenji Kurita, Laura Brown, K. Mavrommatis, Amrita Pati, P. Godfrey, M. Koehrsen, J. Clardy, B. Birren, E. Takano, A. Sali, Roger Linington, M. Fischbach (2014)
Insights into Secondary Metabolism from a Global Analysis of Prokaryotic Biosynthetic Gene ClustersCell, 158
Michael Harpham (1855)
DecemberThe Hospital, 9
S. Lax, Daniel Smith, Jarrad Hampton-Marcell, S. Owens, K. Handley, Nicole Scott, S. Gibbons, Peter Larsen, Benjamin Shogan, Sophie Weiss, J. Metcalf, L. Ursell, Y. Vázquez-Baeza, W. Treuren, Nur Hasan, Molly Gibson, R. Colwell, G. Dantas, R. Knight, J. Gilbert (2014)
Longitudinal analysis of microbial interaction between humans and the indoor environmentScience, 345
MI Love, W Huber, S Anders (2014)
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2Genome Biol., 15
Rapid advances in DNA sequencing, metabolomics, proteomics and computational tools are dramatically increasing access to the microbiome and identification of its links with disease. In particular, time-series studies and multiple molecular perspectives are facilitating microbiome-wide association studies, which are analogous to genome-wide association studies. Early findings point to actionable outcomes of microbiome-wide association studies, although their clinical application has yet to be approved. An appreciation of the complexity of interactions among the microbiome and the host's diet, chemistry and health, as well as determining the frequency of observations that are needed to capture and integrate this dynamic interface, is paramount for developing precision diagnostics and therapies that are based on the microbiome.
Nature – Springer Journals
Published: Jul 6, 2016
Read and print from thousands of top scholarly journals.
Already have an account? Log in
Bookmark this article. You can see your Bookmarks on your DeepDyve Library.
To save an article, log in first, or sign up for a DeepDyve account if you don’t already have one.
Copy and paste the desired citation format or use the link below to download a file formatted for EndNote
Access the full text.
Sign up today, get DeepDyve free for 14 days.
All DeepDyve websites use cookies to improve your online experience. They were placed on your computer when you launched this website. You can change your cookie settings through your browser.