{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T22:36:01Z","timestamp":1792794961934,"version":"4.5.0"},"reference-count":204,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2024,12,19]],"date-time":"2024-12-19T00:00:00Z","timestamp":1734566400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>Gut microbiota regulates the immune system, the development and progression of autoimmune diseases (AIDs) and overall health. Recent studies have played a crucial part in understanding the specific role of different gut bacterial strains and their metabolites in different AIDs. Microbial signatures in AIDs are revealed by advanced sequencing and metabolomics studies. Microbes such as <jats:italic>Faecalibacterium prausnitzii, Akkermansia muciniphila, Anaerostipes caccae, Bacteroides<\/jats:italic> sp.<jats:italic>, Roseburia<\/jats:italic> sp.<jats:italic>, Blautia<\/jats:italic> sp.<jats:italic>, Blautia faecis<\/jats:italic>, <jats:italic>Clostridium lavalense<\/jats:italic>, <jats:italic>Christensenellaceae<\/jats:italic> sp.<jats:italic>, Coprococcus<\/jats:italic> sp.<jats:italic>, Firmicutes<\/jats:italic> sp.<jats:italic>, Ruminococcaceae<\/jats:italic> sp.<jats:italic>, Lachnospiraceae<\/jats:italic> sp.<jats:italic>, Megamonas<\/jats:italic> sp., <jats:italic>Monoglobus<\/jats:italic> sp.<jats:italic>, Streptococcus pneumoniae<\/jats:italic> and <jats:italic>Bifidobacterium<\/jats:italic> sp. help maintain immune homeostasis; whereas, <jats:italic>Prevotella copri, Ruminococcus gnavus, Lactobacillus salivarius, Enterococcus gallinarum, Elizabeth menigoseptica, Collinsella<\/jats:italic> sp.<jats:italic>, Escherichia<\/jats:italic> sp.<jats:italic>, Fusobacterium<\/jats:italic> sp.<jats:italic>, Enterobacter ludwigii, Enterobacteriaceae<\/jats:italic> sp.<jats:italic>, Proteobacteria<\/jats:italic>, <jats:italic>Porphyromonas gingivalis<\/jats:italic>, <jats:italic>Porphyromonas nigrescens<\/jats:italic>, <jats:italic>Dorea<\/jats:italic> sp., and <jats:italic>Clostridium<\/jats:italic> sp. cause immuno-pathogenesis. A complex web of interactions is revealed by understanding the influence of gut microbiota on immune cells and various T cell subsets such as CD4+ T cells, CD8+ T cells, natural killer T cells, \u03b3\u03b4 T cells, etc. Certain AIDs, including rheumatoid arthritis, diabetes mellitus, atopic asthma, inflammatory bowel disease and non-alcoholic fatty liver disease exhibit a state of dysbiosis, characterized by alterations in microbial diversity and relative abundance of specific taxa. This review summarizes recent developments in understanding the role of certain microbiota composition in specific AIDs, and the factors affecting specific regulatory T cells through certain microbial metabolites and also focuses the potential application and therapeutic significance of gut microbiota-based interventions as novel adjunctive therapies for AIDs. Further research to determine the precise association of each gut bacterial strain in specific diseases is required.<\/jats:p>","DOI":"10.3389\/fmicb.2024.1477187","type":"journal-article","created":{"date-parts":[[2024,12,19]],"date-time":"2024-12-19T16:46:43Z","timestamp":1734626803000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":76,"title":["Gut microbiota mediated T cells regulation and autoimmune diseases"],"prefix":"10.3389","volume":"15","author":[{"given":"Nabeel Khalid","family":"Bhutta","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiujin","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cuiqin","family":"Jian","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yifan","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jinlyu","family":"Sun","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bingnan","family":"Han","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shandong","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ansar","family":"Javeed","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2024,12,19]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","DOI":"10.3389\/fendo.2023.1265696","article-title":"Gut microbiome and blood glucose control in type 1 diabetes: a systematic review","volume":"14","author":"Abuqwider","year":"2023","journal-title":"Front. Endocrinol."},{"key":"ref2","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1111\/imm.13150","article-title":"Understanding immune\u2013microbiota interactions in the intestine","volume":"159","author":"Ahern","year":"2020","journal-title":"Immunology"},{"key":"ref3","doi-asserted-by":"publisher","first-page":"590","DOI":"10.1136\/annrheumdis-2018-214514","article-title":"Prevotella copri in individuals at risk for rheumatoid arthritis","volume":"78","author":"Alpizar-Rodriguez","year":"2019","journal-title":"Ann. Rheum. Dis."},{"key":"ref4","doi-asserted-by":"publisher","first-page":"123","DOI":"10.1016\/j.cell.2013.11.042","article-title":"Sphingolipids from a symbiotic microbe regulate homeostasis of host intestinal natural killer T cells","volume":"156","author":"An","year":"2014","journal-title":"Cell"},{"key":"ref5","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1038\/nrgastro.2017.136","article-title":"Environmental triggers in IBD: a review of progress and evidence","volume":"15","author":"Ananthakrishnan","year":"2018","journal-title":"Nat. Rev. Gastroenterol. Hepatol."},{"key":"ref6","doi-asserted-by":"publisher","first-page":"3300","DOI":"10.3390\/ijms24043300","article-title":"Type I diabetes pathoetiology and pathophysiology: roles of the gut microbiome, pancreatic cellular interactions, and the \u2018bystander\u2019 activation of memory CD8+ T cells","volume":"24","author":"Anderson","year":"2023","journal-title":"Int. J. Mol. Sci."},{"key":"ref7","doi-asserted-by":"publisher","first-page":"188","DOI":"10.1186\/s40168-021-01125-7","article-title":"Commensal microbe-derived acetate suppresses NAFLD\/NASH development via hepatic FFAR2 signalling in mice","volume":"9","author":"Aoki","year":"2021","journal-title":"Microbiome"},{"key":"ref8","doi-asserted-by":"publisher","first-page":"353","DOI":"10.1016\/B978-0-12-812215-0.00012-1","article-title":"Epigenetic basis of autoimmune disorders in humans","volume":"6","author":"Araki","year":"2018","journal-title":"Epigenetics Human Dis."},{"key":"ref9","doi-asserted-by":"publisher","first-page":"119311","DOI":"10.1016\/j.lfs.2021.119311","article-title":"Unravelling the involvement of gut microbiota in type 2 diabetes mellitus","volume":"273","author":"Arora","year":"2021","journal-title":"Life Sci."},{"key":"ref10","doi-asserted-by":"publisher","first-page":"2151","DOI":"10.1002\/art.39681","article-title":"Perturbed mucosal immunity and Dysbiosis accompany clinical disease in a rat model of Spondyloarthritis","volume":"68","author":"Asquith","year":"2016","journal-title":"Arthritis Rheumatol."},{"key":"ref11","doi-asserted-by":"publisher","first-page":"359","DOI":"10.1126\/science.aan4526","article-title":"Ectopic colonization of oral bacteria in the intestine drives T(H)1 cell induction and inflammation","volume":"358","author":"Atarashi","year":"2017","journal-title":"Science"},{"key":"ref12","doi-asserted-by":"publisher","first-page":"367","DOI":"10.1016\/j.cell.2015.08.058","article-title":"Th17 cell induction by adhesion of microbes to intestinal epithelial cells","volume":"163","author":"Atarashi","year":"2015","journal-title":"Cell"},{"key":"ref13","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1126\/science.1198469","article-title":"Induction of colonic regulatory T cells by indigenous Clostridium species","volume":"331","author":"Atarashi","year":"2011","journal-title":"Science"},{"key":"ref14","doi-asserted-by":"publisher","first-page":"947","DOI":"10.1136\/annrheumdis-2018-214856","article-title":"Lupus nephritis is linked to disease-activity associated expansions and immunity to a gut commensal","volume":"78","author":"Azzouz","year":"2019","journal-title":"Ann. Rheum. Dis."