Jacque Young, C. Chehoud, K. Bittinger, Aubrey Bailey, J. Diamond, E. Cantu, A. Haas, A. Abbas, Laura Frye, Jason Christie, F. Bushman, R. Collman (2015)
Viral Metagenomics Reveal Blooms of Anelloviruses in the Respiratory Tract of Lung Transplant RecipientsAmerican Journal of Transplantation, 15
C. Huttenhower, A. Kostic, R. Xavier (2014)
Inflammatory bowel disease as a model for translating the microbiome.Immunity, 40 6
Khor (2011)
307Nature, 474
R. Sartor (2008)
Therapeutic correction of bacterial dysbiosis discovered by molecular techniquesProceedings of the National Academy of Sciences, 105
Sahar Abubucker, N. Segata, Johannes Goll, Alyxandria Schubert, J. Izard, B. Cantarel, B. Rodriguez-Mueller, Jeremy Zucker, M. Thiagarajan, B. Henrissat, O. White, S. Kelley, B. Methé, P. Schloss, D. Gevers, M. Mitreva, C. Huttenhower (2012)
Metabolic Reconstruction for Metagenomic Data and Its Application to the Human MicrobiomePLoS Computational Biology, 8
P. Rutgeerts, G. Assche, W. Sandborn, D. Wolf, K. Geboes, J. Colombel, W. Reinisch, Ashish Kumar, A. Lazar, A. Camez, K. Lomax, P. Pollack, G. D'Haens (2012)
Adalimumab induces and maintains mucosal healing in patients with Crohn's disease: data from the EXTEND trial.Gastroenterology, 142 5
Winter (2014)
71Gut Microbes, 5
Rajca (2014)
978Inflamm. Bowel Dis., 20
Jostins (2012)
119Nature, 491
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
C. Chehoud, L. Albenberg, Colleen Judge, C. Hoffmann, Stephanie Grunberg, K. Bittinger, R. Baldassano, J. Lewis, F. Bushman, Gary Wu (2015)
Fungal Signature in the Gut Microbiota of Pediatric Patients With Inflammatory Bowel DiseaseInflammatory Bowel Diseases, 21
K. Gerasimidis, Martin Bertz, L. Hanske, Jana Junick, Olga Biskou, M. Aguilera, V. Garrick, R. Russell, M. Blaut, P. Mcgrogan, C. Edwards (2014)
Decline in Presumptively Protective Gut Bacterial Species and Metabolites Are Paradoxically Associated with Disease Improvement in Pediatric Crohn’s Disease During Enteral NutritionInflammatory Bowel Diseases, 20
Mathias Richard, B. Lamas, G. Liguori, Thomas Hoffmann, H. Sokol (2015)
Gut Fungal Microbiota: The Yin and Yang of Inflammatory Bowel DiseaseInflammatory Bowel Diseases, 21
Lawrence David, Corinne Maurice, Rachel Carmody, David Gootenberg, J. Button, Benjamin Wolfe, Alisha Ling, A. Devlin, Yug Varma, M. Fischbach, S. Biddinger, Rachel Dutton, P. Turnbaugh (2013)
Diet rapidly and reproducibly alters the human gut microbiomeNature, 505
J. Quinton, B. Sendid, D. Reumaux, P. Duthilleul, A. Cortot, B. Grandbastien, G. Charrier, S. Targan, J. Colombel, D. Poulain, Hôpital Huriez, J-Fcolombel Clinique (1998)
Anti-Saccharomyces cerevisiae mannan antibodies combined with antineutrophil cytoplasmic autoantibodies in inflammatory bowel disease: prevalence and diagnostic roleGut, 42
(2012)
Materials for : Host-microbe interactions shape genetic risk for inflammatory bowel disease
B. Methé, K. Nelson, Mihai Pop, H. Creasy, M. Giglio, C. Huttenhower, D. Gevers, J. Petrosino, Sahar Abubucker, J. Badger, A. Chinwalla, A. Earl, Michael Fitzgerald, R. Fulton, 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, J. Bonazzi, Paul 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, 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, Susan Kinder-Haake, N. King, R. Knight, D. Knights, H. Kong, O. Koren, S. Koren, Karthik Kota, C. Kovar, N. Kyrpides, Patricio 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. Mavrommatis, 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, 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, J. Sankar, Fah 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, Todd 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, G. Weinstock, R. Wilson, O. White (2012)
A framework for human microbiome researchNature, 486
