Microbiotas from Humans with Inflammatory Bowel Disease Alter the Balance of Gut Th17 and RORγt+ Regulatory T Cells and Exacerbate Colitis in Mice

QIIME allows analysis of high-throughput community sequencing data

Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Peña, A. G., Goodrich, J. K., Gordon, J. I., et al. (2010) · Nature Methods · doi:10.1038/nmeth.f.303 · Cited by 34,887 · see citing works

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

McMurdie, P. J., & Holmes, S. (2013) · PLoS ONE · doi:10.1371/journal.pone.0061217 · Cited by 21,013 · see citing works

Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB

DeSantis, T. Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E. L., Keller, K., Huber, T., Dalevi, D., Hu, P., & Andersen, G. L. (2006) · Applied and Environmental Microbiology · doi:10.1128/aem.03006-05 · Cited by 10,891 · see citing works

Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors

Routy, B., Le Chatelier, E., Derosa, L., Duong, C. P. M., Alou, M. T., Daillère, R., Fluckiger, A., Messaoudene, M., Rauber, C., Roberti, M. P., et al. (2018) · Science · doi:10.1126/science.aan3706 · Cited by 5,671 · see citing works

The Orphan Nuclear Receptor RORγt Directs the Differentiation Program of Proinflammatory IL-17+ T Helper Cells

Ivanov, I. I., McKenzie, B. S., Zhou, L., Tadokoro, C. E., Lepelley, A., Lafaille, J. J., Cua, D. J., & Littman, D. R. (2006) · Cell · doi:10.1016/j.cell.2006.07.035 · Cited by 5,145 · see citing works

Host–microbe interactions have shaped the genetic architecture of inflammatory bowel disease

The International IBD Genetics Consortium (IIBDGC), Jostins, L., Ripke, S., Weersma, R. K., Duerr, R. H., McGovern, D. P., Hui, K. Y., Lee, J. C., Philip Schumm, L., Sharma, Y., et al. (2012) · Nature · doi:10.1038/nature11582 · Cited by 4,722 · see citing works

Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases

Frank, D. N., St. Amand, A. L., Feldman, R. A., Boedeker, E. C., Harpaz, N., & Pace, N. R. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0706625104 · Cited by 4,611 · see citing works

Induction of Intestinal Th17 Cells by Segmented Filamentous Bacteria

Ivanov, I. I., Atarashi, K., Manel, N., Brodie, E. L., Shima, T., Karaoz, U., Wei, D., Goldfarb, K. C., Santee, C. A., Lynch, S. V., et al. (2009) · Cell · doi:10.1016/j.cell.2009.09.033 · Cited by 4,554 · see citing works

<i>Faecalibacterium prausnitzii</i> is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients

Sokol, H., Pigneur, B., Watterlot, L., Lakhdari, O., Bermúdez-Humarán, L. G., Gratadoux, J.-J., Blugeon, S., Bridonneau, C., Furet, J.-P., Corthier, G., et al. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0804812105 · Cited by 4,413 · see citing works

Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice

Ridaura, V. K., Faith, J. J., Rey, F. E., Cheng, J., Duncan, A. E., Kau, A. L., Griffin, N. W., Lombard, V., Henrissat, B., Bain, J. R., et al. (2013) · Science · doi:10.1126/science.1241214 · Cited by 3,788 · see citing works

Induction of Colonic Regulatory T Cells by Indigenous <i>Clostridium</i> Species

Atarashi, K., Tanoue, T., Shima, T., Imaoka, A., Kuwahara, T., Momose, Y., Cheng, G., Yamasaki, S., Saito, T., Ohba, Y., et al. (2011) · Science · doi:10.1126/science.1198469 · Cited by 3,752 · see citing works

Gut microbiota regulate motor deficits and neuroinflammation in a model of Parkinson's disease

Sampson, T. R., Debelius, J. W., Thron, T., Janssen, S., Shastri, G. G., Ilhan, Z. E., Challis, C., Schretter, C. E., Rocha, S., Gradinaru, V., et al. (2016) · Cell · doi:10.1016/j.cell.2016.11.018 · Cited by 3,622 · see citing works

