{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T04:18:29Z","timestamp":1791260309619,"version":"4.1.0"},"reference-count":67,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,10,17]],"date-time":"2025-10-17T00:00:00Z","timestamp":1760659200000},"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. Vet. Sci."],"abstract":"<jats:sec>\n                    <jats:title>Introduction<\/jats:title>\n                    <jats:p>Bile acid (BA) metabolism by gut microbiota plays a crucial role in host health by influencing nutrient absorption, immune responses, and resistance to pathogens. Elucidating how enteric infections disrupt the BA-microbiota axis is crucial for advancing microbiota-based therapeutics, precision nutrition, and post-antibiotic disease control strategies.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>We reconstructed 9,990 high-quality microbial genomes from the gut microbiota of chicken and performed genome-resolved metabolic profiling. Comparative analyses were conducted across host species, including humans and pigs. Also, 135 intestinal samples collected from different regions of the chicken gut were analyzed. Additional samples from chickens infected with Salmonella typhimurium and Eimeria tenella were included to assess infection-associated alterations.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Our results reveal that the phylum\n                      <jats:italic>Bacillota_A<\/jats:italic>\n                      is predominant, with key BA-transforming enzymes, including bile salt hydrolase (BSH) and 7\u03b1-hydroxysteroid dehydrogenase (7\u03b1-HSDH), present in a substantial proportion of the genomes. Chickens harbored a higher proportion of BSH genes compared to humans and pigs, with\n                      <jats:italic>Ligilactobacillus<\/jats:italic>\n                      and\n                      <jats:italic>Alistipes<\/jats:italic>\n                      identified as major contributors. Region-specific analysis showed that BA-metabolizing microbes are unevenly distributed along the intestinal tract, with the highest diversity observed in the cecum and colon. Experimental pathogen challenges revealed that\n                      <jats:italic>S. typhimurium<\/jats:italic>\n                      infection altered BSH gene abundance and overall microbial community structure, whereas\n                      <jats:italic>E. tenella<\/jats:italic>\n                      infection increased taxonomic richness but reduced community evenness.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Discussion<\/jats:title>\n                    <jats:p>Together, these findings advance our understanding of microbial contributions to BA dynamics in poultry and offer insights into the role of BA metabolism in gut health and pathogen resistance.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fvets.2025.1669620","type":"journal-article","created":{"date-parts":[[2025,10,17]],"date-time":"2025-10-17T05:30:24Z","timestamp":1760679024000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":3,"title":["Genome-centric investigation of bile acid-metabolizing microbiota in chickens and their association with Eimeria tenella and Salmonella typhimurium infections"],"prefix":"10.3389","volume":"12","author":[{"given":"Kai-Meng","family":"Shang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hany M.","family":"Elsheikha","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yong-Jie","family":"Wei","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiao-Xuan","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xin-Wen","family":"Hou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hai-Long","family":"Yu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanan","family":"Cai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hong-Bo","family":"Ni","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rui","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"He","family":"Ma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jing","family":"Jiang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fulong","family":"Nan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xing","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2025,10,17]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"236","DOI":"10.1038\/s41579-022-00805-x","article-title":"Bile