},{"key":"ref15","doi-asserted-by":"publisher","first-page":"285","DOI":"10.1016\/j.immuni.2019.06.002","article-title":"Microbiota-derived short-chain fatty acids promote the memory potential of antigen-activated CD8(+) T cells","volume":"51","author":"Bachem","year":"2019","journal-title":"Immunity"},{"key":"ref16","doi-asserted-by":"publisher","first-page":"2120","DOI":"10.2337\/db10-1201","article-title":"Defective differentiation of regulatory FoxP3+ T cells by small-intestinal dendritic cells in patients with type 1 diabetes","volume":"60","author":"Badami","year":"2011","journal-title":"Diabetes"},{"key":"ref17","doi-asserted-by":"publisher","first-page":"1809","DOI":"10.4049\/jimmunol.178.3.1809","article-title":"Commensal bacteria exacerbate intestinal inflammation but are not essential for the development of murine ileitis","volume":"178","author":"Bamias","year":"2007","journal-title":"J. Immunol."},{"key":"ref18","doi-asserted-by":"publisher","first-page":"e000324","DOI":"10.1136\/bmjresp-2018-000324","article-title":"Gut microbiota relationships to lung function and adult asthma phenotype: a pilot study","volume":"5","author":"Begley","year":"2018","journal-title":"BMJ Open Respir. Res."},{"key":"ref19","doi-asserted-by":"publisher","first-page":"1291","DOI":"10.3390\/jcm8091291","article-title":"Identification of a shared microbiomic and metabolomic profile in systemic autoimmune diseases","volume":"8","author":"Bellocchi","year":"2019","journal-title":"J. Clin. Med."},{"key":"ref20","doi-asserted-by":"publisher","first-page":"727474","DOI":"10.3389\/fimmu.2021.727474","article-title":"A pulmonary Lactobacillus murinus strain induces Th17 and ROR\u03b3t+ regulatory T cells and reduces lung inflammation","volume":"12","author":"Bernard-Raichon","year":"2021","journal-title":"Front. Immunol."},{"key":"ref21","doi-asserted-by":"publisher","first-page":"356","DOI":"10.1038\/nrmicro2546","article-title":"Paneth cells, antimicrobial peptides and maintenance of intestinal homeostasis","volume":"9","author":"Bevins","year":"2011","journal-title":"Nat. Rev. Microbiol."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"764","DOI":"10.1002\/hep.28356","article-title":"The severity of nonalcoholic fatty liver disease is associated with gut dysbiosis and shift in the metabolic function of the gut microbiota","volume":"63","author":"Boursier","year":"2016","journal-title":"Hepatology"},{"key":"ref23","doi-asserted-by":"publisher","first-page":"1686","DOI":"10.1111\/febs.15238","article-title":"NKT cells and the regulation of intestinal immunity: a two-way street","volume":"287","author":"Brailey","year":"2020","journal-title":"FEBS J."},{"key":"ref24","doi-asserted-by":"publisher","first-page":"e1001610","DOI":"10.1371\/journal.pbio.1001610","article-title":"Production of \u03b1-galactosylceramide by a prominent member of the human gut microbiota","volume":"11","author":"Brown","year":"2021","journal-title":"PLoS Biol."},{"key":"ref25","doi-asserted-by":"publisher","first-page":"785","DOI":"10.1038\/mi.2017.75","article-title":"Microbiome-driven allergic lung inflammation is ameliorated by short-chain fatty acids","volume":"11","author":"Cait","year":"2018","journal-title":"Mucosal Immunol."},{"key":"ref26","doi-asserted-by":"publisher","first-page":"322","DOI":"10.1016\/j.chom.2024.02.003","article-title":"Inflammation and bacteriophages affect DNA inversion states and functionality of the gut microbiota","volume":"32","author":"Carasso","year":"2024","journal-title":"Cell Host Microbe"},{"key":"ref27","doi-asserted-by":"publisher","first-page":"1406","DOI":"10.1038\/s41467-019-09455-9","article-title":"A gut microbiome signature for cirrhosis due to nonalcoholic fatty liver disease","volume":"10","author":"Caussy","year":"2019","journal-title":"Nat. Commun."},{"key":"ref28","doi-asserted-by":"publisher","first-page":"10713","DOI":"10.1073\/pnas.1711235114","article-title":"Gut bacteria from multiple sclerosis patients modulate human T cells and exacerbate symptoms in mouse models","volume":"114","author":"Cekanaviciute","year":"2017","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref29","doi-asserted-by":"publisher","first-page":"5486","DOI":"10.3748\/wjg.v23.i30.5486","article-title":"Influence of gut microbiota on neuropsychiatric disorders","volume":"23","author":"Cenit","year":"2017","journal-title":"World J. Gastroenterol."},{"key":"ref30","doi-asserted-by":"publisher","first-page":"11596","DOI":"10.1038\/ncomms11596","article-title":"Th2 and eosinophil responses suppress inflammatory arthritis","volume":"7","author":"Chen","year":"","journal-title":"Nat. Commun."},{"key":"ref31","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2021.761981","article-title":"Interaction between commensal bacteria, immune response and the intestinal barrier in inflammatory bowel disease","volume":"12","author":"Chen","year":"","journal-title":"Front. Immunol."},{"key":"ref32","doi-asserted-by":"publisher","first-page":"1901","DOI":"10.3748\/wjg.v26.i16.1901","article-title":"Therapeutic advances in non-alcoholic fatty liver disease: a microbiota-centered view","volume":"26","author":"Chen","year":"2020","journal-title":"World J. Gastroenterol."},{"key":"ref33","doi-asserted-by":"publisher","first-page":"621995","DOI":"10.1101\/621995","article-title":"Proinflammatory and autoimmunogenic gut microbiome in systemic lupus erythematosus","author":"Chen","year":"2019","journal-title":"bioRxiv"},{"key":"ref34","doi-asserted-by":"publisher","first-page":"e2118811","DOI":"10.1001\/jamanetworkopen.2021.18811","article-title":"Association of Insulin Resistance and Type 2 diabetes with gut microbial diversity: a microbiome-wide analysis from population studies","volume":"4","author":"Chen","year":"","journal-title":"JAMA Netw. Open"},{"key":"ref35","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2021.803101","article-title":"Gut microbiota as regulators of Th17\/Treg balance in patients with myasthenia gravis","volume":"12","author":"Chen","year":"2021","journal-title":"Front. Immunol."},{"key":"ref36","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1186\/s13073-016-0299-7","article-title":"An expansion of rare lineage intestinal microbes characterizes rheumatoid arthritis","volume":"8","author":"Chen","year":"","journal-title":"Genome Med."},{"key":"ref37","doi-asserted-by":"publisher","first-page":"e2321686121","DOI":"10.1073\/pnas.2321686121","article-title":"Lipidomic scanning of self-lipids identifies headless antigens for natural killer T cells","volume":"121","author":"Cheng","year":"2024","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref38","doi-asserted-by":"publisher","first-page":"4030","DOI":"10.1158\/0008-5472.CAN-13-2462","article-title":"Microbiota modulate tumoral immune surveillance in lung through a \u03b3\u03b4T17 immune cell-dependent mechanism","volume":"74","author":"Cheng","year":"2014","journal-title":"Cancer Res."},{"key":"ref39","doi-asserted-by":"publisher","DOI":"10.3390\/jcm8111770","article-title":"An Association of gut Microbiota with different phenotypes in Chinese patients with rheumatoid arthritis","volume":"8","author":"Chiang","year":"2019","journal-title":"J. Clin. Med."},{"key":"ref40","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1146\/annurev-immunol-032713-120216","article-title":"\u03b3\u03b4 T cells: first line of defense and beyond","volume":"32","author":"Chien","year":"2014","journal-title":"Annu. Rev. Immunol."},{"key":"ref41","doi-asserted-by":"publisher","first-page":"1813","DOI":"10.3390\/microorganisms11071813","article-title":"Evaluation of gut microbiota in healthy persons and type 1 diabetes mellitus patients in North-Western Russia","volume":"11","author":"Chukhlovin","year":"2023","journal-title":"Microorganisms"},{"key":"ref42","doi-asserted-by":"publisher","DOI":"10.1128\/microbiolspec.MBP-0006-2014","article-title":"Commensal and pathogenic Escherichia coli metabolism in the gut","volume":"3","author":"Conway","year":"2015","journal-title":"Microbiol. Spectr."