The Treatment-Naive Microbiome in New-Onset Crohn’s Disease

Gevers, D., Kugathasan, S., Denson, L. A., Vázquez-Baeza, Y., Van Treuren, W., Ren, B., Schwager, E., Knights, D., Song, S. J., Yassour, M., et al. (2014) · Cell Host &amp; Microbe · doi:10.1016/j.chom.2014.02.005 · Cited by 3,220 · see citing works

Genetics and pathogenesis of inflammatory bowel disease

Khor, B., Gardet, A., & Xavier, R. J. (2011) · Nature · doi:10.1038/nature10209 · Cited by 2,629 · see citing works

Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations

Liu, J. Z., van Sommeren, S., Huang, H., Ng, S. C., Alberts, R., Takahashi, A., Ripke, S., Lee, J. C., Jostins, L., Shah, T., et al. (2015) · Nature Genetics · doi:10.1038/ng.3359 · Cited by 2,603 · see citing works

The Long-Term Stability of the Human Gut Microbiota

Faith, J. J., Guruge, J. L., Charbonneau, M., Subramanian, S., Seedorf, H., Goodman, A. L., Clemente, J. C., Knight, R., Heath, A. C., Leibel, R. L., et al. (2013) · Science · doi:10.1126/science.1237439 · Cited by 2,058 · see citing works

Microbial Influences in Inflammatory Bowel Diseases

Sartor, R. B. (2008) · Gastroenterology · doi:10.1053/j.gastro.2007.11.059 · Cited by 1,927 · see citing works

The Microbiome in Inflammatory Bowel Disease: Current Status and the Future Ahead

Kostic, A. D., Xavier, R. J., & Gevers, D. (2014) · Gastroenterology · doi:10.1053/j.gastro.2014.02.009 · Cited by 1,789 · see citing works

Gut microbiota and IBD: causation or correlation?

Ni, J., Wu, G. D., Albenberg, L., & Tomov, V. T. (2017) · Nature Reviews Gastroenterology &amp; Hepatology · doi:10.1038/nrgastro.2017.88 · Cited by 1,778 · see citing works

Specific Microbiota Direct the Differentiation of IL-17-Producing T-Helper Cells in the Mucosa of the Small Intestine

Ivanov, I. I., Frutos, R. D. L., Manel, N., Yoshinaga, K., Rifkin, D. B., Sartor, R. B., Finlay, B. B., & Littman, D. R. (2008) · Cell Host &amp; Microbe · doi:10.1016/j.chom.2008.09.009 · Cited by 1,770 · see citing works

Increased expression of interleukin 17 in inflammatory bowel disease

Fujino, S., Andoh, A., Bamba, S., Ogawa, A., Hata, K., Araki, Y., Bamba, T., & Fujiyama, Y. (2003) · Gut · doi:10.1136/gut.52.1.65 · Cited by 1,713 · see citing works

High prevalence of adherent-invasive Escherichia coli associated with ileal mucosa in Crohn’s disease

Darfeuille-Michaud, A., Boudeau, J., Bulois, P., Neut, C., Glasser, A.-L., Barnich, N., Bringer, M.-A., Swidsinski, A., Beaugerie, L., & Colombel, J.-F. (2004) · Gastroenterology · doi:10.1053/j.gastro.2004.04.061 · Cited by 1,566 · see citing works

Fecal Microbiota Transplantation Induces Remission in Patients With Active Ulcerative Colitis in a Randomized Controlled Trial

Moayyedi, P., Surette, M. G., Kim, P. T., Libertucci, J., Wolfe, M., Onischi, C., Armstrong, D., Marshall, J. K., Kassam, Z., Reinisch, W., et al. (2015) · Gastroenterology · doi:10.1053/j.gastro.2015.04.001 · Cited by 1,499 · see citing works

Immunoglobulin A Coating Identifies Colitogenic Bacteria in Inflammatory Bowel Disease

Palm, N. W., de Zoete, M. R., Cullen, T. W., Barry, N. A., Stefanowski, J., Hao, L., Degnan, P. H., Hu, J., Peter, I., Zhang, W., et al. (2014) · Cell · doi:10.1016/j.cell.2014.08.006 · Cited by 1,286 · see citing works

Multidonor intensive faecal microbiota transplantation for active ulcerative colitis: a randomised placebo-controlled trial

Paramsothy, S., Kamm, M. A., Kaakoush, N. O., Walsh, A. J., van den Bogaerde, J., Samuel, D., Leong, R. W. L., Connor, S., Ng, W., Paramsothy, R., et al. (2017) · The Lancet · doi:10.1016/s0140-6736(17)30182-4 · Cited by 1,276 · see citing works