acids and the gut microbiota: metabolic interactions and impacts on disease","volume":"21","author":"Collins","year":"2023","journal-title":"Nat Rev Microbiol"},{"key":"ref2","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1080\/19490976.2015.1127483","article-title":"Consequences of bile salt biotransformations by intestinal bacteria","volume":"7","author":"Ridlon","year":"2016","journal-title":"Gut Microbes"},{"key":"ref3","doi-asserted-by":"publisher","first-page":"625","DOI":"10.1016\/j.femsre.2004.09.003","article-title":"The interaction between bacteria and bile","volume":"29","author":"Begley","year":"2005","journal-title":"FEMS Microbiol Rev"},{"key":"ref4","doi-asserted-by":"publisher","first-page":"250","DOI":"10.1016\/j.foodres.2018.06.035","article-title":"New insights into bacterial bile resistance mechanisms: the role of bile salt hydrolase and its impact on human health","volume":"112","author":"Bustos","year":"2018","journal-title":"Food Res Int"},{"key":"ref5","doi-asserted-by":"publisher","first-page":"1581","DOI":"10.3389\/fmicb.2017.01581","article-title":"In vitro antibacterial activity of unconjugated and conjugated bile salts on Staphylococcus aureus","volume":"8","author":"Sannasiddappa","year":"2017","journal-title":"Front Microbiol"},{"key":"ref6","doi-asserted-by":"publisher","first-page":"140","DOI":"10.1186\/s40168-021-01101-1","article-title":"Review: microbial transformations of human bile acids","volume":"9","author":"Guzior","year":"2021","journal-title":"Microbiome"},{"key":"ref7","doi-asserted-by":"publisher","first-page":"1119","DOI":"10.1021\/acschembio.9b00813","article-title":"Chemical mechanisms of colonization resistance by the gut microbial metabolome","volume":"15","author":"Chang","year":"2020","journal-title":"ACS Chem Biol"},{"key":"ref8","doi-asserted-by":"publisher","first-page":"1463","DOI":"10.1016\/j.jcmgh.2021.02.007","article-title":"Regulation of intestinal barrier function by microbial metabolites","volume":"11","author":"Ghosh","year":"2021","journal-title":"Cell Mol Gastroenterol Hepatol"},{"key":"ref9","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1016\/j.mib.2016.10.003","article-title":"Microbiome, metabolites and host immunity","volume":"35","author":"Levy","year":"2017","journal-title":"Curr Opin Microbiol"},{"key":"ref10","doi-asserted-by":"publisher","first-page":"3143","DOI":"10.3390\/nu13093143","article-title":"Bile acid-gut microbiota axis in inflammatory bowel disease: from bench to bedside","volume":"13","author":"Yang","year":"2021","journal-title":"Nutrients"},{"key":"ref11","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1038\/s41522-019-0096-3","article-title":"Host transcriptome and microbiome interaction modulates physiology of full-sibs broilers with divergent feed conversion ratio","volume":"5","author":"Shah","year":"2019","journal-title":"NPJ Biofilms Microbiomes"},{"key":"ref12","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1186\/s40104-024-01071-y","article-title":"Dietary bile acids supplementation decreases hepatic fat deposition with the involvement of altered gut microbiota and liver bile acids profile in broiler chickens","volume":"15","author":"Wang","year":"2024","journal-title":"J Anim Sci Biotechnol."