},{"key":"ref43","doi-asserted-by":"publisher","first-page":"4103","DOI":"10.4049\/jimmunol.1301970","article-title":"Periodontal pathogens directly promote autoimmune experimental arthritis by inducing a TLR2-and IL-1\u2013driven Th17 response","volume":"192","author":"de Aquino","year":"2014","journal-title":"J. Immunol."},{"key":"ref44","doi-asserted-by":"publisher","first-page":"1569","DOI":"10.1007\/s00125-014-3274-0","article-title":"Aberrant gut microbiota composition at the onset of type 1 diabetes in young children","volume":"57","author":"de Goffau","year":"2014","journal-title":"Diabetologia"},{"key":"ref45","doi-asserted-by":"publisher","first-page":"1238","DOI":"10.2337\/db12-0526","article-title":"Fecal microbiota composition differs between children with \u03b2-cell autoimmunity and those without","volume":"62","author":"de Goffau","year":"2013","journal-title":"Diabetes"},{"key":"ref46","doi-asserted-by":"publisher","first-page":"201","DOI":"10.1097\/BOR.0000000000000574","article-title":"The microbiome in systemic autoimmune disease: mechanistic insights from recent studies","volume":"31","author":"Dehner","year":"2019","journal-title":"Curr. Opin. Rheumatol."},{"key":"ref47","doi-asserted-by":"publisher","DOI":"10.3390\/ijms25137062","article-title":"Inflammatory bowel disease: a comprehensive analysis of molecular bases, predictive biomarkers, diagnostic methods, and therapeutic options","volume":"25","author":"Diez-Martin","year":"2024","journal-title":"Int. J. Mol. Sci."},{"key":"ref48","doi-asserted-by":"publisher","DOI":"10.1128\/aem.00235-18","article-title":"Metabolism of Oxo-bile acids and characterization of recombinant 12\u03b1-Hydroxysteroid dehydrogenases from bile acid 7\u03b1-Dehydroxylating human gut Bacteria","volume":"84","author":"Doden","year":"2018","journal-title":"Appl. Environ. Microbiol."},{"key":"ref49","doi-asserted-by":"publisher","first-page":"665","DOI":"10.1038\/s41590-018-0120-4","article-title":"Regulatory T cells in autoimmune disease","volume":"19","author":"Dominguez-Villar","year":"2018","journal-title":"Nat. Immunol."},{"key":"ref50","doi-asserted-by":"publisher","first-page":"140","DOI":"10.1016\/j.chom.2010.01.005","article-title":"Microbial colonization drives expansion of IL-1 receptor 1-expressing and IL-17-producing \u03b3\/\u03b4 T cells","volume":"7","author":"Duan","year":"2010","journal-title":"Cell Host Microbe"},{"key":"ref51","doi-asserted-by":"publisher","first-page":"109332","DOI":"10.1016\/j.celrep.2021.109332","article-title":"Gut microbiota-derived short-chain fatty acids regulate IL-17 production by mouse and human intestinal \u03b3\u03b4 T cells","volume":"36","author":"Dupraz","year":"2021","journal-title":"Cell Rep."},{"key":"ref52","doi-asserted-by":"publisher","first-page":"1971","DOI":"10.1002\/art.40657","article-title":"Microbiota-dependent involvement of Th17 cells in murine models of inflammatory arthritis","volume":"70","author":"Evans-Marin","year":"2018","journal-title":"Arthritis Rheumatol."},{"key":"ref53","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1016\/j.immuni.2013.01.009","article-title":"Luminal bacteria recruit CD103+ dendritic cells into the intestinal epithelium to sample bacterial antigens for presentation","volume":"38","author":"Farache","year":"2013","journal-title":"Immunity"},{"key":"ref54","doi-asserted-by":"publisher","first-page":"104","DOI":"10.1016\/j.jim.2015.03.020","article-title":"Induction of Th17 cells by segmented filamentous bacteria in the murine intestine","volume":"421","author":"Farkas","year":"2015","journal-title":"J. Immunol. Methods"},{"key":"ref55","doi-asserted-by":"publisher","first-page":"302","DOI":"10.2174\/1573399810666141030125830","article-title":"Glucagon-like peptide 1 and the cardiovascular system","volume":"10","author":"Fava","year":"2014","journal-title":"Curr. Diabetes Rev."},{"key":"ref56","doi-asserted-by":"publisher","first-page":"561","DOI":"10.1164\/rccm.200606-821OC","article-title":"Oral treatment with live Lactobacillus reuteri inhibits the allergic airway response in mice","volume":"175","author":"Forsythe","year":"2007","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"ref57","doi-asserted-by":"publisher","first-page":"677","DOI":"10.1016\/j.immuni.2009.08.020","article-title":"The key role of segmented filamentous bacteria in the coordinated maturation of gut helper T cell responses","volume":"31","author":"Gaboriau-Routhiau","year":"2009","journal-title":"Immunity"},{"key":"ref58","doi-asserted-by":"publisher","first-page":"102590","DOI":"10.1016\/j.ebiom.2019.11.051","article-title":"Role of gut microbiota in type 2 diabetes pathophysiology","volume":"51","author":"Gurung","year":"2020","journal-title":"EBioMedicine"},{"key":"ref59","doi-asserted-by":"publisher","first-page":"5477","DOI":"10.4049\/jimmunol.0804267","article-title":"CD4+ T cells and Lactobacillus casei control relapsing colitis mediated by CD8+ T cells","volume":"183","author":"Hacini-Rachinel","year":"2009","journal-title":"J. Immunol."},{"key":"ref60","doi-asserted-by":"publisher","first-page":"17004","DOI":"10.1038\/nmicrobiol.2017.4","article-title":"Dynamics of the human gut microbiome in inflammatory bowel disease","volume":"2","author":"Halfvarson","year":"2017","journal-title":"Nat. Microbiol."},{"key":"ref61","doi-asserted-by":"publisher","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":"ref62","doi-asserted-by":"publisher","first-page":"982349","DOI":"10.3389\/fvets.2022.982349","article-title":"Lactobacillus delbrueckii might lower serum triglyceride levels via colonic microbiota modulation and SCFA-mediated fat metabolism in parenteral tissues of growing-finishing pigs","volume":"9","author":"Hou","year":"2022","journal-title":"Front. Vet. Sci."},{"key":"ref63","doi-asserted-by":"publisher","first-page":"1070","DOI":"10.1038\/s41591-018-0061-3","article-title":"Molecular phenomics and metagenomics of hepatic steatosis in non-diabetic obese women","volume":"24","author":"Hoyles","year":"2018","journal-title":"Nat. Med."},{"key":"ref64","doi-asserted-by":"publisher","first-page":"226","DOI":"10.1016\/j.intimp.2019.01.018","article-title":"Butyrate inhibit collagen-induced arthritis via Treg\/IL-10\/Th17 axis","volume":"68","author":"Hui","year":"2019","journal-title":"Int. Immunopharmacol."},{"key":"ref65","doi-asserted-by":"publisher","first-page":"8210","DOI":"10.1038\/s41598-018-26509-y","article-title":"Combining amplicon sequencing and metabolomics in cirrhotic patients highlights distinctive microbiota features involved in bacterial translocation, systemic inflammation and hepatic encephalopathy","volume":"8","author":"Iebba","year":"2018","journal-title":"Sci. Rep."},{"key":"ref66","doi-asserted-by":"publisher","first-page":"485","DOI":"10.1016\/j.cell.2009.09.033","article-title":"Induction of intestinal Th17 cells by segmented filamentous bacteria","volume":"139","author":"Ivanov","year":"2009","journal-title":"Cell"},{"key":"ref67","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1016\/j.chom.2008.09.009","article-title":"Specific microbiota direct the differentiation of IL-17-producing T-helper cells in the mucosa of the small intestine","volume":"4","author":"Ivanov","year":"2008","journal-title":"Cell Host Microbe"},{"key":"ref68","doi-asserted-by":"publisher","first-page":"2655","DOI":"10.1038\/s41467-018-05184-7","article-title":"Gut microbiota associations with common diseases and prescription medications in a population-based cohort","volume":"9","author":"Jackson","year":"2018","journal-title":"Nat. Commun."},{"key":"ref69","doi-asserted-by":"publisher","first-page":"12015","DOI":"10.1038\/ncomms12015","article-title":"Alterations of the human gut microbiome in multiple sclerosis","volume":"7","author":"Jangi","year":"2016","journal-title":"Nat. Commun."