Identification of the Uncultured Bacillus of Whipple’s Disease

Relman, D. A., Schmidt, T. M., MacDermott, R. P., & Falkow, S. (1992) · New England Journal of Medicine · doi:10.1056/nejm199207303270501 · Cited by 1,150 · see citing works

Phenotypically distinct subsets of CD4 ⁺ T cells induce or protect from chronic intestinal inflammation in C. B-17 <i>scid</i> mice

Powrie, F., Leach, M. W., Mauze, S., Caddie, L. B., & Coffman, R. L. (1993) · International Immunology · doi:10.1093/intimm/5.11.1461 · Cited by 1,078 · see citing works

Th17 cell induction by adhesion of microbes to intestinal epithelial cells

Atarashi, K., Tanoue, T., Ando, M., Kamada, N., Nagano, Y., Narushima, S., Suda, W., Imaoka, A., Setoyama, H., Nagamori, T., et al. (2015) · Cell · doi:10.1016/j.cell.2015.08.058 · Cited by 1,071 · see citing works

Gut bacteria from multiple sclerosis patients modulate human T cells and exacerbate symptoms in mouse models

Cekanaviciute, E., Yoo, B. B., Runia, T. F., Debelius, J. W., Singh, S., Nelson, C., Kanner, R., Bencosme, Y., Lee, Y. K., Hauser, S. L., et al. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1711235114 · Cited by 1,040 · see citing works

The alarmin IL-33 promotes regulatory T-cell function in the intestine

Schiering, C., Krausgruber, T., Chomka, A., Fröhlich, A., Adelmann, K., Wohlfert, E. A., Pott, J., Griseri, T., Bollrath, J., Hegazy, A. N., et al. (2014) · Nature · doi:10.1038/nature13577 · Cited by 1,007 · see citing works

Ectopic colonization of oral bacteria in the intestine drives T _H 1 cell induction and inflammation

Atarashi, K., Suda, W., Luo, C., Kawaguchi, T., Motoo, I., Narushima, S., Kiguchi, Y., Yasuma, K., Watanabe, E., Tanoue, T., et al. (2017) · Science · doi:10.1126/science.aan4526 · Cited by 957 · see citing works

Individual intestinal symbionts induce a distinct population of RORγ ⁺ regulatory T cells

Sefik, E., Geva-Zatorsky, N., Oh, S., Konnikova, L., Zemmour, D., McGuire, A. M., Burzyn, D., Ortiz-Lopez, A., Lobera, M., Yang, J., et al. (2015) · Science · doi:10.1126/science.aaa9420 · Cited by 879 · see citing works

The microbiota regulates type 2 immunity through RORγt ⁺ T cells

Ohnmacht, C., Park, J.-H., Cording, S., Wing, J. B., Atarashi, K., Obata, Y., Gaboriau-Routhiau, V., Marques, R., Dulauroy, S., Fedoseeva, M., et al. (2015) · Science · doi:10.1126/science.aac4263 · Cited by 863 · see citing works

Intestinal Bacterial Colonization Induces Mutualistic Regulatory T Cell Responses

Geuking, M. B., Cahenzli, J., Lawson, M. A. E., Ng, D. C. K., Slack, E., Hapfelmeier, S., McCoy, K. D., & Macpherson, A. J. (2011) · Immunity · doi:10.1016/j.immuni.2011.03.021 · Cited by 840 · see citing works

Microbiota-dependent crosstalk between macrophages and ILC3 promotes intestinal homeostasis

Mortha, A., Chudnovskiy, A., Hashimoto, D., Bogunovic, M., Spencer, S. P., Belkaid, Y., & Merad, M. (2014) · Science · doi:10.1126/science.1249288 · Cited by 820 · see citing works

Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice

Goodman, A. L., Kallstrom, G., Faith, J. J., Reyes, A., Moore, A. M., Dantas, G. A., & Gordon, J. I. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1102938108 · Cited by 779 · see citing works

Mining the Human Gut Microbiota for Immunomodulatory Organisms

Geva-Zatorsky, N., Sefik, E., Kua, L., Pasman, L., Tan, T. G., Ortiz-Lopez, A., Yanortsang, T. B., Yang, L., Jupp, R., Mathis, D., et al. (2017) · Cell · doi:10.1016/j.cell.2017.01.022 · Cited by 762 · see citing works

