{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,6]],"date-time":"2026-04-06T12:09:07Z","timestamp":1775477347505,"version":"3.50.1"},"reference-count":61,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,10,29]],"date-time":"2025-10-29T00:00:00Z","timestamp":1761696000000},"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>For small ruminants, meat quality\u2014an economically significant characteristic\u2014results from the combined effects of genetic, dietary, and physiological elements. However, the contribution of gastrointestinal (GI) tract gene expression to meat quality remains unclear.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>Here, we performed bulk RNA-seq on 130 samples from Liangshan Black Sheep and Meigu Black Goats, including 10 GI tract segments and semitendinosus muscle, integrating these data with measurements of amino acid composition, fatty acid profiles, and volatile flavor compounds.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results and discussion<\/jats:title>\n                    <jats:p>\n                      We found distinct, segment-specific transcriptional programs across the GI tract, with major functional shifts at the rumen\u2013reticulum, omasum\u2013abomasum, and abomasum\u2013duodenum transitions. In the ileum and jejunum, genes involved in lipid metabolism showed links to fatty acid profiles, whereas genes governing amino acid metabolism in the small intestine were connected to the amino acid composition of muscle. Cecum- and colon-enriched genes were linked to flavor precursor biosynthesis. Species-specific differences revealed that sheep muscle contained higher levels of key amino acids (Asp, Glu, Hyp, Cys, Tyr), whereas goats showed higher \u03b1-linolenic acid and other polyunsaturated fatty acids. This work establishes a gut\u2013muscle transcriptomic axis in small ruminants, identifying candidate genes (e.g.,\n                      <jats:italic>GKN2<\/jats:italic>\n                      ,\n                      <jats:italic>APOC3<\/jats:italic>\n                      ,\n                      <jats:italic>AQP5<\/jats:italic>\n                      ) and pathways that may be involved in regulating amino acid, fatty acid, and flavor traits of meat quality.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fvets.2025.1687258","type":"journal-article","created":{"date-parts":[[2025,10,29]],"date-time":"2025-10-29T05:30:42Z","timestamp":1761715842000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["The expression of genes in different sites of gut tract regulates the meat quality of semitendinosus muscle in sheep and goats"],"prefix":"10.3389","volume":"12","author":[{"given":"Binlong","family":"Chen","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhiying","family":"Huang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhongkun","family":"Cai","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Siyu","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guangwen","family":"Yan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Weihua","family":"Chang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yi","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shizhong","family":"Yang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2025,10,29]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"1060","DOI":"10.3390\/agriculture14071060","article-title":"Meat of sheep: insights into mutton evaluation, nutritive value, influential factors, and interventions","volume":"14","author":"Ding","year":"2024","journal-title":"Agriculture (Basel)"},{"key":"ref2","doi-asserted-by":"publisher","first-page":"105693","DOI":"10.1016\/j.fbio.2024.105693","article-title":"Insights into the differences in meat quality among different sheep breeds in the Qilian Mountains from the perspective of metabolomics and transcriptomics","volume":"63","author":"Ma","year":"2025","journal-title":"Food Biosci"},{"key":"ref3","doi-asserted-by":"publisher","first-page":"1390","DOI":"10.1038\/s41597-024-04260-6","article-title":"Gene expression profiles in specific skeletal muscles and meat quality characteristics of sheep and goats","volume":"11","author":"Leng","year":"2024","journal-title":"Sci