},{"key":"ref70","doi-asserted-by":"publisher","first-page":"1001778","DOI":"10.3389\/fmicb.2022.1001778","article-title":"Yinchen Linggui Zhugan decoction ameliorates high fat diet-induced nonalcoholic fatty liver disease by modulation of SIRT1\/Nrf2 signaling pathway and gut microbiota","volume":"13","author":"Jiang","year":"2022","journal-title":"Front. Microbiol."},{"key":"ref71","doi-asserted-by":"publisher","first-page":"282","DOI":"10.3389\/fimmu.2020.00282","article-title":"Crosstalk between gut microbiota and innate immunity and its implication in autoimmune diseases","volume":"11","author":"Jiao","year":"2020","journal-title":"Front. Immunol."},{"key":"ref72","doi-asserted-by":"publisher","first-page":"1220","DOI":"10.1002\/art.40490","article-title":"Modulation of inflammatory arthritis in mice by gut microbiota through mucosal inflammation and autoantibody generation","volume":"70","author":"Jubair","year":"2018","journal-title":"Arthritis Rheumatol."},{"key":"ref73","doi-asserted-by":"publisher","first-page":"186","DOI":"10.1164\/rccm.200806-951OC","article-title":"Lactobacillus reuteri-induced regulatory T cells protect against an allergic airway response in mice","volume":"179","author":"Karimi","year":"2009","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"ref74","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1016\/j.cotox.2017.10.012","article-title":"Environmental agents, oxidative stress and autoimmunity","volume":"7","author":"Khan","year":"2018","journal-title":"Curr Opin Toxicol"},{"key":"ref75","doi-asserted-by":"publisher","first-page":"1525","DOI":"10.3389\/fimmu.2018.01525","article-title":"Attenuation of rheumatoid inflammation by sodium butyrate through reciprocal targeting of HDAC2 in osteoclasts and HDAC8 in T cells","volume":"9","author":"Kim","year":"2018","journal-title":"Front. Immunol."},{"key":"ref76","doi-asserted-by":"publisher","first-page":"520","DOI":"10.1038\/nature03407","article-title":"Recognition of bacterial glycosphingolipids by natural killer T cells","volume":"434","author":"Kinjo","year":"2005","journal-title":"Nature"},{"key":"ref77","doi-asserted-by":"publisher","first-page":"32","DOI":"10.1186\/s13075-023-03013-x","article-title":"Factors associated with the composition of the gut microbiome in patients with established rheumatoid arthritis and its value for predicting treatment responses","volume":"25","author":"Koh","year":"2023","journal-title":"Arthritis Res. Ther."},{"key":"ref78","doi-asserted-by":"publisher","first-page":"260","DOI":"10.1016\/j.chom.2015.01.001","article-title":"The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes","volume":"17","author":"Kostic","year":"2015","journal-title":"Cell Host Microbe"},{"key":"ref79","doi-asserted-by":"publisher","first-page":"e9085","DOI":"10.1371\/journal.pone.0009085","article-title":"Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults","volume":"5","author":"Larsen","year":"2010","journal-title":"PLoS One"},{"key":"ref80","doi-asserted-by":"publisher","first-page":"e340","DOI":"10.1038\/emm.2017.36","article-title":"Microbiota in T-cell homeostasis and inflammatory diseases","volume":"49","author":"Lee","year":"2017","journal-title":"Exp. Mol. Med."},{"key":"ref81","doi-asserted-by":"publisher","first-page":"1191","DOI":"10.1016\/j.cell.2024.01.029","article-title":"High fat intake sustains sorbitol intolerance after antibiotic-mediated Clostridia depletion from the gut microbiota","volume":"187","author":"Lee","year":"2024","journal-title":"Cell"},{"key":"ref82","doi-asserted-by":"publisher","first-page":"227","DOI":"10.1053\/j.gastro.2011.04.011","article-title":"Twin study indicates loss of interaction between microbiota and mucosa of patients with ulcerative colitis","volume":"141","author":"Lepage","year":"2011","journal-title":"Gastroenterology"},{"key":"ref83","doi-asserted-by":"publisher","first-page":"5450","DOI":"10.1038\/s41598-020-62224-3","article-title":"Implication of the gut microbiome composition of type 2 diabetic patients from northern China","volume":"10","author":"Li","year":"2020","journal-title":"Sci. Rep."},{"key":"ref84","doi-asserted-by":"publisher","first-page":"959","DOI":"10.3389\/fphar.2017.00959","article-title":"Traditional herbal medicine-derived sulforaphene LFS-01 reverses colitis in mice by selectively altering the gut microbiota and promoting intestinal gamma-delta T cells","volume":"8","author":"Li","year":"2018","journal-title":"Front. Pharmacol."},{"key":"ref85","doi-asserted-by":"publisher","first-page":"13839","DOI":"10.1038\/ncomms13839","article-title":"The microbiota maintain homeostasis of liver-resident \u03b3\u03b4T-17 cells in a lipid antigen\/CD1d-dependent manner","volume":"8","author":"Li","year":"","journal-title":"Nat. Commun."},{"key":"ref86","doi-asserted-by":"publisher","first-page":"111308","DOI":"10.1016\/j.celrep.2022.111308","article-title":"Enterobacter ludwigii protects DSS-induced colitis through choline-mediated immune tolerance","volume":"40","author":"Li","year":"","journal-title":"Cell Rep."},{"key":"ref87","doi-asserted-by":"publisher","first-page":"821","DOI":"10.1042\/CS20180841","article-title":"Disordered intestinal microbes are associated with the activity of systemic lupus erythematosus","volume":"133","author":"Li","year":"2019","journal-title":"Clin. Sci."},{"key":"ref88","doi-asserted-by":"publisher","first-page":"824","DOI":"10.3389\/fimmu.2017.00824","article-title":"Upregulation of intestinal barrier function in mice with DSS-induced colitis by a defined bacterial consortium is associated with expansion of IL-17A producing gamma delta T cells","volume":"8","author":"Li","year":"","journal-title":"Front. Immunol."},{"key":"ref89","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2022.844335","article-title":"Effects of gut microbiota on host adaptive immunity under immune homeostasis and tumor pathology state","volume":"13","author":"Li","year":"","journal-title":"Front. Immunol."},{"key":"ref90","doi-asserted-by":"publisher","first-page":"1537","DOI":"10.3390\/nu10101537","article-title":"Probiotics in autoimmune and inflammatory disorders","volume":"10","author":"Liu","year":"2018","journal-title":"Nutrients"},{"key":"ref91","doi-asserted-by":"publisher","first-page":"331","DOI":"10.1007\/s13238-020-00745-3","article-title":"The microbiome in inflammatory bowel diseases: from pathogenesis to therapy","volume":"12","author":"Liu","year":"2021","journal-title":"Protein Cell"},{"key":"ref92","doi-asserted-by":"publisher","first-page":"170","DOI":"10.1007\/s00284-013-0338-1","article-title":"Analysis of fecal Lactobacillus community structure in patients with early rheumatoid arthritis","volume":"67","author":"Liu","year":"2013","journal-title":"Curr. Microbiol."},{"key":"ref93","doi-asserted-by":"publisher","first-page":"655","DOI":"10.1038\/s41586-019-1237-9","article-title":"Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases","volume":"569","author":"Lloyd-Price","year":"2019","journal-title":"Nature"},{"key":"ref94","doi-asserted-by":"publisher","first-page":"523","DOI":"10.1016\/j.jaci.2012.05.049","article-title":"Prenatal and early-life exposures alter expression of innate immunity genes: the PASTURE cohort study","volume":"130","author":"Loss","year":"2012","journal-title":"J. Allergy Clin. Immunol."},{"key":"ref95","doi-asserted-by":"publisher","first-page":"760","DOI":"10.1038\/s41467-019-08711-2","article-title":"The short-chain fatty acid pentanoate suppresses autoimmunity by modulating the metabolic-epigenetic crosstalk in lymphocytes","volume":"10","author":"Luu","year":"2019","journal-title":"Nat. Commun."},{"key":"ref96","doi-asserted-by":"publisher","first-page":"4077","DOI":"10.1038\/s41467-021-24331-1","article-title":"Microbial short-chain fatty acids modulate CD8(+) T cell responses and improve adoptive immunotherapy for cancer","volume":"12","author":"Luu","year":"2021","journal-title":"Nat. Commun."