Gut bacteria that prevent growth impairments transmitted by microbiota from malnourished children

Blanton, L. V., Charbonneau, M. R., Salih, T., Barratt, M. J., Venkatesh, S., Ilkaveya, O., Subramanian, S., Manary, M. J., Trehan, I., Jorgensen, J. M., et al. (2016) · Science · doi:10.1126/science.aad3311 · Cited by 735 · see citing works

Identification of IL-17-producing FOXP3 + regulatory T cells in humans

Voo, K. S., Wang, Y., Santori, F. R., Boggiano, C., Wang, Y.-H., Arima, K., Bover, L. C., Hanabuchi, S., Khalili, J. S., Marinova, E., et al. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0900408106 · Cited by 693 · see citing works

Oxazolone colitis, a Th2 colitis model resembling ulcerative colitis, is mediated by IL-13-producing NK-T cells.

Heller, F., Fuss, I., Nieuwenhuis, E., Blumberg, R., & Strober, W. (2002) · Immunity · doi:10.1016/s1074-7613(02)00453-3 · Cited by 648 · see citing works

GATA3 controls Foxp3+ regulatory T cell fate during inflammation in mice

Wohlfert, E. A., Grainger, J. R., Bouladoux, N., Konkel, J. E., Oldenhove, G., Ribeiro, C. H., Hall, J. A., Yagi, R., Naik, S., Bhairavabhotla, R., et al. (2011) · Journal of Clinical Investigation · doi:10.1172/jci57456 · Cited by 556 · see citing works

Fecal Lipocalin 2, a Sensitive and Broadly Dynamic Non-Invasive Biomarker for Intestinal Inflammation

Chassaing, B., Srinivasan, G., Delgado, M. A., Young, A. N., Gewirtz, A. T., & Vijay–Kumar, M. (2012) · PLoS ONE · doi:10.1371/journal.pone.0044328 · Cited by 555 · see citing works

An IL-23R/IL-22 Circuit Regulates Epithelial Serum Amyloid A to Promote Local Effector Th17 Responses

Sano, T., Huang, W., Hall, J. A., Yang, Y., Chen, A., Gavzy, S. J., Lee, J.-Y., Ziel, J. W., Miraldi, E. R., Domingos, A. I., et al. (2015) · Cell · doi:10.1016/j.cell.2015.08.061 · Cited by 547 · see citing works

Linking T-cell receptor sequence to functional phenotype at the single-cell level

Han, A. S., Glanville, J., Hansmann, L., & Davis, M. M. (2014) · Nature Biotechnology · doi:10.1038/nbt.2938 · Cited by 534 · see citing works

Interleukin-23 Drives Intestinal Inflammation through Direct Activity on T Cells

Ahern, P. P., Schiering, C., Buonocore, S., McGeachy, M. J., Cua, D. J., Maloy, K. J., & Powrie, F. (2010) · Immunity · doi:10.1016/j.immuni.2010.08.010 · Cited by 528 · see citing works

The Treg/Th17 Axis: A Dynamic Balance Regulated by the Gut Microbiome

Omenetti, S., & Pizarro, T. T. (2015) · Frontiers in Immunology · doi:10.3389/fimmu.2015.00639 · Cited by 528 · see citing works

Focused specificity of intestinal TH17 cells towards commensal bacterial antigens

Yang, Y., Torchinsky, M. B., Gobert, M., Xiong, H., Xu, M., Linehan, J. L., Alonzo, F., Ng, C., Chen, A., Lin, X., et al. (2014) · Nature · doi:10.1038/nature13279 · Cited by 520 · see citing works

Transplantation of fecal microbiota from patients with irritable bowel syndrome alters gut function and behavior in recipient mice

De Palma, G., Lynch, M. D. J., Lu, J., Dang, V. T., Deng, Y., Jury, J., Umeh, G., Miranda, P. M., Pigrau Pastor, M., Sidani, S., et al. (2017) · Science Translational Medicine · doi:10.1126/scitranslmed.aaf6397 · Cited by 505 · see citing works

c-MAF-dependent regulatory T cells mediate immunological tolerance to a gut pathobiont