},{"key":"ref13","doi-asserted-by":"publisher","first-page":"992","DOI":"10.3390\/ani14070992","article-title":"Exploring bile-acid changes and microflora profiles in chicken fatty liver disease model","volume":"14","author":"Yang","year":"2024","journal-title":"Animals (Basel)"},{"key":"ref14","doi-asserted-by":"publisher","first-page":"104746","DOI":"10.1016\/j.psj.2024.104746","article-title":"Exploring the metabolic patterns and response mechanisms of bile acids during fasting: a study with poultry as an example","volume":"104","author":"Zhang","year":"2025","journal-title":"Poult Sci"},{"key":"ref15","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1038\/s41522-018-0070-5","article-title":"Lactobacillus elicits a'Marmite effect'on the chicken cecal microbiome","volume":"4","author":"Zou","year":"2018","journal-title":"NPJ Biofilms Microbiomes"},{"key":"ref16","doi-asserted-by":"publisher","first-page":"716","DOI":"10.1080\/00071660802449145","article-title":"Relationship between digesta transit time and apparent metabolisable energy value of wheat in chickens","volume":"49","author":"Hughes","year":"2008","journal-title":"Br Poult Sci"},{"key":"ref17","doi-asserted-by":"publisher","first-page":"4941","DOI":"10.1038\/s41598-020-61723-7","article-title":"Evaluation of bile salt hydrolase inhibitor efficacy for modulating host bile profile and physiology using a chicken model system","volume":"10","author":"Geng","year":"2020","journal-title":"Sci Rep"},{"key":"ref18","doi-asserted-by":"publisher","first-page":"S2090-1232(25)00307-8","DOI":"10.1016\/j.jare.2025.05.015","article-title":"The functions of gut microbiota-mediated bile acid metabolism in intestinal immunity","volume":"10","author":"He","year":"2025","journal-title":"J Adv Res"},{"key":"ref19","doi-asserted-by":"publisher","DOI":"10.29261\/pakvetj\/2024.253","article-title":"Evaluation of antibiotic resistance profile and multiple antibiotic resistance index in avian adapted Salmonella enterica serovar gallinarum isolates. Pak","volume":"44","author":"Durrani","year":"2024","journal-title":"Vet J"},{"key":"ref20","doi-asserted-by":"publisher","first-page":"659","DOI":"10.29261\/pakvetj\/2023.103","article-title":"Probiotic effect of Limosilactobacillus fermentum on growth performance and competitive exclusion of Salmonella gallinarum in poultry","volume":"43","author":"Mehmood","year":"2023","journal-title":"Pak Vet J"},{"key":"ref21","doi-asserted-by":"publisher","first-page":"266","DOI":"10.47278\/journal.ijvs\/2023.099","article-title":"Efficacy of phyto-genic products to control field coccidiosis in broiler chickens","volume":"13","author":"Hailat","year":"2023","journal-title":"Int J Vet Sci"},{"key":"ref22","doi-asserted-by":"publisher","first-page":"34","DOI":"10.47278\/journal.ijvs\/2023.054","article-title":"Drug resistance and coccidiosis affects immunity, performance, blood micronutrients, and intestinal integrity in broiler chickens","volume":"13","author":"Hayajneh","year":"2024","journal-title":"Int J Vet Sci"},{"key":"ref23","doi-asserted-by":"publisher","first-page":"803","DOI":"10.9775\/kvfd.2024.32618","article-title":"Evaluating Linum usitatissimum seeds extract as potential alternative biochemical and therapeutic agent against induced coccidiosis in broiler chicken","volume":"30","author":"Hussain","year":"2024","journal-title":"Kafkas Univ Vet Fak"},{"key":"ref24","doi-asserted-by":"publisher","first-page":"377","DOI":"10.21162\/PAKJAS\/23.54","article-title":"Anticoccidial activities of essential oil of Amomum subulatum in broiler chicks","volume":"60","author":"Saeed","year":"2023","journal-title":"Pak J Agr Sci"},{"key":"ref25","doi-asserted-by":"publisher","first-page":"292","DOI":"10.29261\/pakvetj\/2024.176","article-title":"Coccidiostat activity of Mahonia bealei (fort.) leaves extract against Eimeria tenella in chickens","volume":"44","author":"Zhang","year":"2024","journal-title":"Front Vet Sci."