},{"key":"ref97","doi-asserted-by":"publisher","first-page":"14430","DOI":"10.1038\/s41598-018-32860-x","article-title":"Regulation of the effector function of CD8+ T cells by gut microbiota-derived metabolite butyrate","volume":"8","author":"Luu","year":"2018","journal-title":"Sci. Rep."},{"key":"ref98","doi-asserted-by":"publisher","DOI":"10.1126\/science.aan5931","article-title":"Gut microbiome-mediated bile acid metabolism regulates liver cancer via NKT cells","volume":"360","author":"Ma","year":"2018","journal-title":"Science"},{"key":"ref99","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1186\/s10020-019-0102-5","article-title":"Gut microbiota promote the inflammatory response in the pathogenesis of systemic lupus erythematosus","volume":"25","author":"Ma","year":"2019","journal-title":"Mol. Med."},{"key":"ref100","doi-asserted-by":"publisher","first-page":"2646","DOI":"10.1002\/art.39783","article-title":"Dysbiosis contributes to arthritis development via activation of autoreactive T cells in the intestine","volume":"68","author":"Maeda","year":"2016","journal-title":"Arthritis Rheumatol."},{"key":"ref101","doi-asserted-by":"publisher","first-page":"700","DOI":"10.1002\/dmrr.2790","article-title":"Association between intestinal permeability and faecal microbiota composition in Italian children with beta cell autoimmunity at risk for type 1 diabetes","volume":"32","author":"Maffeis","year":"2016","journal-title":"Diab. Metabol. Res Rev"},{"key":"ref102","doi-asserted-by":"publisher","first-page":"237","DOI":"10.1186\/s13075-017-1446-2","article-title":"Severe intestinal dysbiosis is prevalent in primary Sj\u00f6gren's syndrome and is associated with systemic disease activity","volume":"19","author":"Mandl","year":"2017","journal-title":"Arthritis Res. Ther."},{"key":"ref103","doi-asserted-by":"publisher","first-page":"1156","DOI":"10.1126\/science.aar7201","article-title":"Translocation of a gut pathobiont drives autoimmunity in mice and humans","volume":"359","author":"Manfredo Vieira","year":"2018","journal-title":"Science"},{"key":"ref104","doi-asserted-by":"publisher","first-page":"546","DOI":"10.1021\/pr060470d","article-title":"Rapid and noninvasive metabonomic characterization of inflammatory bowel disease","volume":"6","author":"Marchesi","year":"2007","journal-title":"J. Proteome Res."},{"key":"ref105","doi-asserted-by":"publisher","first-page":"552","DOI":"10.1038\/ni.3713","article-title":"Gut microbial metabolites limit the frequency of autoimmune T cells and protect against type 1 diabetes","volume":"18","author":"Mari\u00f1o","year":"2017","journal-title":"Nat. Immunol."},{"key":"ref106","doi-asserted-by":"publisher","first-page":"1282","DOI":"10.1038\/nature08530","article-title":"Regulation of inflammatory responses by gut microbiota and chemoattractant receptor GPR43","volume":"461","author":"Maslowski","year":"2009","journal-title":"Nature"},{"key":"ref107","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1007\/s00281-014-0454-4","article-title":"The gut microbiota and inflammatory bowel disease","volume":"37","author":"Matsuoka","year":"2015","journal-title":"Semin. Immunopathol."},{"key":"ref108","doi-asserted-by":"publisher","first-page":"320","DOI":"10.1016\/j.intimp.2016.08.001","article-title":"Augmentation of T helper type 1 immune response through intestinal immunity in murine cutaneous herpes simplex virus type 1 infection by probiotic Lactobacillus plantarum strain 06CC2","volume":"39","author":"Matsusaki","year":"2016","journal-title":"Int. Immunopharmacol."},{"key":"ref109","doi-asserted-by":"publisher","first-page":"525","DOI":"10.1038\/nature03408","article-title":"Exogenous and endogenous glycolipid antigens activate NKT cells during microbial infections","volume":"434","author":"Mattner","year":"2005","journal-title":"Nature"},{"key":"ref110","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1016\/j.cell.2005.05.007","article-title":"An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system","volume":"122","author":"Mazmanian","year":"2005","journal-title":"Cell"},{"key":"ref111","doi-asserted-by":"publisher","first-page":"473","DOI":"10.1016\/j.ebiom.2019.07.048","article-title":"Soluble fibre supplementation with and without a probiotic in adults with asthma: a 7-day randomised, double blind, three way cross-over trial","volume":"46","author":"Mcloughlin","year":"2019","journal-title":"EBioMedicine"},{"key":"ref112","doi-asserted-by":"publisher","first-page":"3814","DOI":"10.1038\/srep03814","article-title":"Fecal microbiota imbalance in Mexican children with type 1 diabetes","volume":"4","author":"Mej\u00eda-Le\u00f3n","year":"2014","journal-title":"Sci. Rep."},{"key":"ref113","doi-asserted-by":"publisher","first-page":"1632","DOI":"10.1080\/19490976.2020.1778261","article-title":"Serum metabolites reflecting gut microbiome alpha diversity predict type 2 diabetes","volume":"11","author":"Menni","year":"2020","journal-title":"Gut Microbes"},{"key":"ref114","doi-asserted-by":"publisher","first-page":"336","DOI":"10.1039\/c7np00056a","article-title":"Role of antimicrobial peptides in controlling symbiotic bacterial populations","volume":"35","author":"Mergaert","year":"2018","journal-title":"Nat. Prod. Rep."},{"key":"ref115","doi-asserted-by":"publisher","first-page":"3522","DOI":"10.1002\/art.34595","article-title":"Porphyromonas gingivalis and disease-related autoantibodies in individuals at increased risk of rheumatoid arthritis","volume":"64","author":"Mikuls","year":"2012","journal-title":"Arthritis Rheum."},{"key":"ref116","doi-asserted-by":"publisher","first-page":"255","DOI":"10.1016\/j.mib.2013.06.003","article-title":"Faecalibacterium prausnitzii and human intestinal health","volume":"16","author":"Miquel","year":"2013","journal-title":"Curr. Opin. Microbiol."},{"key":"ref117","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1186\/s13052-017-0340-5","article-title":"Bifidobacterium mixture (B. longum BB536, B. infantis M-63, B. breve M-16V) treatment in children with seasonal allergic rhinitis and intermittent asthma","volume":"43","author":"Miraglia Del Giudice","year":"2017","journal-title":"Ital. J. Pediatr."},{"key":"ref118","first-page":"656","article-title":"Synovial inflammation in active rheumatoid arthritis and psoriatic arthritis facilitates trapping of a variety of oral bacterial DNAs","volume":"24","author":"Moen","year":"2006","journal-title":"Clin. Exp. Rheumatol."},{"key":"ref119","doi-asserted-by":"publisher","first-page":"791","DOI":"10.1111\/jgh.16147","article-title":"A metagenomic study identifies a Prevotella copri enriched microbial profile associated with non-alcoholic steatohepatitis in subjects with obesity","volume":"38","author":"Moran-Ramos","year":"2023","journal-title":"J. Gastroenterol. Hepatol."},{"key":"ref120","doi-asserted-by":"publisher","first-page":"405","DOI":"10.1038\/s41577-018-0002-x","article-title":"To respond or not to respond - a personal perspective of intestinal tolerance","volume":"18","author":"Mowat","year":"2018","journal-title":"Nat. Rev. Immunol."},{"key":"ref121","doi-asserted-by":"crossref","DOI":"10.2741\/e777","article-title":"Genes associated with T helper 17 cell differentiation and function","volume-title":"Frontiers in Bioscience","author":"Nalbant","year":"2016"},{"key":"ref122","doi-asserted-by":"publisher","first-page":"655","DOI":"10.1016\/j.cell.2017.09.022","article-title":"A gut microbial mimic that hijacks diabetogenic autoreactivity to suppress colitis","volume":"171","author":"Nanjundappa","year":"2017","journal-title":"Cell"},{"key":"ref123","doi-asserted-by":"publisher","first-page":"14516","DOI":"10.1038\/s41598-017-15099-w","article-title":"Butyrate and propionate inhibit antigen-specific CD8(+) T cell activation by suppressing IL-12 production by antigen-presenting cells","volume":"7","author":"Nastasi","year":"2017","journal-title":"Sci. Rep."},{"key":"ref124","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1007\/s11892-016-0781-z","article-title":"The role of the intestinal microbiome in type 1 diabetes pathogenesis","volume":"16","author":"Needell","year":"2016","journal-title":"Curr. Diab. Rep."