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The development of autoimmune diseases is phenotypically associated with gut microbiota-modulated features at the molecular and cellular levels. The etiology and pathogenesis of autoimmune diseases comprise the alterations of immune systems with the innate and adaptive immune cell infiltration into specific organs and the augmented production of proinflammatory cytokines stimulated by commensal microbiota. However, the relative importance and mechanistic interrelationships between the gut microbial community and the immune system during progression of autoimmune diseases are still not well understood. In this review, we describe studies on the profiling of gut microbial signatures for the modulation of immunological homeostasis in multiple inflammatory diseases, elucidate their critical roles in the etiology and pathogenesis of autoimmune diseases, and discuss the implications of these findings for these disorders. Targeting intestinal microbiome and its metabolomic associations with the phenotype of autoimmunity will enable the progress of developing new therapeutic strategies to counteract microorganism-related immune dysfunction in these autoimmune diseases.<\/jats:p>","DOI":"10.3390\/microorganisms9091930","type":"journal-article","created":{"date-parts":[[2021,9,12]],"date-time":"2021-09-12T21:45:57Z","timestamp":1631483157000},"page":"1930","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":20,"title":["Gut Microbiota-Modulated Metabolomic Profiling Shapes the Etiology and Pathogenesis of Autoimmune Diseases"],"prefix":"10.3390","volume":"9","author":[{"given":"Yi-Wen","family":"Tsai","sequence":"first","affiliation":[{"name":"Department of Family Medicine, Chang Gung Memorial Hospital, Keelung, No.222, Maijin Road, Keelung 204, Taiwan"},{"name":"College of Medicine, Chang-Gung University, No.259, Wenhua 1st Road, Guishan Dist., Taoyuan City 333, Taiwan"},{"name":"Graduate Institute of Medical Sciences, National Defense Medical Center, No.161, Section 6, Min Chuan East Road, Neihu, Taipei 114, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jia-Ling","family":"Dong","sequence":"additional","affiliation":[{"name":"Department and Graduate Institute of Microbiology and Immunology, National Defense Medical Center, No.161, Section 6, Min Chuan East Road, Neihu, Taipei 114, Taiwan"},{"name":"National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, No.35, Keyan Road, Zhunan, Miaoli 350, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yun-Jie","family":"Jian","sequence":"additional","affiliation":[{"name":"Department and Graduate Institute of Microbiology and Immunology, National Defense Medical Center, No.161, Section 6, Min Chuan East Road, Neihu, Taipei 114, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9697-6814","authenticated-orcid":false,"given":"Shin-Huei","family":"Fu","sequence":"additional","affiliation":[{"name":"Department and Graduate Institute of Microbiology and Immunology, National Defense Medical Center, No.161, Section 6, Min Chuan East Road, Neihu, Taipei 114, Taiwan"},{"name":"National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, No.35, Keyan Road, Zhunan, Miaoli 350, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ming-Wei","family":"Chien","sequence":"additional","affiliation":[{"name":"Department and Graduate Institute of Microbiology and Immunology, National Defense Medical Center, No.161, Section 6, Min Chuan East Road, Neihu, Taipei 114, Taiwan"},{"name":"National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, No.35, Keyan Road, Zhunan, Miaoli 350, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu-Wen","family":"Liu","sequence":"additional","affiliation":[{"name":"National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, No.35, Keyan Road, Zhunan, Miaoli 350, Taiwan"},{"name":"Graduate Institute of Life Sciences, National Defense Medical Center, No.161, Section 6, Min Chuan East Road, Neihu, Taipei 114, Taiwan"},{"name":"Molecular Cell Biology, Taiwan International Graduate Program, Academia Sinica, No.128, Academia Road, Section 2, Nankang, Taipei 115, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chao-Yuan","family":"Hsu","sequence":"additional","affiliation":[{"name":"Department and Graduate Institute of Microbiology and Immunology, National Defense Medical Center, No.161, Section 6, Min Chuan East Road, Neihu, Taipei 114, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huey-Kang","family":"Sytwu","sequence":"additional","affiliation":[{"name":"Graduate Institute of Medical Sciences, National Defense Medical Center, No.161, Section 6, Min Chuan East Road, Neihu, Taipei 114, Taiwan"},{"name":"Department and Graduate Institute of Microbiology and Immunology, National Defense Medical Center, No.161, Section 6, Min Chuan East Road, Neihu, Taipei 114, Taiwan"},{"name":"National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, No.35, Keyan Road, Zhunan, Miaoli 350, Taiwan"},{"name":"Graduate Institute of Life Sciences, National Defense Medical Center, No.161, Section 6, Min Chuan East Road, Neihu, Taipei 114, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2021,9,10]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1159\/000329169","article-title":"Pathogenesis of Type 1 Diabetes: Implications for Incidence Trends","volume":"76","author":"Knip","year":"2011","journal-title":"Horm. 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