},{"key":"ref26","doi-asserted-by":"publisher","first-page":"324","DOI":"10.2307\/1589700","article-title":"Role of Coccidia in the occurrence of necrotic enteritis of chickens","volume":"24","author":"Al-Sheikhly","year":"1980","journal-title":"Avian Dis"},{"key":"ref27","doi-asserted-by":"publisher","first-page":"56","DOI":"10.1186\/s13071-020-3897-6","article-title":"Dissection of the cecal microbial community in chickens after Eimeria tenella infection","volume":"13","author":"Chen","year":"2020","journal-title":"Parasit Vectors"},{"key":"ref28","doi-asserted-by":"publisher","first-page":"e0184890","DOI":"10.1371\/journal.pone.0184890","article-title":"Effects of Eimeria tenella infection on chicken caecal microbiome diversity, exploring variation associated with severity of pathology","volume":"12","author":"Macdonald","year":"2017","journal-title":"PLoS One"},{"key":"ref29","doi-asserted-by":"publisher","first-page":"1646825","DOI":"10.3389\/fvets.2025.1646825","article-title":"Insights from metagenomics on microbial biosynthesis of vitamins B and K2 in chicken gut microbiota","volume":"12","author":"Yu","year":"2025","journal-title":"Front Vet Sci"},{"key":"ref30","doi-asserted-by":"publisher","first-page":"30","DOI":"10.1016\/j.vetpar.2018.06.005","article-title":"Eimeria tenella infection perturbs the chicken gut microbiota from the onset of oocyst shedding","volume":"258","author":"Huang","year":"2018","journal-title":"Vet Parasitol"},{"key":"ref31","doi-asserted-by":"publisher","first-page":"127773","DOI":"10.1016\/j.micres.2024.127773","article-title":"Dietary \u03b1-linolenic acid supplementation enhances resistance to Salmonella typhimurium challenge in chickens by altering the intestinal mucosal barrier integrity and cecal microbes","volume":"285","author":"Ma","year":"2024","journal-title":"Microbiol Res"},{"key":"ref32","doi-asserted-by":"publisher","first-page":"1191939","DOI":"10.3389\/fcimb.2023.1191939","article-title":"Comprehensive analysis of gut microbiome and host transcriptome in chickens after Eimeria tenella infection","volume":"13","author":"Yu","year":"2023","journal-title":"Front Cell Infect Microbiol"},{"key":"ref33","doi-asserted-by":"publisher","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"Fastp: an ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"ref34","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat Methods"},{"key":"ref35","doi-asserted-by":"publisher","first-page":"1203","DOI":"10.1038\/s41592-023-01940-w","article-title":"CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning","volume":"20","author":"Chklovski","year":"2023","journal-title":"Nat Methods"},{"key":"ref36","doi-asserted-by":"publisher","first-page":"2864","DOI":"10.1038\/ismej.2017.126","article-title":"DRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication","volume":"11","author":"Olm","year":"2017","journal-title":"ISME J"},{"key":"ref37","doi-asserted-by":"publisher","first-page":"5315","DOI":"10.1093\/bioinformatics\/btac672","article-title":"GTDB-Tk v2: memory friendly classification with the genome taxonomy database","volume":"38","author":"Chaumeil","year":"2022","journal-title":"Bioinformatics"},{"key":"ref38","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1186\/1471-2105-11-119","article-title":"Prodigal: prokaryotic gene recognition and translation initiation site identification","volume":"11","author":"Hyatt","year":"2010","journal-title":"BMC Bioinform"},{"key":"ref39","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1038\/nmeth.3176","article-title":"Fast and sensitive protein alignment using DIAMOND","volume":"12","author":"Buchfink","year":"2015","journal-title":"Nat Methods"},{"key":"ref40","doi-asserted-by":"publisher","first-page":"323","DOI":"10.1186\/1471-2105-12-323","article-title":"RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome","volume":"12","author":"Li","year":"2011","journal-title":"BMC Bioinform"},{"key":"ref41","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1007\/s12064-012-0162-3","article-title":"Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples","volume":"131","author":"Wagner","year":"2012","journal-title":"Theory Biosci"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1007\/978-3-319-24277-4_9","article-title":"Data analysis","volume-title":"ggplot2: Elegant graphics for data analysis","author":"Wickham","year":"2016"},{"key":"ref43","doi-asserted-by":"publisher","first-page":"505","DOI":"10.1038\/s41586-019-1058-x","article-title":"New insights from