},{"key":"ref9001","first-page":"65","article-title":"Microbes in gastrointestinal health and disease","author":"Neish","year":"2009"},{"key":"ref125","doi-asserted-by":"publisher","first-page":"763","DOI":"10.14218\/JCTH.2022.00415","article-title":"Akkermansia muciniphila and Bifidobacterium bifidum prevent NAFLD by regulating FXR expression and gut microbiota","volume":"11","author":"Nian","year":"2023","journal-title":"J. Clin. Transl. Hepatol."},{"key":"ref126","doi-asserted-by":"publisher","first-page":"642","DOI":"10.1038\/s41467-023-36323-4","article-title":"Microbiota-derived acetate enhances host antiviral response via NLRP3","volume":"14","author":"Niu","year":"2023","journal-title":"Nat. Commun."},{"key":"ref127","doi-asserted-by":"publisher","first-page":"489","DOI":"10.1126\/science.1219328","article-title":"Microbial exposure during early life has persistent effects on natural killer T cell function","volume":"336","author":"Olszak","year":"2012","journal-title":"Science"},{"key":"ref128","doi-asserted-by":"publisher","first-page":"15","DOI":"10.5217\/ir.2023.00080","article-title":"Gut microbiota in pathophysiology, diagnosis, and therapeutics of inflammatory bowel disease","volume":"22","author":"Pandey","year":"2024","journal-title":"Intest Res"},{"key":"ref129","doi-asserted-by":"publisher","first-page":"426","DOI":"10.3390\/ijms23010426","article-title":"Role of microbiota-derived metabolites in alcoholic and non-alcoholic fatty liver diseases","volume":"23","author":"Park","year":"2022","journal-title":"Int. J. Mol. Sci."},{"key":"ref130","doi-asserted-by":"publisher","first-page":"e10220","DOI":"10.7717\/peerj.10220","article-title":"Acetate correlates with disability and immune response in multiple sclerosis","volume":"8","author":"P\u00e9rez-P\u00e9rez","year":"2020","journal-title":"PeerJ"},{"key":"ref131","doi-asserted-by":"publisher","first-page":"3147","DOI":"10.2174\/0929867328666210922161913","article-title":"Gut microbiota and autoimmune diseases: a charming real world together with probiotics","volume":"29","author":"Piccioni","year":"2022","journal-title":"Curr. Med. Chem."},{"key":"ref132","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1002\/hep.30036","article-title":"Hepatocellular carcinoma is associated with gut microbiota profile and inflammation in nonalcoholic fatty liver disease","volume":"69","author":"Ponziani","year":"2019","journal-title":"Hepatology"},{"key":"ref133","doi-asserted-by":"publisher","first-page":"162021","DOI":"10.1155\/2014\/162021","article-title":"Evidence for the gut microbiota short-chain fatty acids as key pathophysiological molecules improving diabetes","volume":"2014","author":"Puddu","year":"2014","journal-title":"Mediat. Inflamm."},{"key":"ref134","doi-asserted-by":"publisher","first-page":"1353881","DOI":"10.1080\/16512235.2017.1353881","article-title":"A wide diversity of bacteria from the human gut produces and degrades biogenic amines","volume":"28","author":"Pugin","year":"2017","journal-title":"Microb. Ecol. Health Dis."},{"key":"ref135","first-page":"108764","article-title":"Collinsella aerofaciens linked with increased ethanol production and liver inflammation contribute to the pathophysiology of NAFLD","volume-title":"Science","author":"Purohit","year":"2024"},{"key":"ref136","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1038\/nature11450","article-title":"A metagenome-wide association study of gut microbiota in type 2 diabetes","volume":"490","author":"Qin","year":"2012","journal-title":"Nature"},{"key":"ref137","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1038\/nature08821","article-title":"A human gut microbial gene catalogue established by metagenomic sequencing","volume":"464","author":"Qin","year":"2010","journal-title":"Nature"},{"key":"ref138","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1080\/09540105.2019.1579785","article-title":"Two strains of probiotic Lactobacillus enhance immune response and promote naive T cell polarization to Th1","volume":"30","author":"Ren","year":"2019","journal-title":"Food Agric. Immunol."},{"key":"ref139","doi-asserted-by":"publisher","first-page":"221","DOI":"10.1038\/s41577-020-00452-4","article-title":"\u03b3\u03b4 T cells in tissue physiology and surveillance","volume":"21","author":"Ribot","year":"2021","journal-title":"Nat. Rev. Immunol."},{"key":"ref140","doi-asserted-by":"publisher","first-page":"179","DOI":"10.1016\/j.jaci.2010.10.010","article-title":"Prenatal animal contact and gene expression of innate immunity receptors at birth are associated with atopic dermatitis","volume":"127","author":"Roduit","year":"2011","journal-title":"J. Allergy Clin. Immunol."},{"key":"ref141","doi-asserted-by":"publisher","first-page":"1526","DOI":"10.1002\/ibd.20961","article-title":"Prevention of TNBS-induced colitis by different Lactobacillus and Bifidobacterium strains is associated with an expansion of \u03b3\u03b4T and regulatory T cells of intestinal intraepithelial lymphocytes","volume":"15","author":"Roselli","year":"2009","journal-title":"Inflamm. Bowel Dis."},{"key":"ref142","doi-asserted-by":"publisher","first-page":"12204","DOI":"10.1073\/pnas.0909122107","article-title":"Inducible Foxp3+ regulatory T-cell development by a commensal bacterium of the intestinal microbiota","volume":"107","author":"Round","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref143","doi-asserted-by":"publisher","first-page":"440","DOI":"10.1038\/embor.2012.32","article-title":"Early life antibiotic-driven changes in microbiota enhance susceptibility to allergic asthma","volume":"13","author":"Russell","year":"2012","journal-title":"EMBO Rep."},{"key":"ref144","doi-asserted-by":"publisher","first-page":"108983","DOI":"10.1016\/j.intimp.2022.108983","article-title":"The emerging role of microbiota-derived short-chain fatty acids in immunometabolism","volume":"110","author":"Saade","year":"2022","journal-title":"Int. Immunopharmacol."},{"key":"ref145","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1007\/s40588-023-00213-6","article-title":"Gut microbiota and autoimmune diseases: mechanisms, treatment, challenges, and future recommendations","volume":"11","author":"Sadeghpour Heravi","year":"2024","journal-title":"Curr. Clin. Microbiol. Rep."},{"key":"ref146","doi-asserted-by":"publisher","first-page":"634","DOI":"10.1038\/s41423-019-0220-6","article-title":"Helper T cell differentiation","volume":"16","author":"Saravia","year":"2019","journal-title":"Cell. Mol. Immunol."},{"key":"ref147","doi-asserted-by":"publisher","first-page":"e01202","DOI":"10.7554\/eLife.01202","article-title":"Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis","volume":"2","author":"Scher","year":"2013","journal-title":"eLife"},{"key":"ref148","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1038\/nature14027","article-title":"Growth and host interaction of mouse segmented filamentous bacteria in vitro","volume":"520","author":"Schnupf","year":"2015","journal-title":"Nature"},{"key":"ref149","doi-asserted-by":"publisher","first-page":"612","DOI":"10.1248\/bpb.35.612","article-title":"Lactobacillus acidophilus strain L-92 induces CD4(+)CD25(+)Foxp3(+) regulatory T cells and suppresses allergic contact dermatitis","volume":"35","author":"Shah","year":"2012","journal-title":"Biol. Pharm. Bull."},{"key":"ref150","doi-asserted-by":"publisher","first-page":"1922","DOI":"10.1038\/s41467-020-15857-x","article-title":"CD8+ regulatory T cells are critical in prevention of autoimmune-mediated diabetes","volume":"11","author":"Shimokawa","year":"2020","journal-title":"Nat. Commun."},{"key":"ref151","doi-asserted-by":"publisher","first-page":"25","DOI":"10.3389\/fendo.2020.00025","article-title":"The role of short-chain fatty acids from gut microbiota in gut-brain communication","volume":"11","author":"Silva","year":"2020","journal-title":"Front. Endocrinol."