{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,3]],"date-time":"2026-11-03T02:28:00Z","timestamp":1793672880927,"version":"4.5.1"},"reference-count":94,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,7,11]],"date-time":"2026-07-11T00:00:00Z","timestamp":1783728000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2026,11,3]],"date-time":"2026-11-03T00:00:00Z","timestamp":1793664000000},"content-version":"vor","delay-in-days":115,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"name":"Yunnan Provincial Universities Service Key Industry Technology Project - Doctoral Student Industry-Oriented Scientific Research Innovation Training Project","award":["CY22624109"],"award-info":[{"award-number":["CY22624109"]}]},{"name":"Graduate Research and Innovation Project of Yunnan University","award":["KC-242410789"],"award-info":[{"award-number":["KC-242410789"]}],"id":[{"id":"https:\/\/ror.org\/0040axw97","id-type":"ROR","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2021YFD1200904"],"award-info":[{"award-number":["2021YFD1200904"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32470654"],"award-info":[{"award-number":["32470654"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Special funds for central guidance of local scientific and technological development","award":["202407AA110003"],"award-info":[{"award-number":["202407AA110003"]}]},{"name":"Major Program of Yunnan Fundamental Research Projects","award":["202601BC070001"],"award-info":[{"award-number":["202601BC070001"]}]},{"name":"\u201cXingdian Talent Support Program\u201d Grant of Yunnan Province","award":["XDYC-QNRC-2023-0371"],"award-info":[{"award-number":["XDYC-QNRC-2023-0371"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["npj Biofilms Microbiomes"],"DOI":"10.1038\/s41522-026-01095-4","type":"journal-article","created":{"date-parts":[[2026,7,11]],"date-time":"2026-07-11T03:33:47Z","timestamp":1783740827000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["A rugged life: how host-microbiome adaptations associated with the semi-feral lifestyle of gayal (Bos frontalis)"],"prefix":"10.1038","volume":"12","author":[{"given":"Yuming","family":"Chen","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juntao","family":"Ma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhifan","family":"Guo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junren","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaonan","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jian","family":"Xiao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dexiang","family":"Hu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jifan","family":"Yan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weidong","family":"Deng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhizhong","family":"Nu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Husheng","family":"He","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenliang","family":"He","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jing","family":"Luo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ya-Ping","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8643-4931","authenticated-orcid":false,"given":"Yan","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,7,11]]},"reference":[{"key":"1095_CR1","unstructured":"Simoons F. J. Gayal or Mithan. in Evolution of domesticated animals 34\u201339 (Longman, 1984)."},{"key":"1095_CR2","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1186\/s13002-017-0153-z","volume":"13","author":"Y Geng","year":"2017","unstructured":"Geng, Y. et al. Prioritizing fodder species based on traditional knowledge: a case study of mithun (Bos frontalis) in Dulongjiang area, Yunnan Province, Southwest China. J. Ethnobiol. Ethnomed. 13, 24 (2017).","journal-title":"J. Ethnobiol. Ethnomed."},{"key":"1095_CR3","doi-asserted-by":"publisher","first-page":"1139","DOI":"10.1038\/s41559-018-0562-y","volume":"2","author":"DD Wu","year":"2018","unstructured":"Wu, D. D. et al. Pervasive introgression facilitated domestication and adaptation in the Bos species complex. Nat. Ecol. Evol. 2, 1139\u20131145 (2018).","journal-title":"Nat. Ecol. Evol."},{"key":"1095_CR4","doi-asserted-by":"publisher","first-page":"353","DOI":"10.1038\/s42003-022-03298-9","volume":"5","author":"Y Chen","year":"2022","unstructured":"Chen, Y. et al. A draft genome of Drung cattle reveals clues to its chromosomal fusion and environmental adaptation. Commun. Biol. 5, 353 (2022).","journal-title":"Commun. Biol."},{"key":"1095_CR5","unstructured":"Jiang, Z. et al. China\u2019s red list of biodiversity: vertebrates. in China\u2019s Red List of Biodiversity (Science Press, 2021)."},{"key":"1095_CR6","doi-asserted-by":"publisher","first-page":"1368","DOI":"10.5713\/ajas.2014.14159","volume":"27","author":"R Md Uzzaman","year":"2014","unstructured":"Md Uzzaman, R., Md Bhuiyan, S. A., Edea, Z. & Kim, K.-S. Semi-domesticated and Irreplaceable Genetic Resource Gayal (Bos frontalis) Needs Effective Genetic Conservation in Bangladesh: A Review. Asian-Australas. J. Anim. Sci. 27, 1368\u20131372 (2014).","journal-title":"Asian-Australas. J. Anim. Sci."},{"key":"1095_CR7","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msad006","volume":"40","author":"Y Li","year":"2023","unstructured":"Li, Y. et al. Large-scale chromosomal changes lead to genome-level expression alterations, environmental adaptation, and speciation in the gayal (Bos frontalis). Mol. Biol. Evol. 40, msad006 (2023).","journal-title":"Mol. Biol. Evol."