Xu, M., Pokrovskii, M., Ding, Y., Yi, R., Au, C., Harrison, O. J., Galan, C., Belkaid, Y., Bonneau, R., & Littman, D. R. (2018) · Nature · doi:10.1038/nature25500 · Cited by 498 · see citing works

Characterization of Foxp3+CD4+CD25+ and IL-10-Secreting CD4+CD25+ T Cells during Cure of Colitis

Uhlig, H. H., Coombes, J. L., Mottet, C., Ízcue, A., Thompson, C., Fanger, A., Tannapfel, A., Fontenot, J. D., Ramsdell, F., & Powrie, F. M. (2006) · The Journal of Immunology · doi:10.4049/jimmunol.177.9.5852 · Cited by 463 · see citing works

Foxp3+ T cells expressing RORγt represent a stable regulatory T-cell effector lineage with enhanced suppressive capacity during intestinal inflammation

Yang, B.-H., Hagemann, S., Mamareli, P., Lauer, U., Hoffmann, U., Beckstette, M., Föhse, L., Prinz, I., Pezoldt, J., Suerbaum, S., et al. (2015) · Mucosal Immunology · doi:10.1038/mi.2015.74 · Cited by 435 · see citing works

Identifying species of symbiont bacteria from the human gut that, alone, can induce intestinal Th17 cells in mice

Tan, T. G., Sefik, E., Geva-Zatorsky, N., Kua, L., Naskar, D., Teng, F., Pasman, L., Ortiz-Lopez, A., Jupp, R., Wu, H.-J. J., et al. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1617460113 · Cited by 427 · see citing works

Identifying gut microbe-host phenotype relationships using combinatorial communities in gnotobiotic mice

Faith, J. J., Ahern, P. P., Ridaura, V. K., Cheng, J., & Gordon, J. I. (2014) · Science Translational Medicine · doi:10.1126/scitranslmed.3008051 · Cited by 373 · see citing works

Interactions between diet and the intestinal Microbiota alter intestinal permeability and colitis severity in mice

Llewellyn, S. R., Britton, G. J., Contijoch, E. J., Vennaro, O. H., Mortha, A., Colombel, J.-F., Grinspan, A., Clemente, J. C., Merad, M., & Faith, J. J. (2018) · Gastroenterology · doi:10.1053/j.gastro.2017.11.030 · Cited by 364 · see citing works

Gnotobiotic mouse model of phage–bacterial host dynamics in the human gut

Reyes, A., Wu, M., McNulty, N. P., Rohwer, F. L., & Gordon, J. I. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1319470110 · Cited by 355 · see citing works

Regulation of Adaptive Immunity; The Role of Interleukin-10

Ng, T. H. S., Britton, G. J., Hill, E. V., Verhagen, J., Burton, B. R., & Wraith, D. C. (2013) · Frontiers in Immunology · doi:10.3389/fimmu.2013.00129 · Cited by 354 · see citing works

Characterization of Interleukin-17–Producing Regulatory T Cells in Inflamed Intestinal Mucosa From Patients With Inflammatory Bowel Diseases

Hovhannisyan, Z., Treatman, J. D., Littman, D. R., & Mayer, L. (2010) · Gastroenterology · doi:10.1053/j.gastro.2010.12.002 · Cited by 339 · see citing works

Circulating and Tissue-Resident CD4+ T Cells With Reactivity to Intestinal Microbiota Are Abundant in Healthy Individuals and Function Is Altered During Inflammation

Hegazy, A. N., West, N. R., Stubbington, M. J. T., Wendt, E., Suijker, K. I. M., Datsi, A., This, S., Danne, C., Campion, S., Duncan, S. H., et al. (2017) · Gastroenterology · doi:10.1053/j.gastro.2017.07.047 · Cited by 338 · see citing works

Host-Protozoan Interactions Protect from Mucosal Infections through Activation of the Inflammasome

Chudnovskiy, A., Mortha, A., Kana, V., Kennard, A., Ramirez, J. D., Rahman, A., Remark, R., Mogno, I., Ng, R., Gnjatic, S., et al. (2016) · Cell · doi:10.1016/j.cell.2016.08.076 · Cited by 325 · see citing works

IgA-coated E. coli enriched in Crohn’s disease spondyloarthritis promote T H 17-dependent inflammation

