Willing, B. P., Russell, S. L. & Finlay, B. B. Shifting the balance: antibiotic effects on host-microbiota mutualism. Nat. Rev. Microbiol. 9, 233–243 (2011).

CAS  PubMed  Article  Google Scholar 

Ivanov, I. I. et al. Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell 139, 485–498 (2009).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Flannigan K. L. & Denning T.L. Segmented filamentous bacteria-induced immune responses: a balancing act between host protection and autoimmunity. Immunology 154, 537–546 (2018).

Mak, I. W., Evaniew, N. & Ghert, M. Lost in translation: animal models and clinical trials in cancer treatment. Am. J. Transl. Res. 6, 114–118 (2014).

PubMed  PubMed Central  Google Scholar 

Seok, J. et al. Genomic responses in mouse models poorly mimic human inflammatory diseases. Proc. Natl Acad. Sci. USA 110, 3507–3512 (2013).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Beura, L. K. et al. Normalizing the environment recapitulates adult human immune traits in laboratory mice. Nature 532, 512–516 (2016).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Liu, Y. et al. Gut microbiome alterations in high-fat-diet-fed mice are associated with antibiotic tolerance. Nat. Microbiol. 6, 874–884 (2021).

CAS  PubMed  Article  Google Scholar 

Scott N. A. et al. Antibiotics induce sustained dysregulation of intestinal T cell immunity by perturbing macrophage homeostasis. Sci. Transl. Med. 10, eaao4755 (2018).

Strati, F. et al. Antibiotic-associated dysbiosis affects the ability of the gut microbiota to control intestinal inflammation upon fecal microbiota transplantation in experimental colitis models. Microbiome 9, 39 (2021).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Ashley S. L. et al. Lung and gut microbiota are altered by hyperoxia and contribute to oxygen-induced lung injury in mice. Sci. Transl. Med. 12, eaau9959 (2020).

Brown, R. L., Sequeira, R. P. & Clarke, T. B. The microbiota protects against respiratory infection via GM-CSF signaling. Nat. Commun. 8, 1512 (2017).

PubMed  PubMed Central  Article  CAS  Google Scholar 

Hosang, L. et al. The lung microbiome regulates brain autoimmunity. Nature 603, 138–144 (2022).

CAS  PubMed  Article  Google Scholar 

Ichinohe, T. et al. Microbiota regulates immune defense against respiratory tract influenza A virus infection. Proc. Natl Acad. Sci. USA 108, 5354–5359 (2011).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Hurabielle, C. et al. Immunity to commensal skin fungi promotes psoriasiform skin inflammation. Proc. Natl Acad. Sci. USA 117, 16465–16474 (2020).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Naik, S. et al. Commensal-dendritic-cell interaction specifies a unique protective skin immune signature. Nature 520, 104–108 (2015).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Hu, Y. et al. Different immunological responses to early-life antibiotic exposure affecting autoimmune diabetes development in NOD mice. J. Autoimmun. 72, 47–56 (2016).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Hu, Y. et al. Maternal Antibiotic Treatment Protects Offspring from Diabetes Development in Nonobese Diabetic Mice by Generation of Tolerogenic APCs. J. Immunol. 195, 4176–4184 (2015).

CAS  PubMed  Article  Google Scholar 

Kennedy, E. A., King, K. Y. & Baldridge, M. T. Mouse Microbiota Models: comparing Germ-Free Mice and Antibiotics Treatment as Tools for Modifying Gut Bacteria. Front. Physiol. 9, 1534 (2018).

PubMed  PubMed Central  Article  Google Scholar 

Sender, R., Fuchs, S. & Milo, R. Are We Really Vastly Outnumbered? Revisiting the Ratio of Bacterial to Host. Cells Hum. Cell 164, 337–340 (2016).

CAS  Google Scholar 

Sommer, F. & Backhed, F. The gut microbiota–masters of host development and physiology. Nat. Rev. Microbiol. 11, 227–238 (2013).

CAS  PubMed  Article  Google Scholar 

Renz, H., Brandtzaeg, P. & Hornef, M. The impact of perinatal immune development on mucosal homeostasis and chronic inflammation. Nat. Rev. Immunol. 12, 9–23 (2011).