},{"key":"ref152","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1111\/j.1365-2249.2012.04625.x","article-title":"Therapeutic manipulation of natural killer (NK) T cells in autoimmunity: are we close to reality?","volume":"171","author":"Simoni","year":"2013","journal-title":"Clin. Exper. Immunol."},{"key":"ref153","doi-asserted-by":"publisher","first-page":"1260","DOI":"10.1016\/j.jaci.2005.03.036","article-title":"Selective probiotic bacteria induce IL-10-producing regulatory T cells in vitro by modulating dendritic cell function through dendritic cell-specific intercellular adhesion molecule 3-grabbing nonintegrin","volume":"115","author":"Smits","year":"2005","journal-title":"J. Allergy Clin. Immunol."},{"key":"ref154","doi-asserted-by":"publisher","first-page":"2690","DOI":"10.1016\/j.molimm.2007.12.010","article-title":"Lactobacillus casei suppresses experimental arthritis by down-regulating T helper 1 effector functions","volume":"45","author":"So","year":"2008","journal-title":"Mol. Immunol."},{"key":"ref155","doi-asserted-by":"publisher","first-page":"1774","DOI":"10.1038\/s41564-019-0599-y","article-title":"Homing in on 12,13-diHOME in asthma","volume":"4","author":"Stewart","year":"2019","journal-title":"Nat. Microbiol."},{"key":"ref156","doi-asserted-by":"publisher","first-page":"583","DOI":"10.1038\/s41586-018-0617-x","article-title":"Temporal development of the gut microbiome in early childhood from the TEDDY study","volume":"562","author":"Stewart","year":"2018","journal-title":"Nature"},{"key":"ref157","doi-asserted-by":"publisher","first-page":"143","DOI":"10.2147\/ITT.S61528","article-title":"The hygiene hypothesis: current perspectives and future therapies","volume":"4","author":"Stiemsma","year":"2015","journal-title":"Immunotargets Ther."},{"key":"ref158","doi-asserted-by":"publisher","first-page":"27509","DOI":"10.1073\/pnas.1921223117","article-title":"Bifidobacterium alters the gut microbiota and modulates the functional metabolism of T regulatory cells in the context of immune checkpoint blockade","volume":"117","author":"Sun","year":"2020","journal-title":"Proc. Natl. Acad. Sci."},{"key":"ref159","doi-asserted-by":"publisher","first-page":"2129","DOI":"10.1084\/jem.20160526","article-title":"Microbial antigen mimics activate diabetogenic CD8 T cells in NOD mice","volume":"213","author":"Tai","year":"2016","journal-title":"J. Exp. Med."},{"key":"ref160","doi-asserted-by":"publisher","first-page":"102913","DOI":"10.1016\/j.ebiom.2020.102913","article-title":"Microbiota-derived butyrate limits the autoimmune response by promoting the differentiation of follicular regulatory T cells","volume":"58","author":"Takahashi","year":"2020","journal-title":"EBioMedicine"},{"key":"ref161","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1159\/000441768","article-title":"Reduced abundance of butyrate-producing Bacteria species in the fecal microbial Community in Crohn's disease","volume":"93","author":"Takahashi","year":"2016","journal-title":"Digestion"},{"key":"ref162","doi-asserted-by":"publisher","first-page":"1976","DOI":"10.1016\/j.intimp.2011.08.007","article-title":"Efficacy of oral administration of heat-killed probiotics from Mongolian dairy products against influenza infection in mice: alleviation of influenza infection by its immunomodulatory activity through intestinal immunity","volume":"11","author":"Takeda","year":"2011","journal-title":"Int. Immunopharmacol."},{"key":"ref163","doi-asserted-by":"publisher","first-page":"157","DOI":"10.2217\/fmb-2016-0130","article-title":"Roseburia spp.: a marker of health?","volume":"12","author":"Tamanai-Shacoori","year":"2017","journal-title":"Future Microbiol."},{"key":"ref164","doi-asserted-by":"publisher","first-page":"E8141","DOI":"10.1073\/pnas.1617460113","article-title":"Identifying species of symbiont bacteria from the human gut that, alone, can induce intestinal Th17 cells in mice","volume":"113","author":"Tan","year":"2016","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref165","doi-asserted-by":"publisher","first-page":"2300016","DOI":"10.1002\/elsc.202300016","article-title":"Gut microbiota induced epigenetic modifications in the non-alcoholic fatty liver disease pathogenesis","volume":"24","author":"Tang","year":"2024","journal-title":"Eng. Life Sci."},{"key":"ref166","doi-asserted-by":"publisher","first-page":"600","DOI":"10.1038\/s41586-019-0878-z","article-title":"A defined commensal consortium elicits CD8 T cells and anti-cancer immunity","volume":"565","author":"Tanoue","year":"2019","journal-title":"Nature"},{"key":"ref167","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1080\/19490976.2021.1880221","article-title":"Elevated gut microbiome abundance of Christensenellaceae, Porphyromonadaceae and Rikenellaceae is associated with reduced visceral adipose tissue and healthier metabolic profile in Italian elderly","volume":"13","author":"Tavella","year":"2021","journal-title":"Gut Microbes"},{"key":"ref168","doi-asserted-by":"publisher","first-page":"1356540","DOI":"10.1155\/2019\/1356540","article-title":"Intracellular pathogens: host immunity and microbial persistence strategies","volume":"2019","author":"Thakur","year":"2019","journal-title":"J Immunol Res"},{"key":"ref169","doi-asserted-by":"publisher","first-page":"667","DOI":"10.1038\/s41591-019-0405-7","article-title":"Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation","volume":"25","author":"Thomas","year":"2019","journal-title":"Nat. Med."},{"key":"ref170","doi-asserted-by":"publisher","first-page":"4611","DOI":"10.4049\/jimmunol.1101299","article-title":"Components of Streptococcus pneumoniae suppress allergic airways disease and NKT cells by inducing regulatory T cells","volume":"188","author":"Thorburn","year":"2012","journal-title":"J. Immunol."},{"key":"ref171","doi-asserted-by":"publisher","first-page":"1823","DOI":"10.1042\/bcj20160510","article-title":"Introduction to the human gut microbiota","volume":"474","author":"Thursby","year":"2017","journal-title":"Biochem. J."},{"key":"ref172","doi-asserted-by":"publisher","first-page":"2555","DOI":"10.2337\/db08-0331","article-title":"The \"perfect storm\" for type 1 diabetes: the complex interplay between intestinal microbiota, gut permeability, and mucosal immunity","volume":"57","author":"Vaarala","year":"2008","journal-title":"Diabetes"},{"key":"ref173","doi-asserted-by":"publisher","first-page":"k2179","DOI":"10.1136\/bmj.k2179","article-title":"Role of the gut microbiota in nutrition and health","volume":"361","author":"Valdes","year":"2018","journal-title":"BMJ"},{"key":"ref174","doi-asserted-by":"publisher","first-page":"77","DOI":"10.1016\/j.jaut.2018.10.009","article-title":"Shared gut, but distinct oral microbiota composition in primary Sj\u00f6gren's syndrome and systemic lupus erythematosus","volume":"97","author":"Van Der Meulen","year":"2019","journal-title":"J. Autoimmun."},{"key":"ref175","doi-asserted-by":"publisher","first-page":"350","DOI":"10.1007\/s12016-018-8719-7","article-title":"The human microbiota and asthma","volume":"57","author":"Ver Heul","year":"2019","journal-title":"Clin. Rev. Allergy Immunol."},{"key":"ref176","doi-asserted-by":"publisher","first-page":"824","DOI":"10.1016\/j.jhep.2013.11.034","article-title":"Impact of oral vancomycin on gut microbiota, bile acid metabolism, and insulin sensitivity","volume":"60","author":"Vrieze","year":"2014","journal-title":"J. Hepatol."},{"key":"ref177","doi-asserted-by":"publisher","first-page":"552","DOI":"10.4161\/gmic.29797","article-title":"A commensal bacterial product elicits and modulates migratory capacity of CD39(+) CD4 T regulatory subsets in the suppression of neuroinflammation","volume":"5","author":"Wang","year":"2014","journal-title":"Gut Microbes"},{"key":"ref178","doi-asserted-by":"publisher","first-page":"697","DOI":"10.1111\/cea.14089","article-title":"Microbiota associations with inflammatory pathways in asthma","volume":"52","author":"Wang","year":"","journal-title":"Clin. Exp. Allergy"},{"key":"ref179","doi-asserted-by":"publisher","first-page":"2853","DOI":"10.1084\/jem.20062008","article-title":"A bacterial carbohydrate links innate and adaptive responses through toll-like receptor 2","volume":"203","author":"Wang","year":"2006","journal-title":"J. Exp. Med."