Data"},{"key":"ref4","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1186\/s13002-022-00537-5","article-title":"An ethnobiological study on traditional knowledge associated with black-boned sheep (Ovis Aries) in Northwest Yunnan, China","volume":"18","author":"Fan","year":"2022","journal-title":"J Ethnobiol Ethnomed"},{"key":"ref5","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1079\/PNS2003248","article-title":"Determinants of meat quality: tenderness","volume":"62","author":"Maltin","year":"2003","journal-title":"Proc Nutr Soc"},{"key":"ref6","doi-asserted-by":"publisher","first-page":"918","DOI":"10.3390\/ijms17060918","article-title":"Nutrigenomics and beef quality: a review about lipogenesis","volume":"17","author":"Ladeira","year":"2016","journal-title":"Int J Mol Sci"},{"key":"ref7","doi-asserted-by":"publisher","first-page":"100330","DOI":"10.1016\/j.animal.2021.100330","article-title":"Review: factors affecting sheep carcass and meat quality attributes","volume":"16","author":"Prache","year":"2022","journal-title":"Animal"},{"key":"ref8","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1016\/j.jfca.2016.08.001","article-title":"Influence of commercial cut on proximate composition and fatty acid profile of rasa Aragonesa light lamb","volume":"53","author":"Campo","year":"2016","journal-title":"J Food Compos Anal"},{"key":"ref9","doi-asserted-by":"publisher","first-page":"982","DOI":"10.5713\/ab.23.0316","article-title":"Multiomics analyses of Jining Grey goat and Boer goat reveal genomic regions associated with fatty acid and amino acid metabolism and muscle development","volume":"37","author":"Liu","year":"2024","journal-title":"Anim Biosci"},{"key":"ref10","doi-asserted-by":"publisher","first-page":"2738","DOI":"10.3390\/ani14182738","article-title":"Effects of feeding systems on the growth performance, carcass characteristics, and meat quality in sheep: a meta-analysis","volume":"14","author":"Wang","year":"2024","journal-title":"Animals"},{"key":"ref11","doi-asserted-by":"publisher","first-page":"102159","DOI":"10.1016\/j.fochx.2025.102159","article-title":"Effects of intramuscular fat on the flavor of fresh sheep and goat meat: recent insights into pre-mortem and post-mortem factors","volume":"25","author":"Su","year":"2025","journal-title":"Food Chem X"},{"key":"ref12","doi-asserted-by":"publisher","first-page":"e0100522","DOI":"10.1128\/spectrum.01005-22","article-title":"Dynamic changes in the gut microbial community and function during broiler growth","volume":"10","author":"Yang","year":"2022","journal-title":"Microbiol Spectr"},{"key":"ref13","doi-asserted-by":"publisher","first-page":"812","DOI":"10.24272\/j.issn.2095-8137.2024.467","article-title":"Single-cell Rna-Seq provides insight into the underdeveloped immune system of germ-free mice","volume":"46","author":"Sheng","year":"2025","journal-title":"Zool Res"},{"key":"ref14","doi-asserted-by":"publisher","first-page":"101422","DOI":"10.1016\/j.psj.2021.101422","article-title":"The digestive and reproductive tract microbiotas and their association with body weight in laying hens","volume":"100","author":"Su","year":"2021","journal-title":"Poult Sci"},{"key":"ref15","doi-asserted-by":"publisher","first-page":"e185","DOI":"10.1002\/imt2.185","article-title":"Vaginal microbiota are associated with in vitro fertilization during female infertility","volume":"3","author":"Wang","year":"2024","journal-title":"iMeta"},{"key":"ref16","doi-asserted-by":"publisher","first-page":"1460","DOI":"10.1002\/jcsm.12964","article-title":"Gut microbes and muscle function: can probiotics make our muscles stronger?","volume":"13","author":"Giron","year":"2022","journal-title":"J Cachexia Sarcopenia Muscle"},{"key":"ref17","doi-asserted-by":"publisher","first-page":"388","DOI":"10.1016\/j.ymthe.2021.08.025","article-title":"Fecal mir-142a-3p from dextran Sulfate sodium-challenge recovered mice prevents colitis by promoting the growth of Lactobacillus Reuteri","volume":"30","author":"He","year":"2022","journal-title":"Mol Ther"},{"key":"ref18","doi-asserted-by":"publisher","first-page":"2263207","DOI":"10.1080\/19490976.2023.2263207","article-title":"Progress of linking gut microbiota and musculoskeletal health: casualty, mechanisms, and translational