Caruso, R., Lo, B. C. & Nunez, G. Host–microbiota interactions in inflammatory bowel disease. Nat. Rev. Immunol. 20, 411–426 (2020).
Article CAS PubMed Google Scholar
Xavier, R. J. & Podolsky, D. K. Unravelling the pathogenesis of inflammatory bowel disease. Nature 448, 427–434 (2007).
Article CAS PubMed Google Scholar
Caballero-Flores, G., Pickard, J. M. & Nunez, G. Microbiota-mediated colonization resistance: mechanisms and regulation. Nat. Rev. Microbiol. 21, 347–360 (2023).
Article CAS PubMed Google Scholar
Ni, J., Wu, G. D., Albenberg, L. & Tomov, V. T. Gut microbiota and IBD: causation or correlation? Nat. Rev. Gastroenterol. Hepatol. 14, 573–584 (2017).
Article PubMed PubMed Central Google Scholar
Caruso, R. et al. A specific gene-microbe interaction drives the development of Crohn’s disease-like colitis in mice. Sci. Immunol. 4, eaaw4341 (2019). This study demonstrates the requirement for a specific mucus-dwelling pathobiont for triggering early-onset Crohn’s disease-like colitis in Nod2 Cybb double-deficient mice.
Article CAS PubMed PubMed Central Google Scholar
Berry, D. et al. Host-compound foraging by intestinal microbiota revealed by single-cell stable isotope probing. Proc. Natl Acad. Sci. USA 110, 4720–4725 (2013).
Article CAS PubMed PubMed Central Google Scholar
Sonnenburg, J. L. et al. Glycan foraging in vivo by an intestine-adapted bacterial symbiont. Science 307, 1955–1959 (2005).
Article CAS PubMed Google Scholar
Albenberg, L. et al. Correlation between intraluminal oxygen gradient and radial partitioning of intestinal microbiota. Gastroenterology 147, 1055–1063.e8 (2014).
Byndloss, M. X. et al. Microbiota-activated PPAR-γ signaling inhibits dysbiotic Enterobacteriaceae expansion. Science 357, 570–575 (2017).
Article CAS PubMed PubMed Central Google Scholar
Friedman, E. S. et al. Microbes vs. chemistry in the origin of the anaerobic gut lumen. Proc. Natl Acad. Sci. USA 115, 4170–4175 (2018).
Article CAS PubMed PubMed Central Google Scholar
Spees, A. M. et al. Streptomycin-induced inflammation enhances Escherichia coli gut colonization through nitrate respiration. mBio 4, e00430-13 (2013).
Article PubMed PubMed Central Google Scholar
Duncan, S. H., Louis, P., Thomson, J. M. & Flint, H. J. The role of pH in determining the species composition of the human colonic microbiota. Env. Microbiol. 11, 2112–2122 (2009).
Campbell, C. et al. Extrathymically generated regulatory T cells establish a niche for intestinal border-dwelling bacteria and affect physiologic metabolite balance. Immunity 48, 1245–1257.e9 (2018).
Article CAS PubMed PubMed Central Google Scholar
Vaishnava, S. et al. The antibacterial lectin RegIIIγ promotes the spatial segregation of microbiota and host in the intestine. Science 334, 255–258 (2011).
Article CAS PubMed PubMed Central Google Scholar
Cremer, J. et al. Effect of flow and peristaltic mixing on bacterial growth in a gut-like channel. Proc. Natl Acad. Sci. USA 113, 11414–11419 (2016).
Article CAS PubMed PubMed Central Google Scholar
Kashyap, P. C. et al. Complex interactions among diet, gastrointestinal transit, and gut microbiota in humanized mice. Gastroenterology 144, 967–977 (2013).
Donaldson, G. P., Lee, S. M. & Mazmanian, S. K. Gut biogeography of the bacterial microbiota. Nat. Rev. Microbiol. 14, 20–32 (2016).
Article CAS PubMed Google Scholar
McCallum, G. & Tropini, C. The gut microbiota and its biogeography. Nat. Rev. Microbiol. 22, 105–118 (2024).
Article CAS PubMed Google Scholar
Kamada, N., Chen, G. Y., Inohara, N. & Nunez, G. Control of pathogens and pathobionts by the gut microbiota. Nat. Immunol. 14, 685–690 (2013).
Article CAS PubMed PubMed Central Google Scholar
Miller, B. M., Liou, M. J., Lee, J. Y. & Baumler, A. J. The longitudinal and cross-sectional heterogeneity of the intestinal microbiota. Curr. Opin. Microbiol. 63, 221–230 (2021).
Article CAS PubMed Google Scholar
Gu, S. et al. Bacterial community mapping of the mouse gastrointestinal tract. PLoS ONE 8, e74957 (2013).
Article CAS PubMed PubMed Central Google Scholar
Nava, G. M., Friedrichsen, H. J. & Stappenbeck, T. S. Spatial organization of intestinal microbiota in the mouse ascending colon. ISME J. 5, 627–638 (2011).
Article CAS PubMed Google Scholar
Sender, R. & Milo, R. The distribution of cellular turnover in the human body. Nat. Med. 27, 45–48 (2021).
Article CAS PubMed Google Scholar
Litvak, Y., Byndloss, M. X. & Baumler, A. J. Colonocyte metabolism shapes the gut microbiota. Science 362, eaat9076 (2018).
Article PubMed PubMed Central Google Scholar
Furusawa, Y. et al. Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells. Nature 504, 446–450 (2013).
Article CAS PubMed Google Scholar
Buffie, C. G. et al. Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile. Nature 517, 205–208 (2015).
Article CAS PubMed Google Scholar
Whitaker, W. R., Shepherd, E. S. & Sonnenburg, J. L. Tunable expression tools enable single-cell strain distinction in the gut microbiome. Cell 169, 538–546.e12 (2017).
Article CAS PubMed PubMed Central Google Scholar
Nagara, Y., Takada, T., Nagata, Y., Kado, S. & Kushiro, A. Microscale spatial analysis provides evidence for adhesive monopolization of dietary nutrients by specific intestinal bacteria. PLoS ONE 12, e0175497 (2017).
Article PubMed PubMed Central Google Scholar
Pedron, T. et al. A crypt-specific core microbiota resides in the mouse colon. mBio 3, e00116-12 (2012).
Article PubMed PubMed Central Google Scholar
Tropini, C., Earle, K. A., Huang, K. C. & Sonnenburg, J. L. The gut microbiome: connecting spatial organization to function. Cell Host Microbe 21, 433–442 (2017).
Article CAS PubMed PubMed Central Google Scholar
Lee, S. M. et al. Bacterial colonization factors control specificity and stability of the gut microbiota. Nature 501, 426–429 (2013).
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