{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,20]],"date-time":"2026-10-20T13:50:09Z","timestamp":1792504209993,"version":"4.5.0"},"reference-count":43,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,4,7]],"date-time":"2026-04-07T00:00:00Z","timestamp":1775520000000},"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:sec>\n                    <jats:title>Introduction<\/jats:title>\n                    <jats:p>The global incidence of inflammatory bowel disease (IBD) is increasing, with dysbiosis of the gut microbiota identified as a significant factor contributing to chronic intestinal inflammation. This study aims to elucidate the gut microbiota and serum bile acid profiles in patients with ulcerative colitis (UC) and Crohn\u2019s disease (CD), and to explore the relationship between bacterial taxa and bile acids.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>We recruited 31 UC patients, 41 CD patients, and 32 healthy controls from The First Affiliated Hospital of Zhejiang Chinese Medical University. Gut microbiota composition was analyzed by 16S rDNA sequencing of stool samples, and serum bile acid profiles were quantified using LC\u2013MS\/MS. Alpha and beta diversity were assessed, and differential abundance of bacterial genera was evaluated using non-parametric tests with false discovery rate (FDR) correction. Correlations between differentially abundant genera and bile acid levels were examined by Spearman\u2019s rank correlation.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Both UC and CD groups exhibited significant alterations in alpha and beta diversity compared to controls. At the genus level, pro-inflammatory taxa, including\n                      <jats:italic>Escherichia-Shigella<\/jats:italic>\n                      and\n                      <jats:italic>Ruminococcus_gnavus_group,<\/jats:italic>\n                      were enriched, while short-chain fatty acid (SCFA)-producing genera such as\n                      <jats:italic>Coprococcus<\/jats:italic>\n                      were depleted. Notably, SCFA-producing\n                      <jats:italic>Romboutsia<\/jats:italic>\n                      and\n                      <jats:italic>Butyricicoccus<\/jats:italic>\n                      were exclusively depleted in CD. A consistent depletion of secondary bile acids\u2014lithocholic acid (LCA), glycolithocholic acid (GLCA), deoxycholic acid (DCA), taurodeoxycholic acid (TDCA), and glycodeoxycholic acid (GDCA)\u2014was observed in both patient groups. Correlation analysis revealed positive associations between several\n                      <jats:italic>Lachnospiraceae<\/jats:italic>\n                      genera and DCA\/LCA levels.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Discussion<\/jats:title>\n                    <jats:p>\n                      This study confirms gut microbiota dysbiosis and altered bile acid profiles in UC and CD, with CD displaying a more pronounced disruption of SCFA-producing bacteria. The observed depletion of\n                      <jats:italic>Lachnospiraceae<\/jats:italic>\n                      and secondary bile acids suggests a link between microbial metabolic dysfunction and IBD pathogenesis. Although\n                      <jats:italic>Lachnospiraceae<\/jats:italic>\n                      may represent a candidate for next-generation probiotic development, further mechanistic and clinical studies are required to validate its therapeutic potential.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fmicb.2026.1782415","type":"journal-article","created":{"date-parts":[[2026,4,7]],"date-time":"2026-04-07T05:34:10Z","timestamp":1775540050000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":3,"title":["Gut microbiota and bile acids profiles study of ulcerative colitis and Crohn\u2019s disease patients"],"prefix":"10.3389","volume":"17","author":[{"given":"Zhejiong","family":"Wang","sequence":"first","affiliation":[{"name":"Department of Laboratory Medicine, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine)","place":["Hangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiayi","family":"Shi","sequence":"additional","affiliation":[{"name":"Haining Hospital of Traditional Chinese Medicine","place":["Jiaxing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yan","family":"Yu","sequence":"additional","affiliation":[{"name":"Hangzhou Health-Bank Medical Laboratory Co., Ltd.","place":["Hangzhou, China"]},{"name":"Faculty of Medicine, The First School of Clinical Medicine, Yangzhou