uncultivated genomes of the global human gut microbiome","volume":"568","author":"Nayfach","year":"2019","journal-title":"Nature"},{"key":"ref44","doi-asserted-by":"publisher","first-page":"000501","DOI":"10.1099\/mgen.0.000501","article-title":"Post-weaning shifts in microbiome composition and metabolism revealed by over 25000 pig gut metagenome-assembled genomes","volume":"7","author":"Gaio","year":"2021","journal-title":"Microb Genom"},{"key":"ref45","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1111\/j.1574-6968.2002.tb11051.x","article-title":"Diversity and phylogenetic analysis of bacteria in the mucosa of chicken ceca and comparison with bacteria in the cecal lumen","volume":"208","author":"Gong","year":"2002","journal-title":"FEMS Microbiol Lett"},{"key":"ref46","doi-asserted-by":"publisher","first-page":"858","DOI":"10.3390\/nu3100858","article-title":"Regulation of inflammation by short chain fatty acids","volume":"3","author":"Vinolo","year":"2011","journal-title":"Nutrients"},{"key":"ref47","doi-asserted-by":"publisher","first-page":"25","DOI":"10.2741\/3603","article-title":"Beneficial effects of Bacteroides fragilis polysaccharides on the immune system","volume":"15","author":"Troy","year":"2010","journal-title":"Front Biosci (Landmark Ed)"},{"key":"ref48","doi-asserted-by":"publisher","first-page":"100","DOI":"10.1111\/1574-6968.12608","article-title":"The chicken gastrointestinal microbiome","volume":"360","author":"Oakley","year":"2014","journal-title":"FEMS Microbiol Lett"},{"key":"ref49","doi-asserted-by":"publisher","first-page":"316","DOI":"10.1007\/s13205-019-1834-1","article-title":"Comparative metagenomic sequencing analysis of cecum microbiotal diversity and function in broilers and layers","volume":"9","author":"Qi","year":"2019","journal-title":"3 Biotech"},{"key":"ref50","doi-asserted-by":"publisher","first-page":"678","DOI":"10.1128\/am.27.4.678-687.1974","article-title":"Isolation, culture characteristics, and identification of anaerobic bacteria from the chicken cecum","volume":"27","author":"Salanitro","year":"1974","journal-title":"Appl Microbiol"},{"key":"ref51","doi-asserted-by":"publisher","first-page":"671","DOI":"10.3382\/ps.2012-02822","article-title":"Bacterial census of poultry intestinal microbiome","volume":"92","author":"Wei","year":"2013","journal-title":"Poult Sci"},{"key":"ref52","doi-asserted-by":"publisher","first-page":"653","DOI":"10.1016\/j.psj.2019.12.013","article-title":"Influential factors on the composition of the conventionally raised broiler gastrointestinal microbiomes","volume":"99","author":"Feye","year":"2020","journal-title":"Poult Sci"},{"key":"ref53","doi-asserted-by":"publisher","first-page":"4301","DOI":"10.1007\/s00253-014-5646-2","article-title":"Microbiota of the chicken gastrointestinal tract: influence on health, productivity and disease","volume":"98","author":"Stanley","year":"2014","journal-title":"Appl Microbiol Biotechnol"},{"key":"ref54","doi-asserted-by":"publisher","first-page":"2773","DOI":"10.2527\/2002.80112773x","article-title":"Xylanase and beta-glucanase supplementation improve conjugated bile acid fraction in intestinal contents and increase villus size of small intestine wall in broiler chickens fed a rye-based diet","volume":"80","author":"Mathlouthi","year":"2002","journal-title":"J Anim Sci"},{"key":"ref55","doi-asserted-by":"publisher","first-page":"skae338","DOI":"10.1093\/jas\/skae338","article-title":"Dietary bile acids alleviate corticosterone-induced fatty liver and hepatic glucocorticoid receptor suppression in broiler chickens","volume":"102","author":"Liu","year":"2024","journal-title":"J Anim Sci"},{"key":"ref56","doi-asserted-by":"publisher","first-page":"skad393","DOI":"10.1093\/jas\/skad393","article-title":"Growth performance, bile acid profile, fecal microbiome and serum metabolomics of growing-finishing pigs fed diets with bile acids supplementation","volume":"101","author":"Zhou","year":"2023","journal-title":"J Anim Sci"},{"key":"ref57","doi-asserted-by":"publisher","first-page":"630","DOI":"10.3390\/ani11030630","article-title":"Effects of bile acids on growth performance and lipid metabolism during chronic heat stress in broiler chickens","volume":"11","author":"Yin","year":"2021","journal-title":"Animals (Basel)."