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Rev. Immunol."},{"key":"10.1016\/j.celrep.2026.117556_bib61","doi-asserted-by":"crossref","first-page":"451","DOI":"10.1038\/nature12726","article-title":"Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation","volume":"504","author":"Arpaia","year":"2013","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2026.117556_bib62","doi-asserted-by":"crossref","first-page":"410","DOI":"10.1038\/s41586-019-1865-0","article-title":"Microbial bile acid metabolites modulate gut RORgamma(+) regulatory T cell homeostasis","volume":"577","author":"Song","year":"2020","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2026.117556_bib63","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1038\/s41586-019-1785-z","article-title":"Bile acid metabolites control T(H)17 and T(reg) cell differentiation","volume":"576","author":"Hang","year":"2019","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2026.117556_bib64","doi-asserted-by":"crossref","first-page":"475","DOI":"10.1038\/s41586-020-2193-0","article-title":"Bacterial metabolism of bile acids promotes generation of peripheral regulatory T cells","volume":"581","author":"Campbell","year":"2020","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2026.117556_bib65","doi-asserted-by":"crossref","first-page":"256","DOI":"10.1126\/science.1145697","article-title":"Reciprocal TH17 and regulatory T cell differentiation mediated by retinoic acid","volume":"317","author":"Mucida","year":"2007","journal-title":"Science"},{"key":"10.1016\/j.celrep.2026.117556_bib66","doi-asserted-by":"crossref","DOI":"10.1126\/sciimmunol.adj4775","article-title":"Gut bacteria-derived serotonin promotes immune tolerance in early life","volume":"9","author":"Sanidad","year":"2024","journal-title":"Sci. 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Med."},{"key":"10.1016\/j.celrep.2026.117556_bib74","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2501030122","article-title":"Human milk IgA promotes normal immune development by limiting Th17-inducing Erysipelatoclostridium ramosum in the infant gut","volume":"122","author":"Donald","year":"2025","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.celrep.2026.117556_bib75","doi-asserted-by":"crossref","first-page":"1017","DOI":"10.1016\/j.jaci.2016.06.047","article-title":"Aberrant IgA responses to the gut microbiota during infancy precede asthma and allergy development","volume":"139","author":"Dzidic","year":"2017","journal-title":"J. Allergy Clin. 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