University","place":["Yangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Linchao","family":"Zhu","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine)","place":["Hangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lichen","family":"Zhu","sequence":"additional","affiliation":[{"name":"Artificial Intelligence and Big Data Center (Information Center), The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine)","place":["Hangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenjuan","family":"Tuo","sequence":"additional","affiliation":[{"name":"Hangzhou Health-Bank Medical Laboratory Co., Ltd.","place":["Hangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juntao","family":"Ni","sequence":"additional","affiliation":[{"name":"The Second Affiliated Hospital of Zhejiang University","place":["Hangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi","family":"Wu","sequence":"additional","affiliation":[{"name":"The First School of Clinical Medicine, Zhejiang Chinese Medical University","place":["Zhejiang, Hangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shengliang","family":"Qiu","sequence":"additional","affiliation":[{"name":"The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine)","place":["Hangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ying","family":"Yu","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine)","place":["Hangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,4,7]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"e70304","DOI":"10.1002\/mnfr.70304","article-title":"Modulation of intestinal microbiota through kefir-based beverages in a murine model of acute pancreatitis","volume":"69","author":"Aguirre-Ram\u00edrez","year":"2025","journal-title":"Mol. Nutr. Food Res."},{"key":"ref2","doi-asserted-by":"publisher","first-page":"101567","DOI":"10.1016\/j.nmni.2025.101567","article-title":"Comparative analysis of dominant gut microbiota in inflammatory bowel disease patients and healthy individuals: a case-control study","volume":"64","author":"Ahmadi","year":"2025","journal-title":"New Microbes New Infect"},{"key":"ref3","doi-asserted-by":"publisher","first-page":"1573","DOI":"10.1084\/jem.20101330","article-title":"An innately dangerous balancing act: intestinal homeostasis, inflammation, and colitis-associated cancer","volume":"207","author":"Asquith","year":"2010","journal-title":"J. Exp. Med."},{"key":"ref4","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1016\/j.chom.2022.02.004","article-title":"Gut microbiota-derived bile acids in intestinal immunity, inflammation, and tumorigenesis","volume":"30","author":"Cai","year":"2022","journal-title":"Cell Host Microbe"},{"key":"ref5","doi-asserted-by":"publisher","first-page":"101624","DOI":"10.1016\/j.xcrm.2024.101624","article-title":"Enhanced microbiota profiling in patients with quiescent Crohn's disease through comparison with paired healthy first-degree relatives","volume":"5","author":"Chen","year":"2024","journal-title":"Cell Rep. Med."},{"key":"ref6","doi-asserted-by":"publisher","first-page":"103293","DOI":"10.1016\/j.ebiom.2021.103293","article-title":"Short chain fatty acids and its producing organisms: an overlooked therapy for IBD?","volume":"66","author":"Deleu","year":"2021","journal-title":"EBioMedicine"},{"key":"ref7","doi-asserted-by":"publisher","first-page":"1745","DOI":"10.1136\/gutjnl-2012-303611","article-title":"Butyricicoccus pullicaecorum in inflammatory bowel disease","volume":"62","author":"Eeckhaut","year":"2013","journal-title":"Gut"},{"key":"ref8","doi-asserted-by":"publisher","first-page":"115993","DOI":"10.1016\/j.foodres.2025.115993","article-title":"Western diet-based NutriCol medium: a high-pectin, low-inulin culture medium promoted gut microbiota stability and diversity in PolyFermS and M-ARCOL continuous in vitro models","volume":"206","author":"Esmail","year":"2025","journal-title":"Food Res. 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Sci."},{"key":"ref12","doi-asserted-by":"publisher","first-page":"8343","DOI":"10.3390\/ijms23158343","article-title":"Interactive relationships between intestinal flora and bile acids","volume":"23","author":"Guo","year":"2022","journal-title":"Int. J. Mol. Sci."},{"key":"ref13","doi-asserted-by":"publisher","first-page":"103","DOI":"10.1186\/s13073-017-0490-5","article-title":"A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients","volume":"9","author":"Hall","year":"2017","journal-title":"Genome Med."},{"key":"ref14","doi-asserted-by":"publisher","first-page":"e2007595118","DOI":"10.1073\/pnas.2007595118","article-title":"Capsular polysaccharide correlates with immune response to the human gut microbe Ruminococcus gnavus","volume":"118","author":"Henke","year":"2021","journal-title":"Proc. Natl. Acad. Sci. 