S. Rajca, V. Grondin, E. Louis, G. Vernier‐Massouille, Jean-Charle Grimaud, Y. Bouhnik, D. Laharie, J. Dupas, H. Pillant, L. Picon, M. Veyrac, M. Flamant, G. Savoye, R. Jian, M. Devos, G. Paintaud, E. Piver, M. Allez, J. Mary, H. Sokol, J. Colombel, P. Seksik (2014)
Alterations in the Intestinal Microbiome (Dysbiosis) as a Predictor of Relapse After Infliximab Withdrawal in Crohn's DiseaseInflammatory Bowel Diseases, 20
I. Iliev, Vincent Funari, K. Taylor, Quoclinh Nguyen, C. Reyes, Samuel Strom, Jordan Brown, Courtney Becker, P. Fleshner, Marla Dubinsky, Jerome Rotter, Hanlin Wang, D. McGovern, Gordon Brown, D. Underhill (2012)
Interactions Between Commensal Fungi and the C-Type Lectin Receptor Dectin-1 Influence ColitisScience, 336
Nabeetha Nagalingam, S. Lynch (2012)
Role of the microbiota in inflammatory bowel diseases.Inflammatory bowel diseases, 18 5
S. Samuel, E. Jr, W. Sandborn (2010)
The effects of itraconazole on inflammatory bowel disease activity in patients treated for histoplasmosisAlimentary Pharmacology & Therapeutics, 32
S. Ott, T. Kühbacher, M. Musfeldt, P. Rosenstiel, S. Hellmig, A. Rehman, O. Drews, W. Weichert, K. Timmis, S. Schreiber (2008)
Fungi and inflammatory bowel diseases: Alterations of composition and diversityScandinavian Journal of Gastroenterology, 43
R. Sartor (2006)
Mechanisms of Disease: pathogenesis of Crohn's disease and ulcerative colitisNature Clinical Practice Gastroenterology &Hepatology, 3
K. Khan, T. Ullman, A. Ford, M. Abreu, A. Abadir, J. Marshall, N. Talley, P. Moayyedi (2011)
Antibiotic Therapy in Inflammatory Bowel Disease: A Systematic Review and Meta-AnalysisThe American Journal of Gastroenterology, 106
Ta-Chiang Liu, T. Stappenbeck (2016)
Genetics and Pathogenesis of Inflammatory Bowel Disease.Annual review of pathology, 11
Khalid Metwalli, Shariq Khan, B. Krom, M. Jabra-Rizk (2013)
Streptococcus mutans, Candida albicans, and the Human Mouth: A Sticky SituationPLoS Pathogens, 9
H. Alvarez, A. Steinbüchel (2002)
Triacylglycerols in prokaryotic microorganismsApplied Microbiology and Biotechnology, 60
M. Nairz, Andrea Schroll, T. Sonnweber, G. Weiss (2010)
The struggle for iron – a metal at the host–pathogen interfaceCellular Microbiology, 12
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
C. Summerton, M. Longlands, K. Wiener, D. Shreeve (2002)
Faecal calprotectin: a marker of inflammation throughout the intestinal tractEuropean Journal of Gastroenterology & Hepatology, 14
T. Card, R. Logan, L. Rodrigues, J. Wheeler (2004)
Antibiotic use and the development of Crohn’s diseaseGut, 53
N. Segata, L. Waldron, Annalisa Ballarini, Vagheesh Narasimhan, O. Jousson, C. Huttenhower (2012)
Metagenomic microbial community profiling using unique clade-specific marker genesNature methods, 9
D. Knights, M. Silverberg, R. Weersma, D. Gevers, G. Dijkstra, Hailiang Huang, A. Tyler, S. Sommeren, F. Imhann, J. Stempak, Hu Huang, Pajau Vangay, Gabriel Al-Ghalith, C. Russell, J. Sauk, J. Knight, M. Daly, C. Huttenhower, R. Xavier (2014)
Complex host genetics influence the microbiome in inflammatory bowel diseaseGenome Medicine, 6
Jin-Feng Lin, Jin-Min Chen, Junhua Zuo, Allen Yu, Zhu-Jun Xiao, Feihong Deng, Biao Nie, B. Jiang (2014)
Meta-analysis: Fecal Calprotectin for Assessment of Inflammatory Bowel Disease ActivityInflammatory Bowel Diseases, 20
L. Albenberg, T. Esipova, Colleen Judge, K. Bittinger, Jun Chen, Alice Laughlin, Stephanie Grunberg, R. Baldassano, J. Lewis, Hongzhe Li, S. Thom, F. Bushman, S. Vinogradov, Gary Wu (2014)
Correlation between intraluminal oxygen gradient and radial partitioning of intestinal microbiota.Gastroenterology, 147 5
J. Norman, S. Handley, Megan Baldridge, L. Droit, Catherine Liu, B. Keller, Amal Kambal, Cynthia Monaco, Guoyan Zhao, P. Fleshner, T. Stappenbeck, D. McGovern, A. Keshavarzian, E. Mutlu, J. Sauk, D. Gevers, R. Xavier, David Wang, M. Parkes, H. Virgin (2015)
Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel DiseaseCell, 160