Viladomiu, M., Kivolowitz, C., Abdulhamid, A., Dogan, B., Victorio, D., Castellanos, J. G., Woo, V., Teng, F., Tran, N. L., Sczesnak, A., et al. (2017) · Science Translational Medicine · doi:10.1126/scitranslmed.aaf9655 · Cited by 314 · see citing works

Induction of Persistent Colitis by a Human Commensal, EnterotoxigenicBacteroides fragilis, in Wild-Type C57BL/6 Mice

Rhee, K., Wu, S., Wu, X., Huso, D. L., Karim, B. O., Franco, A. A., Rabizadeh, S., Golub, J. E., Mathews, L. E., Shin, J. W., et al. (2009) · Infection and Immunity · doi:10.1128/iai.00814-08 · Cited by 297 · see citing works

Host protective roles of type 2 immunity: Parasite killing and tissue repair, flip sides of the same coin

Allen, J. E., & Sutherland, T. E. (2014) · Seminars in Immunology · doi:10.1016/j.smim.2014.06.003 · Cited by 260 · see citing works

Impaired regulatory T cell function in germ‐free mice

Östman, S., Rask, C., Wold, A. E., Hultkrantz, S., & Telemo, E. (2006) · European Journal of Immunology · doi:10.1002/eji.200535244 · Cited by 256 · see citing works

Functional Characterization of Inflammatory Bowel Disease–Associated Gut Dysbiosis in Gnotobiotic Mice

Nagao‐Kitamoto, H., Shreiner, A. B., Gillilland, M. G., Kitamoto, S., Ishii, C., Hirayama, A., Kuffa, P., Zaatari, M. E., Grasberger, H., Seekatz, A. M., et al. (2016) · Cellular and Molecular Gastroenterology and Hepatology · doi:10.1016/j.jcmgh.2016.02.003 · Cited by 248 · see citing works

A Disease-Associated Microbial and Metabolomics State in Relatives of Pediatric Inflammatory Bowel Disease Patients

Jacobs, J. P., Goudarzi, M., Singh, N., Tong, M., McHardy, I. H., Ruegger, P. M., Asadourian, M., Moon, B., Ayson, A., Borneman, J., et al. (2016) · Cellular and Molecular Gastroenterology and Hepatology · doi:10.1016/j.jcmgh.2016.06.004 · Cited by 230 · see citing works

Segmented filamentous bacteria in a defined bacterial cocktail induce intestinal inflammation in SCID mice reconstituted with CD45RBhigh CD4+ T cells

Štëpánková, R., Powrie, F. M., Kofroňová, O., Kozáková, H., Hudcovic, T., Hrnčíř, T., Uhlig, H. H., Read, S., Šinkorová, Z., Benada, O., et al. (2007) · Inflammatory Bowel Diseases · doi:10.1002/ibd.20221 · Cited by 191 · see citing works

The role of mucosal immunity and host genetics in defining intestinal commensal bacteria

Hansen, J. J., Gulati, A., & Sartor, R. B. (2010) · Current Opinion in Gastroenterology · doi:10.1097/mog.0b013e32833f1195 · Cited by 177 · see citing works

Gut microbiota density influences host physiology and is shaped by host and microbial factors

Contijoch, E. J., Britton, G. J., Yang, C., Mogno, I., Li, Z., Ng, R., Llewellyn, S. R., Hira, S., Johnson, C. N., Rabinowitz, K. M., et al. (2019) · eLife · doi:10.7554/elife.40553 · Cited by 167 · see citing works

Downregulation of Th17 Cells in the Small Intestine by Disruption of Gut Flora in the Absence of Retinoic Acid

Cha, H., Chang, S.-Y., Chang, J., Kim, J., Yang, J., Kim, C., & Kweon, M. (2010) · The Journal of Immunology · doi:10.4049/jimmunol.0902944 · Cited by 165 · see citing works

Induction of Bacterial Antigen-Specific Colitis by a Simplified Human Microbiota Consortium in Gnotobiotic Interleukin-10 −/− Mice

Eun, C. S., Mishima, Y., Wohlgemuth, S., Liu, B., Bower, M., Carroll, I. M., & Sartor, R. B. (2014) · Infection and Immunity · doi:10.1128/iai.01513-13 · Cited by 124 · see citing works