},{"key":"ref58","doi-asserted-by":"publisher","first-page":"196","DOI":"10.3382\/ps\/pex288","article-title":"Effects of dietary supplemental bile acids on performance, carcass characteristics, serum lipid metabolites and intestinal enzyme activities of broiler chickens","volume":"97","author":"Lai","year":"2018","journal-title":"Poult Sci"},{"key":"ref59","doi-asserted-by":"publisher","first-page":"887","DOI":"10.3382\/ps\/pey434","article-title":"Effects of diets with different energy and bile acids levels on growth performance and lipid metabolism in broilers","volume":"98","author":"Ge","year":"2019","journal-title":"Poult Sci"},{"key":"ref60","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1186\/s40104-024-01113-5","article-title":"Dietary bile acids supplementation protects against Salmonella typhimurium infection via improving intestinal mucosal barrier and gut microbiota composition in broilers","volume":"15","author":"Hu","year":"2024","journal-title":"J Anim Sci Biotechnol"},{"key":"ref61","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1186\/s40104-022-00801-4","article-title":"Supplemental N-acyl homoserine lactonase alleviates intestinal disruption and improves gut microbiota in broilers challenged by Salmonella typhimurium","volume":"14","author":"Wang","year":"2023","journal-title":"J Anim Sci Biotechnol"},{"key":"ref62","doi-asserted-by":"publisher","first-page":"463","DOI":"10.1136\/gut.2010.212159","article-title":"Farnesoid X receptor activation inhibits inflammation and preserves the intestinal barrier in inflammatory bowel disease","volume":"60","author":"Gadaleta","year":"2011","journal-title":"Gut"},{"key":"ref63","doi-asserted-by":"publisher","first-page":"1158","DOI":"10.21037\/atm-21-2631","article-title":"TGR5 protects against cholestatic liver disease via suppressing the NF-\u03baB pathway and activating the Nrf2\/HO-1 pathway","volume":"9","author":"Yang","year":"2021","journal-title":"Ann Transl Med"},{"key":"ref64","doi-asserted-by":"publisher","first-page":"e00073","DOI":"10.1128\/IAI.00073-18","article-title":"Influence of Eimeria falciformis infection on gut microbiota and metabolic pathways in mice","volume":"86","author":"Huang","year":"2018","journal-title":"Infect Immun"},{"key":"ref65","doi-asserted-by":"publisher","first-page":"632556","DOI":"10.3389\/fcimb.2020.632556","article-title":"The absence of gut microbiota alters the development of the apicomplexan parasite Eimeria tenella","volume":"10","author":"Gaboriaud","year":"2020","journal-title":"Front Cell Infect Microbiol"},{"key":"ref66","doi-asserted-by":"publisher","first-page":"211","DOI":"10.1186\/s40168-018-0590-5","article-title":"The chicken gut metagenome and the modulatory effects of plant-derived benzylisoquinoline alkaloids","volume":"6","author":"Huang","year":"2018","journal-title":"Microbiome"},{"key":"ref67","doi-asserted-by":"publisher","first-page":"326","DOI":"10.1177\/0004563218817798","article-title":"Bile acids and the metabolic syndrome","volume":"56","author":"McGlone","year":"2019","journal-title":"Ann Clin Biochem"}],"container-title":["Frontiers in Veterinary Science"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fvets.2025.1669620\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,17]],"date-time":"2025-10-17T05:30:26Z","timestamp":1760679026000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fvets.2025.1669620\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,10,17]]},"references-count":67,"alternative-id":["10.3389\/fvets.2025.1669620"],"URL":"https:\/\/doi.org\/10.3389\/fvets.2025.1669620","relation":{},"ISSN":["2297-1769"],"issn-type":[{"value":"2297-1769","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,10,17]]},"article-number":"1669620"}}