B. Samuel, E. Hansen, J. Manchester, P. Coutinho, B. Henrissat, R. Fulton, P. Latreille, Kung Kim, R. Wilson, J. Gordon (2007)
Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gutProceedings of the National Academy of Sciences, 104
Gary Wu, Jun Chen, C. Hoffmann, K. Bittinger, Ying-Yu Chen, S. Keilbaugh, M. Bewtra, D. Knights, W. Walters, R. Knight, R. Sinha, Erin Gilroy, Kernika Gupta, R. Baldassano, Lisa Nessel, Hongzhe Li, F. Bushman, J. Lewis (2011)
Linking Long-Term Dietary Patterns with Gut Microbial EnterotypesScience, 334
I. Vlaminck, K. Khush, C. Strehl, B. Kohli, H. Luikart, N. Neff, Jennifer Okamoto, T. Snyder, D. Cornfield, M. Nicolls, D. Weill, D. Bernstein, H. Valantine, S. Quake (2013)
Temporal Response of the Human Virome to Immunosuppression and Antiviral TherapyCell, 155
S. Dollive, Ying-Yu Chen, Stephanie Grunberg, K. Bittinger, C. Hoffmann, Lee Vandivier, Chris Cuff, J. Lewis, Gary Wu, F. Bushman (2013)
Fungi of the Murine Gut: Episodic Variation and Proliferation during Antibiotic TreatmentPLoS ONE, 8
Dale Lee, R. Baldassano, A. Otley, L. Albenberg, A. Griffiths, Charlene Compher, Eric Chen, Hongzhe Li, Erin Gilroy, Lisa Nessel, A. Grant, C. Chehoud, F. Bushman, Gary Wu, J. Lewis (2015)
Comparative Effectiveness of Nutritional and Biological Therapy in North American Children with Active Crohn's DiseaseInflammatory Bowel Diseases, 21
K. Strijbis, B. Distel (2010)
Intracellular Acetyl Unit Transport in Fungal Carbon MetabolismEukaryotic Cell, 9
J. Lewis (2011)
The utility of biomarkers in the diagnosis and therapy of inflammatory bowel disease.Gastroenterology, 140 6
M. Peeters, S. Joossens, S. Vermeire, R. Vlietinck, X. Bossuyt, P. Rutgeerts (2001)
Diagnostic value of anti-Saccharomyces cerevisiae and antineutrophil cytoplasmic autoantibodies in inflammatory bowel diseaseAmerican Journal of Gastroenterology, 96
M. Tong, Xiaoxiao Li, Laura Parfrey, B. Roth, A. Ippoliti, B. Wei, J. Borneman, D. McGovern, D. Frank, Ellen Li, S. Horvath, R. Knight, J. Braun (2013)
A Modular Organization of the Human Intestinal Mucosal Microbiota and Its Association with Inflammatory Bowel DiseasePLoS ONE, 8
(2014)
Dysbiosis in the inflamed intestine: chance favors the prepared microbe
D. Margolis, M. Fanelli, O. Hoffstad, J. Lewis (2010)
Potential Association Between the Oral Tetracycline Class of Antimicrobials Used to Treat Acne and Inflammatory Bowel DiseaseThe American Journal of Gastroenterology, 105
K. Bittinger, Emily Charlson, Elizabeth Loy, D. Shirley, A. Haas, Alice Laughlin, Y. Yi, Gary Wu, J. Lewis, I. Frank, E. Cantu, J. Diamond, J. Christie, R. Collman, F. Bushman (2014)
Improved characterization of medically relevant fungi in the human respiratory tract using next-generation sequencingGenome Biology, 15
N. Kaakoush, A. Day, S. Leach, D. Lemberg, S. Nielsen, H. Mitchell (2015)
Effect of Exclusive Enteral Nutrition on the Microbiota of Children With Newly Diagnosed Crohn's DiseaseClinical and Translational Gastroenterology, 6
C. Hoffmann, S. Dollive, Stephanie Grunberg, Jun Chen, Hongzhe Li, Gary Wu, J. Lewis, F. Bushman (2013)
Archaea and Fungi of the Human Gut Microbiome: Correlations with Diet and Bacterial ResidentsPLoS ONE, 8
L. Prideaux, P. Cruz, S. Ng, M. Kamm (2012)
Serological Antibodies in Inflammatory Bowel Disease: A Systematic ReviewInflammatory Bowel Diseases, 18
O. Borrelli, L. Cordischi, M. Cirulli, M. Paganelli, V. Labalestra, S. Uccini, P. Russo, S. Cucchiara (2006)
Polymeric diet alone versus corticosteroids in the treatment of active pediatric Crohn's disease: a randomized controlled open-label trial.Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association, 4 6
Z. Grover, R. Muir, P. Lewindon (2013)
Exclusive enteral nutrition induces early clinical, mucosal and transmural remission in paediatric Crohn’s diseaseJournal of Gastroenterology, 49
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