Ecobiotherapy Rich in Firmicutes Decreases Susceptibility to Colitis in a Humanized Gnotobiotic Mouse Model

Natividad, J. M., Pinto-Sánchez, M. I., Galipeau, H. J., Jury, J., Jordana, M., Reinisch, W., Collins, S. M., Bercik, P., Surette, M. G., Allen‐Vercoe, E., et al. (2015) · Inflammatory Bowel Diseases · doi:10.1097/mib.0000000000000422 · Cited by 119 · see citing works

Development of gut inflammation in mice colonized with mucosa-associated bacteria from patients with ulcerative colitis

Du, Z., Hudcovic, T., Mrázek, J., Kozáková, H., Šrůtková, D., Schwarzer, M., Tlaskalová‐Hogenová, H., Kostovčík, M., & Kverka, M. (2015) · Gut Pathogens · doi:10.1186/s13099-015-0080-2 · Cited by 54 · see citing works

Bifidobacterium animalis causes extensive duodenitis and mild colonic inflammation in monoassociated interleukin-10-deficient mice

Moran, J. P., Walter, J., Tannock, G. W., Tonkonogy, S. L., & Sartor, R. B. (2009) · Inflammatory Bowel Diseases · doi:10.1002/ibd.20900 · Cited by 53 · see citing works

Gut microbiota density influences host physiology and is shaped by host and microbial factorsPreprint

Contijoch, E. J., Britton, G. J., Yang, C., et al. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/277095 · Cited by 24 · see citing works

Interaction between microbiota and immunity in health and disease

Zheng, D., Liwinski, T., & Elinav, E. (2020) · Cell Research · doi:10.1038/s41422-020-0332-7 · Cited by 3,947 · see citing works

Pathophysiology of Inflammatory Bowel Diseases

Chang, J. T. (2020) · New England Journal of Medicine · doi:10.1056/nejmra2002697 · Cited by 1,295 · see citing works

Microbial bile acid metabolites modulate gut RORγ+ regulatory T cell homeostasis

Song, X., Sun, X., Oh, S. F., Wu, M., Zhang, Y., Zheng, W., Geva-Zatorsky, N., Jupp, R., Mathis, D., Benoist, C., et al. (2020) · Nature · doi:10.1038/s41586-019-1865-0 · Cited by 1,024 · see citing works

Establishing or Exaggerating Causality for the Gut Microbiome: Lessons from Human Microbiota-Associated Rodents

Walter, J., Armet, A. M., Finlay, B. B., & Shanahan, F. (2020) · Cell · doi:10.1016/j.cell.2019.12.025 · Cited by 596 · see citing works

Ginseng polysaccharides alter the gut microbiota and kynurenine/tryptophan ratio, potentiating the antitumour effect of antiprogrammed cell death 1/programmed cell death ligand 1 (anti-PD-1/PD-L1) immunotherapy

Huang, J., Liu, D., Wang, Y., Liu, L., Li, J., Yuan, J., Jiang, Z., Jiang, Z., Hsiao, W. W., Liu, H., et al. (2022) · Gut · doi:10.1136/gutjnl-2020-321031 · Cited by 539 · see citing works

Microbiota in inflammatory bowel disease: mechanisms of disease and therapeutic opportunities

Iliev, I. D., Ananthakrishnan, A. N., & Guo, C.-J. (2025) · Nature Reviews Microbiology · doi:10.1038/s41579-025-01163-0 · Cited by 249 · see citing works

Fecal IgA Levels Are Determined by Strain-Level Differences in Bacteroides ovatus and Are Modifiable by Gut Microbiota Manipulation

Yang, C., Mogno, I., Contijoch, E. J., Borgerding, J. N., Aggarwala, V., Li, Z., Siu, S., Grasset, E. K., Helmus, D. S., Dubinsky, M. C., et al. (2020) · Cell Host &amp; Microbe · doi:10.1016/j.chom.2020.01.016 · Cited by 221 · see citing works

Novel Fecal Biomarkers That Precede Clinical Diagnosis of Ulcerative Colitis

Galipeau, H. J., Caminero, A., Turpin, W., Bermudez-Brito, M., Santiago, A., Libertucci, J., Constante, M., Raygoza Garay, J. A., Rueda, G., Armstrong, S., et al. (2021) · Gastroenterology · doi:10.1053/j.gastro.2020.12.004 · Cited by 190 · see citing works