values","volume":"15","author":"Wang","year":"2023","journal-title":"Gut Microbes"},{"key":"ref19","doi-asserted-by":"publisher","first-page":"eaan5662","DOI":"10.1126\/scitranslmed.aan5662","article-title":"The gut microbiota influences skeletal muscle mass and function in mice","volume":"11","author":"Lahiri","year":"2019","journal-title":"Sci Transl Med"},{"key":"ref20","doi-asserted-by":"publisher","first-page":"2151191","DOI":"10.1155\/2022\/2151191","article-title":"Mechanisms involved in gut microbiota regulation of skeletal muscle","volume":"2022","author":"Li","year":"2022","journal-title":"Oxidative Med Cell Longev"},{"key":"ref21","doi-asserted-by":"publisher","first-page":"412","DOI":"10.1186\/s12864-025-11607-9","article-title":"Integrated transcriptomics and metabolomics reveal the molecular characteristics and metabolic regulatory mechanisms among different muscles in Minxian black Fur sheep","volume":"26","author":"Wang","year":"2025","journal-title":"BMC Genomics"},{"key":"ref22","doi-asserted-by":"publisher","first-page":"1110","DOI":"10.1186\/s12864-024-10928-5","article-title":"Insights and implications for transcriptomic analysis of heat stress-induced intestinal inflammation in pigs","volume":"25","author":"Yu","year":"2024","journal-title":"BMC Genomics"},{"key":"ref23","doi-asserted-by":"publisher","first-page":"530","DOI":"10.1186\/s12864-025-11712-9","article-title":"Transcriptome analysis reveals age-specific growth characteristics in the rumen of Hanwoo (Korean native cattle) steers","volume":"26","author":"Park","year":"2025","journal-title":"BMC Genomics"},{"key":"ref24","doi-asserted-by":"publisher","first-page":"100262","DOI":"10.1016\/j.vas.2022.100262","article-title":"Nutrigenomics in livestock sector and its human-animal interface-a review","volume":"17","author":"Haq","year":"2022","journal-title":"Vet Anim Sci"},{"key":"ref25","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1093\/gigascience\/giab096","article-title":"An improved ovine reference genome assembly to facilitate in-depth functional annotation of the sheep genome","volume":"11","author":"Davenport","year":"2022","journal-title":"Gigascience"},{"key":"ref26","doi-asserted-by":"publisher","first-page":"643","DOI":"10.1038\/ng.3802","article-title":"Single-molecule sequencing and chromatin conformation capture enable De novo reference assembly of the domestic goat genome","volume":"49","author":"Bickhart","year":"2017","journal-title":"Nat Genet"},{"key":"ref27","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"Star: ultrafast universal Rna-seq aligner","volume":"29","author":"Dobin","year":"2012","journal-title":"Bioinformatics"},{"key":"ref28","doi-asserted-by":"publisher","first-page":"525","DOI":"10.1038\/nbt.3519","article-title":"Near-optimal probabilistic Rna-Seq quantification","volume":"34","author":"Bray","year":"2016","journal-title":"Nat Biotechnol"},{"key":"ref29","first-page":"2579","article-title":"Visualizing high-dimensional data using T-Sne","volume":"9","author":"Maaten","year":"2008","journal-title":"J Mach Learn Res"},{"key":"ref30","first-page":"3221","article-title":"Accelerating T-Sne using tree-based algorithms","volume":"15","author":"Laurens","year":"2014","journal-title":"J Mach Learn Res"},{"key":"ref31","doi-asserted-by":"publisher","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for Rna-Seq data with Deseq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol"},{"key":"ref32","doi-asserted-by":"publisher","first-page":"505","DOI":"10.1038\/s41586-019-1338-5","article-title":"Gene expression across mammalian organ development","volume":"571","author":"Cardoso-Moreira","year":"2019","journal-title":"Nature"},{"key":"ref33","doi-asserted-by":"publisher","first-page":"1523","DOI":"10.1038\/s41467-019-09234-6","article-title":"Metascape provides a biologist-oriented resource for the analysis of systems-level datasets","volume":"10","author":"Zhou","year":"2019","journal-title":"Nat Commun"},{"key":"ref34","doi-asserted-by":"publisher","first-page":"650","DOI":"10.1093\/bioinformatics\/bti042","article-title":"Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification","volume":"21","author":"Yanai","year":"2004","journal-title":"Bioinformatics"},{"key":"ref35","doi-asserted-by":"publisher","first-page":"ELIXIR","DOI":"10.12688\/f1000research.24956.2","article-title":"Gprofiler2 -- an R package for gene list functional enrichment analysis and namespace conversion toolset G:profiler","volume":"9","author":"Kolberg","year":"2020","journal-title":"F1000Res"},{"key":"ref36","doi-asserted-by":"publisher","first-page":"100141","DOI":"10.1016\/j.xinn.2021.100141","article-title":"Clusterprofiler 4.0: a universal enrichment tool for interpreting omics data","volume":"2","author":"Wu","year":"2021","journal-title":"Innovation (Camb)"},{"key":"ref37","doi-asserted-by":"publisher","first-page":"giab067","DOI":"10.1093\/gigascience\/giab067","article-title":"Association of female reproductive tract microbiota with egg production in layer chickens","volume":"10","author":"Su","year":"2021","journal-title":"Gigascience"},{"key":"ref38","doi-asserted-by":"publisher","first-page":"1569196","DOI":"10.3389\/fvets.2025.1569196","article-title":"Insights into high-altitude adaptation and meat quality regulation by gastrointestinal metabolites in Tibetan and black pigs","volume":"12","author":"Bai","year":"2025","journal-title":"Front Vet Sci"},{"key":"ref39","doi-asserted-by":"publisher","first-page":"761","DOI":"10.24272\/j.issn.2095-8137.2024.462","article-title":"Static magnetic field exposure modulates gut microbiota and host metabolism to alleviate high-fat diet-induced metabolic dysfunction-associated fatty liver disease","volume":"46","author":"Chen","year":"2025","journal-title":"Zool Res"},{"key":"ref40","doi-asserted-by":"publisher","first-page":"747","DOI":"10.1007\/s00439-020-02237-0","article-title":"The relationship between the gut microbiome and host gene expression: a review","volume":"140","author":"Nichols","year":"2021","journal-title":"Hum Genet"},{"key":"ref41","doi-asserted-by":"publisher","first-page":"314","DOI":"10.1016\/j.chom.2019.08.011","article-title":"Regional diversity of the gastrointestinal microbiome","volume":"26","author":"Martinez-Guryn","year":"2019","journal-title":"Cell Host Microbe"},{"key":"ref42","doi-asserted-by":"publisher","first-page":"159","DOI":"10.1017\/s1751731107658042","article-title":"Recent advances in cattle functional genomics and their application to beef quality","volume":"1","author":"Hocquette","year":"2007","journal-title":"Animal"},{"key":"ref43","doi-asserted-by":"publisher","first-page":"05","DOI":"10.1093\/gigascience\/giaf006","article-title":"Multiomics analysis provides insights into musk secretion in muskrat and musk deer","volume":"14","author":"Wang","year":"2025","journal-title":"Gigascience"},{"key":"ref44","doi-asserted-by":"publisher","first-page":"1265","DOI":"10.1016\/j.jgg.2024.08.002","article-title":"Insights into left-right asymmetric development of chicken ovary at the single-cell level","volume":"51","author":"Wang","year":"2024","journal-title":"J Genet Genomics"},{"key":"ref45","doi-asserted-by":"publisher","first-page":"1088","DOI":"10.24272\/j.issn.2095-8137.2024.037","article-title":"Single nucleus\/cell Rna-seq of the chicken hypothalamic-pituitary-ovarian axis offers new insights into the molecular regulatory mechanisms of ovarian development","volume":"45","author":"Leng","year":"2024","journal-title":"Zool Res"},{"key":"ref46","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1007\/s13353-020-00577-1","article-title":"Transcriptomic profile of semitendinosus muscle of bulls of different breed and performance","volume":"61","author":"Ciecierska","year":"2020","journal-title":"J Appl Genet"},{"key":"ref47","doi-asserted-by":"publisher","first-page":"116029","DOI":"10.1016\/j.jep.2022.116029","article-title":"Inhibition of Slc7a11-Gpx4 signal pathway is involved in aconitine-induced ferroptosis in vivo and in vitro","volume":"303","author":"Li","year":"2023","journal-title":"J Ethnopharmacol"},{"key":"ref48","doi-asserted-by":"publisher","first-page":"1392418","DOI":"10.3389\/fendo.2024.1392418","article-title":"The short-chain fatty acid receptors Gpr41\/43 regulate bone mass by promoting Adipogenic differentiation of mesenchymal stem cells","volume":"15","author":"Behler-Janbeck","year":"2024","journal-title":"Front Endocrinol (Lausanne)"},{"key":"ref49","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1016\/j.aninu.2020.12.001","article-title":"Ruminal microbiota\u2013host interaction and its effect on nutrient metabolism","volume":"7","author":"Liu","year":"2021","journal-title":"Anim Nutr"},{"key":"ref50","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12899-019-0038-6","article-title":"Exercise endurance capacity is markedly reduced due to impaired energy homeostasis during prolonged fasting in Fabp4\/5 deficient mice","volume":"19","author":"Iso","year":"2019","journal-title":"BMC Physiol"},{"key":"ref51","doi-asserted-by":"publisher","first-page":"1383","DOI":"10.1172\/jci82655","article-title":"Loss of gastrokine-2 drives premalignant gastric inflammation and tumor progression","volume":"126","author":"Menheniott","year":"2016","journal-title":"J Clin Invest"},{"key":"ref52","doi-asserted-by":"publisher","first-page":"225","DOI":"10.1016\/j.cmet.2013.07.003","article-title":"Abca12 regulates Abca1-dependent cholesterol efflux from macrophages and the development of atherosclerosis","volume":"18","author":"Fu","year":"2013","journal-title":"Cell Metab"},{"key":"ref53","doi-asserted-by":"publisher","first-page":"1889","DOI":"10.3390\/ijms24031889","article-title":"Aquaporin-5 dynamic regulation","volume":"24","author":"D'Agostino","year":"2023","journal-title":"Int J Mol Sci"},{"key":"ref54","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1038\/s41586-019-0992-y","article-title":"Colonic epithelial cell diversity in health and inflammatory bowel disease","volume":"567","author":"Parikh","year":"2019","journal-title":"Nature"},{"key":"ref55","doi-asserted-by":"publisher","first-page":"507","DOI":"10.1016\/j.schres.2023.11.007","article-title":"The expression of immune related genes and potential regulatory mechanisms in schizophrenia","volume":"267","author":"Yu","year":"2024","journal-title":"Schizophr Res"},{"key":"ref56","doi-asserted-by":"publisher","first-page":"515","DOI":"10.5851\/kosfa.2024.e29","article-title":"Umami characteristics and taste improvement mechanism of meat","volume":"44","author":"Hossain","year":"2024","journal-title":"Food Sci Anim Resour"},{"key":"ref57","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1038\/s41538-023-00178-2","article-title":"The flavor-enhancing action of glutamate and its mechanism involving the notion of kokumi","volume":"7","author":"Yamamoto","year":"2023","journal-title":"NPJ Sci Food"},{"key":"ref58","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1002\/jsfa.4152","article-title":"Exploitation of dietary tannins to improve rumen metabolism and ruminant nutrition","volume":"91","author":"Patra","year":"2011","journal-title":"J Sci Food Agric"},{"key":"ref59","doi-asserted-by":"publisher","first-page":"205","DOI":"10.1016\/0921-4488(88)90049-1","article-title":"Grazing behavior and diet selection of goats","volume":"1","author":"Lu","year":"1988","journal-title":"Small Rumin Res"},{"key":"ref60","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1016\/j.meatsci.2003.09.004","article-title":"Fatty acid composition and cholesterol content of muscles as related to genotype and vitamin E treatment in crossbred lambs","volume":"67","author":"Salvatori","year":"2004","journal-title":"Meat Sci"},{"key":"ref61","doi-asserted-by":"publisher","first-page":"108996","DOI":"10.1016\/j.meatsci.2022.108996","article-title":"Transcriptome analysis reveals the molecular regulatory network of muscle development and meat quality in Sunit lamb supplemented with dietary probiotic","volume":"194","author":"Zhang","year":"2022","journal-title":"Meat Sci"}],"container-title":["Frontiers in Veterinary Science"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fvets.2025.1687258\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,29]],"date-time":"2025-10-29T05:30:43Z","timestamp":1761715843000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fvets.2025.1687258\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,10,29]]},"references-count":61,"alternative-id":["10.3389\/fvets.2025.1687258"],"URL":"https:\/\/doi.org\/10.3389\/fvets.2025.1687258","relation":{},"ISSN":["2297-1769"],"issn-type":[{"value":"2297-1769","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,10,29]]},"article-number":"1687258"}}