{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T09:59:30Z","timestamp":1790071170266,"version":"4.0.1"},"reference-count":43,"publisher":"MDPI AG","issue":"19","license":[{"start":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T00:00:00Z","timestamp":1790035200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32541116"],"award-info":[{"award-number":["32541116"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"award":["32541116"],"award-info":[{"award-number":["32541116"]}],"id":[{"id":"https:\/\/ror.org\/01h0zpd94","id-type":"ROR","asserted-by":"publisher"}]},{"name":"Central Public-interest Scientific Institution Basal Research Fund","award":["Y2026BF02"],"award-info":[{"award-number":["Y2026BF02"]}]},{"name":"Central Public-interest Scientific Institution Basal Research Fund","award":["No.1610332026014"],"award-info":[{"award-number":["No.1610332026014"]}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2023YFF10009"],"award-info":[{"award-number":["2023YFF10009"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Bayannaoer Research Institute Young Scientist Project","award":["2024BYNECAU004"],"award-info":[{"award-number":["2024BYNECAU004"]}]},{"DOI":"10.13039\/501100005236","name":"Chinese Universities Scientific Fund","doi-asserted-by":"publisher","award":["2026RC017"],"award-info":[{"award-number":["2026RC017"]}],"id":[{"id":"10.13039\/501100005236","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Biology"],"abstract":"<jats:p>The mammalian stomach has conserved digestive functions but also shows major anatomical and physiological differences among species. However, broad comparative transcriptomic analyses across mammals and across ruminant stomach chambers remain limited. Here, we collected and integrated 111 bulk RNA-seq datasets from 11 mammalian species (humans, mice, monkeys, dogs, horses, donkeys, pigs, cattle, deer, goats, and sheep) and analyzed 12,048 shared one-to-one orthologous genes. We identified 56 conserved genes mainly involved in translation, ribosome biogenesis, protein homeostasis, and mitochondrial function. Pairwise comparisons revealed extensive transcriptional differences, with 2070\u20137110 differentially expressed genes across species pairs, together with distinct species-associated transcription-factor activity patterns. We also identified 25 ruminant-enriched genes associated with epithelial differentiation, ion transport, mucosal defense, and metabolism. Analysis of 69 samples from the rumen, reticulum, omasum, and abomasum of sheep, goats, cattle, and deer showed clear chamber-associated transcriptomic differences. The abomasum had a distinct expression program, with 235 enriched genes related to hormone regulation, secretion, transport, and digestion. Weighted gene co-expression network analysis further identified different gene programs in the forestomach and abomasum. Together, these findings reveal conserved, species-associated, and chamber-associated transcriptional features of the mammalian stomach and provide a useful framework for understanding its molecular diversity.<\/jats:p>","DOI":"10.3390\/biology15191677","type":"journal-article","created":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T08:17:54Z","timestamp":1790065074000},"page":"1677","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Multi-Species Transcriptomics of the Mammalian Stomach Reveals Conserved Programs and Ruminant Chamber Specialization"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0009-0007-5863-0039","authenticated-orcid":false,"given":"Qi-Xuan","family":"Huang","sequence":"first","affiliation":[{"name":"Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory of Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhi-Hui","family":"Wang","sequence":"additional","affiliation":[{"name":"Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory of Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8049-5565","authenticated-orcid":false,"given":"Wen-Tian","family":"Wei","sequence":"additional","affiliation":[{"name":"Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory of Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Si-Rui","family":"Liu","sequence":"additional","affiliation":[{"name":"Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory of Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi-Lin","family":"Bai","sequence":"additional","affiliation":[{"name":"Key Laboratory of Innovative Utilization of Local Cattle and Sheep Germplasm Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhengzhou University, Zhengzhou 450001, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yue-Yu","family":"Bai","sequence":"additional","affiliation":[{"name":"Key Laboratory of Innovative Utilization of Local Cattle and Sheep Germplasm Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhengzhou University, Zhengzhou 450001, China"},{"name":"Institute of Livestock Breeding and Reproduction, Henan University, Zhengzhou 450046, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meng-Hua","family":"Li","sequence":"additional","affiliation":[{"name":"Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory of Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Song-Song","family":"Xu","sequence":"additional","affiliation":[{"name":"Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory of Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,22]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1320","DOI":"10.3168\/jds.2009-2071","article-title":"Invited Review: Ruminant Ecology and Evolution: Perspectives Useful to Ruminant Livestock Research and Production","volume":"93","author":"Hackmann","year":"2010","journal-title":"J. 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