Psychological stress in inflammatory bowel disease: Psychoneuroimmunological insights into bidirectional gut–brain communications

Ge, L., Liu, S., Li, S., Yang, J., Hu, G., Xu, C., & Song, W. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.1016578 · Cited by 187 · see citing works

Microbiota maintain colonic homeostasis by activating TLR2/MyD88/PI3K signaling in IL-10–producing regulatory B cells

Mishima, Y., Oka, A., Liu, B., Herzog, J. W., Eun, C. S., Fan, T.-J., Bulik-Sullivan, E., Carroll, I. M., Hansen, J. J., Chen, L., et al. (2019) · Journal of Clinical Investigation · doi:10.1172/jci93820 · Cited by 166 · see citing works

Recipient factors in faecal microbiota transplantation: one stool does not fit all

Danne, C., Rolhion, N., & Sokol, H. (2021) · Nature Reviews Gastroenterology &amp; Hepatology · doi:10.1038/s41575-021-00441-5 · Cited by 154 · see citing works

Advances and novel developments in mechanisms of allergic inflammation

Han, X., Krempski, J. W., & Nadeau, K. (2020) · Allergy · doi:10.1111/all.14632 · Cited by 129 · see citing works

Regulatory T cells in the face of the intestinal microbiota

Ramanan, D., Pratama, A., Zhu, Y., Venezia, O., Sassone-Corsi, M., Chowdhary, K., Galván-Peña, S., Sefik, E., Brown, C., Gélineau, A., et al. (2023) · Nature Reviews Immunology · doi:10.1038/s41577-023-00890-w · Cited by 126 · see citing works

Gut Microbiome as a Potential Factor for Modulating Resistance to Cancer Immunotherapy

Shui, L., Yang, X., Li, J., Yi, C., Sun, Q., & Zhu, H. (2020) · Frontiers in Immunology · doi:10.3389/fimmu.2019.02989 · Cited by 115 · see citing works

Human CD4+CD8α+ Tregs induced by Faecalibacterium prausnitzii protect against intestinal inflammation

Touch, S., Godefroy, E., Rolhion, N., Danne, C., Oeuvray, C., Straube, M., Galbert, C., Brot, L., Alonso Salgueiro, I., Chadi, S., et al. (2022) · JCI Insight · doi:10.1172/jci.insight.154722 · Cited by 80 · see citing works

Geographic Differences in Gut Microbiota Composition Impact Susceptibility to Enteric Infection

Porras, A. M., Shi, Q., Zhou, H., Callahan, R., Montenegro-Bethancourt, G., Solomons, N., & Brito, I. L. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.109457 · Cited by 74 · see citing works

Molecular Communication Between Neuronal Networks and Intestinal Epithelial Cells in Gut Inflammation and Parkinson’s Disease

Drobny, A., Ngo, P. A., Neurath, M. F., Zunke, F., & López-Posadas, R. (2021) · Frontiers in Medicine · doi:10.3389/fmed.2021.655123 · Cited by 24 · see citing works

Methods of Inducing Inflammatory Bowel Disease in Mice

Maxwell, J. R., Brown, W. A., Smith, C. S., Byrne, F. R., & Viney, J. L. (2009) · Current Protocols in Pharmacology · doi:10.1002/0471141755.ph0558s47 · Cited by 64 · see citing works

Mouse Model of Dextran Sodium Sulfate (DSS)-induced Colitis

Das, S., Batra, S. K., & Rachagani, S. (2017) · BIO-PROTOCOL · doi:10.21769/bioprotoc.2515 · Cited by 19 · see citing works

31288 Occurrence of inflammatory bowel disease in patients with chronic inflammatory skin diseases

Schneeweiss, M. C., Kirchgesner, J., & Wyss, R. (2022) · Journal of the American Academy of Dermatology · doi:10.1016/j.jaad.2022.06.378

Special Issue “Dietary Bioactive Components in Inflammatory Bowel Disease”

Gasparrini, M., & Mazzoni, L. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25073569 · Cited by 4 · see citing works

Origins and Directions of Inflammatory Bowel Disease, Early Studies of the “Nonspecific” Inflammatory Bowel Diseases

Levine, J. S. (2003) · Gastroenterology · doi:10.1016/s0016-5085(03)70023-7 · Cited by 6 · see citing works