PubMed  Article  CAS  Google Scholar 

Cash, H. L., Whitham, C. V., Behrendt, C. L. & Hooper, L. V. Symbiotic bacteria direct expression of an intestinal bactericidal lectin. Science 313, 1126–1130 (2006).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Meisel, J. S. et al. Commensal microbiota modulate gene expression in the skin. Microbiome 6, 20 (2018).

PubMed  PubMed Central  Article  Google Scholar 

Sanos, S. L. et al. RORgammat and commensal microflora are required for the differentiation of mucosal interleukin 22-producing NKp46+ cells. Nat. Immunol. 10, 83–91 (2009).

CAS  PubMed  Article  Google Scholar 

Bain, C. C. et al. Constant replenishment from circulating monocytes maintains the macrophage pool in the intestine of adult mice. Nat. Immunol. 15, 929–937 (2014).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Chen Q., Nair S. & Ruedl C. Microbiota regulates the turnover kinetics of gut macrophages in health and inflammation. Life Sci Alliance. 5, e202101178 (2022).

Constantinides M. G. et al. MAIT cells are imprinted by the microbiota in early life and promote tissue repair. Science 366, eaax6624 (2019).

Schwarzer, M. et al. Germ-Free Mice Exhibit Mast Cells With Impaired Functionality and Gut Homing and Do Not Develop Food Allergy. Front. Immunol. 10, 205 (2019).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Shaw, T. N. et al. Tissue-resident macrophages in the intestine are long lived and defined by Tim-4 and CD4 expression. J. Exp. Med. 215, 1507–1518 (2018).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Legoux, F. et al. Microbial metabolites control the thymic development of mucosal-associated invariant T cells. Science 366, 494–499 (2019).

CAS  PubMed  Article  Google Scholar 

Satoh-Takayama, N. et al. Microbial flora drives interleukin 22 production in intestinal NKp46+ cells that provide innate mucosal immune defense. Immunity 29, 958–970 (2008).

CAS  PubMed  Article  Google Scholar 

Ueda, Y. et al. Commensal microbiota induce LPS hyporesponsiveness in colonic macrophages via the production of IL-10. Int. Immunol. 22, 953–962 (2010).

CAS  PubMed  Article  Google Scholar 

McCoy, K. D. & Thomson, C. A. The Impact of Maternal Microbes and Microbial Colonization in Early Life on Hematopoiesis. J. Immunol. 200, 2519–2526 (2018).

CAS  PubMed  Article  Google Scholar 

Wang, Z. et al. Skin microbiome promotes mast cell maturation by triggering stem cell factor production in keratinocytes. J. Allergy Clin. Immunol. 139, 1205–1216 (2017). e1206.

CAS  PubMed  Article  Google Scholar 

Ganal, S. C. et al. Priming of natural killer cells by nonmucosal mononuclear phagocytes requires instructive signals from commensal microbiota. Immunity 37, 171–186 (2012).

CAS  PubMed  Article  Google Scholar 

Almeida, J. I. et al. Hallmarks of the human intestinal microbiome on liver maturation and function. J. Hepatol. 76, 694–725 (2022).

PubMed  Article  Google Scholar 

Erny, D. et al. Host microbiota constantly control maturation and function of microglia in the CNS. Nat. Neurosci. 18, 965–977 (2015).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Geuking, M. B. et al. Intestinal bacterial colonization induces mutualistic regulatory T cell responses. Immunity 34, 794–806 (2011).

CAS  PubMed  Article  Google Scholar 

Kim, K. S. et al. Dietary antigens limit mucosal immunity by inducing regulatory T cells in the small intestine. Science 351, 858–863 (2016).

CAS  PubMed  Article  Google Scholar 

Weiss, J. M. et al. Neuropilin 1 is expressed on thymus-derived natural regulatory T cells, but not mucosa-generated induced Foxp3+ T reg cells. J. Exp. Med. 209, 1723–1742 (2012). S1721.

CAS  PubMed  PubMed Central  Article  Google Scholar 

Bunker J. J. et al. Natural polyreactive IgA antibodies coat the intestinal microbiota. Science 358, eaan6619 (2017).

Cahenzli, J., Koller, Y., Wyss, M., Geuking, M. B. & McCoy, K. D. Intestinal microbial diversity during early-life colonization shapes long-term IgE levels. Cell Host Microbe 14, 559–570 (2013).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Herbst, T. et al. Dysregulation of allergic airway inflammation in the absence of microbial colonization. Am. J. Respir. Crit. Care Med. 184, 198–205 (2011).

CAS