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Ethnopharmacol."},{"key":"ref28","doi-asserted-by":"publisher","first-page":"2769","DOI":"10.1016\/S0140-6736(17)32448-0","article-title":"Worldwide incidence and prevalence of inflammatory bowel disease in the 21st century: a systematic review of population-based studies","volume":"390","author":"Ng","year":"2017","journal-title":"Lancet"},{"key":"ref29","doi-asserted-by":"publisher","first-page":"121699","DOI":"10.1016\/j.lfs.2023.121699","article-title":"Bifidobacterium and Lactobacillus improve inflammatory bowel disease in zebrafish of different ages by regulating the intestinal mucosal barrier and microbiota","volume":"324","author":"Ni","year":"2023","journal-title":"Life Sci."},{"key":"ref30","doi-asserted-by":"publisher","first-page":"907","DOI":"10.1038\/s41586-022-04480-z","article-title":"Human gut bacteria produce \u03a4(\u0397)17-modulating bile acid metabolites","volume":"603","author":"Paik","year":"2022","journal-title":"Nature"},{"key":"ref31","doi-asserted-by":"publisher","first-page":"733992","DOI":"10.3389\/fcimb.2022.733992","article-title":"The gut microbiota in inflammatory bowel disease","volume":"12","author":"Qiu","year":"2022","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref32","doi-asserted-by":"publisher","first-page":"577","DOI":"10.1053\/j.gastro.2007.11.059","article-title":"Microbial influences in inflammatory bowel diseases","volume":"134","author":"Sartor","year":"2008","journal-title":"Gastroenterology"},{"key":"ref33","doi-asserted-by":"publisher","first-page":"1208","DOI":"10.3390\/microorganisms13061208","article-title":"Impact of psychopathology and gut microbiota on disease progression in ulcerative colitis: a five-year follow-up study","volume":"13","author":"Scaldaferri","year":"2025","journal-title":"Microorganisms"},{"key":"ref34","doi-asserted-by":"publisher","first-page":"659","DOI":"10.1016\/j.chom.2020.01.021","article-title":"Dysbiosis-induced secondary bile acid deficiency promotes intestinal inflammation","volume":"27","author":"Sinha","year":"2020","journal-title":"Cell Host Microbe"},{"key":"ref35","doi-asserted-by":"publisher","first-page":"1376","DOI":"10.3390\/ph18091376","article-title":"Metagenomic characterization of gut microbiota in children with autism spectrum disorder: microbial signatures and modulation by anti-inflammatory diet and probiotics","volume":"18","author":"Valencia-Buitrago","year":"2025","journal-title":"Pharmaceuticals (Basel, Switzerland)."},{"key":"ref36","doi-asserted-by":"publisher","first-page":"731","DOI":"10.1016\/j.molmed.2024.12.005","article-title":"Probiotics in inflammatory bowel disease: microbial modulation and therapeutic prospects","volume":"31","author":"Vallejos","year":"2025","journal-title":"Trends Mol. 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Microbiol."},{"key":"ref39","doi-asserted-by":"publisher","first-page":"e38457","DOI":"10.1097\/MD.0000000000038457","article-title":"Bile acid profiles and classification model accuracy for inflammatory bowel disease diagnosis","volume":"103","author":"Xu","year":"2024","journal-title":"Medicine"},{"key":"ref40","doi-asserted-by":"publisher","first-page":"722","DOI":"10.1093\/ibd\/izy359","article-title":"Difference in pathomechanism between Crohn's disease and ulcerative colitis revealed by colon transcriptome","volume":"25","author":"Yang","year":"2019","journal-title":"Inflamm. Bowel Dis."},{"key":"ref41","doi-asserted-by":"publisher","first-page":"874021","DOI":"10.3389\/fimmu.2022.874021","article-title":"Comprehensive analysis of the relationships between the gut microbiota and fecal metabolome in individuals with primary Sjogren's syndrome by 16S rRNA sequencing and LC-MS-based metabolomics","volume":"13","author":"Yang","year":"2022","journal-title":"Front. Immunol."},{"key":"ref42","doi-asserted-by":"publisher","first-page":"3432","DOI":"10.1038\/s41467-022-31171-0","article-title":"Programmable probiotics modulate inflammation and gut microbiota for inflammatory bowel disease treatment after effective oral delivery","volume":"13","author":"Zhou","year":"2022","journal-title":"Nat. Commun."},{"key":"ref43","doi-asserted-by":"publisher","first-page":"110628","DOI":"10.1016\/j.intimp.2023.110628","article-title":"Taurodeoxycholate ameliorates DSS-induced colitis in mice","volume":"122","author":"Zou","year":"2023","journal-title":"Int. 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