},{"key":"ref180","doi-asserted-by":"publisher","first-page":"122274","DOI":"10.1016\/j.lfs.2023.122274","article-title":"EVOO supplement prevents type 1 diabetes by modulating gut microbiota and serum metabolites in NOD mice","volume":"335","author":"Wang","year":"","journal-title":"Life Sci."},{"key":"ref181","doi-asserted-by":"publisher","first-page":"1365554","DOI":"10.3389\/fimmu.2024.1365554","article-title":"Emerging role of gut microbiota in autoimmune diseases","volume":"15","author":"Wang","year":"2024","journal-title":"Front. Immunol."},{"key":"ref182","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2022.799602","article-title":"Characteristics of the gut microbiome and its relationship with peripheral CD4+ T cell subpopulations and cytokines in rheumatoid arthritis","volume":"13","author":"Wang","year":"","journal-title":"Front. Microbiol."},{"key":"ref183","doi-asserted-by":"publisher","first-page":"2285877","DOI":"10.1080\/0886022X.2023.2285877","article-title":"Alterations of the gut microbiota in the lupus nephritis: a systematic review","volume":"45","author":"Wang","year":"","journal-title":"Ren. Fail."},{"key":"ref184","doi-asserted-by":"publisher","first-page":"e418","DOI":"10.1016\/S2665-9913(20)30064-3","article-title":"Associations between gut microbiota and genetic risk for rheumatoid arthritis in the absence of disease: a cross-sectional study","volume":"2","author":"Wells","year":"2020","journal-title":"Lancet Rheumatol."},{"key":"ref185","doi-asserted-by":"publisher","first-page":"142","DOI":"10.1186\/s13059-017-1271-6","article-title":"Quantitative metagenomics reveals unique gut microbiome biomarkers in ankylosing spondylitis","volume":"18","author":"Wen","year":"2017","journal-title":"Genome Biol."},{"key":"ref186","doi-asserted-by":"publisher","first-page":"821","DOI":"10.1097\/MIB.0000000000000019","article-title":"Stat3 activation in murine colitis induced by enterotoxigenic Bacteroides fragilis","volume":"20","author":"Wick","year":"2014","journal-title":"Inflamm. Bowel Dis."},{"key":"ref187","doi-asserted-by":"publisher","first-page":"886","DOI":"10.3390\/nu13030886","article-title":"The interplay between the gut microbiome and the immune system in the context of infectious diseases throughout life and the role of nutrition in optimizing treatment strategies","volume":"13","author":"Wiertsema","year":"2021","journal-title":"Nutrients"},{"key":"ref188","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1155\/2023\/1984200","article-title":"The challenge of applications of probiotics in gastrointestinal diseases","volume":"2023","author":"Wolfe","year":"2023","journal-title":"Adv. Gut Microbiome Res."},{"key":"ref189","doi-asserted-by":"publisher","first-page":"H55","DOI":"10.1111\/j.1750-3841.2010.02031.x","article-title":"Modulation of Th1\/Th2 balance by Lactobacillus strains isolated from kimchi via stimulation of macrophage cell line J774A.1 in vitro","volume":"76","author":"Won","year":"2011","journal-title":"J. Food Sci."},{"key":"ref190","doi-asserted-by":"publisher","first-page":"1162","DOI":"10.1002\/eji.201546160","article-title":"Commensal A4 bacteria inhibit intestinal Th2-cell responses through induction of dendritic cell TGF-\u03b2 production","volume":"46","author":"Wu","year":"2016","journal-title":"Eur. J. Immunol."},{"key":"ref191","doi-asserted-by":"publisher","first-page":"D545","DOI":"10.1093\/nar\/gkz764","article-title":"GMrepo: a database of curated and consistently annotated human gut metagenomes","volume":"48","author":"Wu","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"ref192","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2024.1331486","article-title":"Rheumatoid arthritis and the intestinal microbiome: probiotics as a potential therapy","volume":"15","author":"Yang","year":"2024","journal-title":"Front. Immunol."},{"key":"ref193","doi-asserted-by":"publisher","first-page":"645741","DOI":"10.3389\/fimmu.2021.645741","article-title":"Commensal microbiome expands T\u03b3\u03b417 cells in the lung and promotes particulate matter-induced acute neutrophilia","volume":"12","author":"Yang","year":"2021","journal-title":"Front. Immunol."},{"key":"ref194","doi-asserted-by":"publisher","first-page":"132","DOI":"10.1136\/annrheumdis-2019-215763","article-title":"Shotgun metagenomics reveals an enrichment of potentially cross-reactive bacterial epitopes in ankylosing spondylitis patients, as well as the effects of TNFi therapy upon microbiome composition","volume":"79","author":"Yin","year":"2020","journal-title":"Ann. Rheum. Dis."},{"key":"ref195","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1016\/j.chom.2018.11.009","article-title":"A diet-sensitive commensal Lactobacillus strain mediates TLR7-dependent systemic autoimmunity","volume":"25","author":"Zegarra-Ruiz","year":"2019","journal-title":"Cell Host Microbe"},{"key":"ref196","doi-asserted-by":"publisher","first-page":"161","DOI":"10.1016\/j.immuni.2011.07.010","article-title":"CD8(+) T cells: foot soldiers of the immune system","volume":"35","author":"Zhang","year":"2011","journal-title":"Immunity"},{"key":"ref197","doi-asserted-by":"publisher","first-page":"7551","DOI":"10.1128\/AEM.02676-14","article-title":"Dynamics of gut microbiota in autoimmune lupus","volume":"80","author":"Zhang","year":"2014","journal-title":"Appl. Environ. Microbiol."},{"key":"ref198","doi-asserted-by":"publisher","first-page":"206","DOI":"10.1093\/gastro\/goaa014","article-title":"Influence of microbiota on immunity and immunotherapy for gastric and esophageal cancers","volume":"8","author":"Zhang","year":"2020","journal-title":"Gastroenterol. Rep."},{"key":"ref199","doi-asserted-by":"publisher","first-page":"2813","DOI":"10.1007\/s10238-023-01028-x","article-title":"Autoimmune diseases and gut microbiota: a bibliometric and visual analysis from 2004 to 2022","volume":"23","author":"Zhang","year":"2023","journal-title":"Clin. Exp. Med."},{"key":"ref200","doi-asserted-by":"publisher","first-page":"895","DOI":"10.1038\/nm.3914","article-title":"The oral and gut microbiomes are perturbed in rheumatoid arthritis and partly normalized after treatment","volume":"21","author":"Zhang","year":"2015","journal-title":"Nat. Med."},{"key":"ref201","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2023.1219942","article-title":"The role of gut microbiome in the complex relationship between respiratory tract infection and asthma","volume":"14","author":"Zhao","year":"2023","journal-title":"Front. Microbiol."},{"key":"ref202","doi-asserted-by":"publisher","first-page":"607","DOI":"10.1016\/j.autrev.2018.12.010","article-title":"Emerging role of air pollution in autoimmune diseases","volume":"18","author":"Zhao","year":"2019","journal-title":"Autoimmun. Rev."},{"key":"ref203","doi-asserted-by":"publisher","first-page":"102360","DOI":"10.1016\/j.jaut.2019.102360","article-title":"Metagenomic profiling of the pro-inflammatory gut microbiota in ankylosing spondylitis","volume":"107","author":"Zhou","year":"2020","journal-title":"J. Autoimmun."}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2024.1477187\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,12,19]],"date-time":"2024-12-19T16:46:49Z","timestamp":1734626809000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2024.1477187\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,12,19]]},"references-count":204,"alternative-id":["10.3389\/fmicb.2024.1477187"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2024.1477187","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,12,19]]},"article-number":"1477187"}}