},{"key":"1095_CR8","unstructured":"Food and Agriculture Organization of the United Nations. World Watch List for Domestic Animal Diversity 3rd edition (eds Scherf, B. D.) 651\u2013652 (Food and Agriculture Organization of the United Nations, 2000)."},{"key":"1095_CR9","first-page":"401","volume":"13","author":"Y Tian","year":"1998","unstructured":"Tian, Y., Ge, C. & Xie, P. Studies on the histologic structure and characteristics of striated muscle in Yunnan native cattle. J. Yunnan Agric. Univ. 13, 401\u2013406 (1998).","journal-title":"J. Yunnan Agric. Univ."},{"key":"1095_CR10","doi-asserted-by":"publisher","first-page":"1245","DOI":"10.5713\/ajas.2001.1245","volume":"14","author":"KS Huque","year":"2001","unstructured":"Huque, K. S., Rahman, M. M. & Jalil, M. A. Study on the growth pattern of Gayals (Bos Frontalis) and their crossbred calves. Asian-Australas. J. Anim. Sci. 14, 1245\u20131249 (2001).","journal-title":"Asian-Australas. J. Anim. Sci."},{"key":"1095_CR11","doi-asserted-by":"publisher","first-page":"1599","DOI":"10.5713\/ajas.2003.1599","volume":"16","author":"M Giasuddin","year":"2003","unstructured":"Giasuddin, M. & Islam, M. R. Physical Feature, physiological character and behavior study of Gayal (Bos frontalis). Asian-Australas. J. Anim. Sci. 16, 1599\u20131603 (2003).","journal-title":"Asian-Australas. J. Anim. Sci."},{"key":"1095_CR12","first-page":"103","volume":"69","author":"OJ Babayemi","year":"2004","unstructured":"Babayemi, O. J., Demeyer, D. & Fievez, V. Nutritive value and qualitative assessment of secondary compounds in seeds of eight tropical browse, shrub and pulse legumes. Commun. Agric. Appl. Biol. Sci. 69, 103\u2013110 (2004).","journal-title":"Commun. Agric. Appl. Biol. Sci."},{"key":"1095_CR13","doi-asserted-by":"publisher","first-page":"1208","DOI":"10.5713\/ajas.2007.1208","volume":"20","author":"D Xi","year":"2007","unstructured":"Xi, D. et al. Comparison of Gayal (Bos frontalis) and Yunnan Yellow Cattle (Bos taurus): in vitro dry matter digestibility and gas production for a range of forages. Asian-Australas. J. Anim. Sci. 20, 1208\u20131214 (2007).","journal-title":"Asian-Australas. J. Anim. Sci."},{"key":"1095_CR14","doi-asserted-by":"publisher","first-page":"1559","DOI":"10.3923\/pjbs.2001.1559.1561","volume":"4","author":"K Huque","year":"2001","unstructured":"Huque, K., Rahman, M. & Jalil, M. Nutritive value of major feed ingredients, usually browsed and their responses to Gayals (Bos frontalis) in the hill tract area. Pak. J. Biol. Sci. 4, 1559\u20131561 (2001).","journal-title":"Pak. J. Biol. Sci."},{"key":"1095_CR15","doi-asserted-by":"crossref","unstructured":"Karasov, W. H. & del Rio, C. M. Physiological Ecology: How Animals Process Energy, Nutrients, and Toxins (Princeton University Press, 2007).","DOI":"10.1515\/9780691213316"},{"key":"1095_CR16","doi-asserted-by":"publisher","first-page":"556","DOI":"10.1186\/s12866-025-04199-7","volume":"25","author":"W Peng","year":"2025","unstructured":"Peng, W. et al. Effects of changes in rumen microbial adaptability on rumen fermentation and nutrient digestion in Horqin beef cattle during different seasons of grazing and supplementary feeding. BMC Microbiol. 25, 556 (2025).","journal-title":"BMC Microbiol."},{"key":"1095_CR17","doi-asserted-by":"publisher","DOI":"10.1016\/j.envres.2023.115925","volume":"229","author":"J Gharechahi","year":"2023","unstructured":"Gharechahi, J. et al. Lignocellulose degradation by rumen bacterial communities: new insights from metagenome analyses. Environ. Res. 229, 115925 (2023).","journal-title":"Environ. Res."},{"key":"1095_CR18","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3389\/fvets.2023.1204706","volume":"10","author":"Y Liu","year":"2023","unstructured":"Liu, Y. et al. Transcriptome profiling in rumen, reticulum, omasum, and abomasum tissues during the developmental transition of pre-ruminant to the ruminant in yaks. Front. Vet. Sci. 10, 1\u201310 (2023).","journal-title":"Front. Vet. Sci."},{"key":"1095_CR19","doi-asserted-by":"publisher","first-page":"734","DOI":"10.1007\/s12275-018-8133-0","volume":"56","author":"D Xue","year":"2018","unstructured":"Xue, D. et al. Microbial diversity in the rumen, reticulum, omasum, and abomasum of yak on a rapid fattening regime in an agro-pastoral transition zone. J. Microbiol. 56, 734\u2013743 (2018).","journal-title":"J. Microbiol."},{"key":"1095_CR20","doi-asserted-by":"publisher","DOI":"10.1002\/advs.202514862","volume":"13","author":"C Huang","year":"2025","unstructured":"Huang, C. et al. The high-altitude adaptation characteristics of microbiota-host cross-talk in Yak gastrointestinal track. Adv. Sci. 13, e14862 (2025).","journal-title":"Adv. Sci."},{"key":"1095_CR21","first-page":"1","volume":"13","author":"Y Zhang","year":"2022","unstructured":"Zhang, Y. et al. Transcriptome analysis of bovine rumen tissue in three developmental stages. Front. Genet. 13, 1\u201310 (2022).","journal-title":"Front. Genet."},{"key":"1095_CR22","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41597-025-04927-8","volume":"12","author":"G Z","year":"2025","unstructured":"Z, G. et al. De novo transcriptome assembly and annotation of the semi-wild Gayal (Bos frontalis). Sci. Data 12, 1\u20139 (2025).","journal-title":"Sci. Data"},{"key":"1095_CR23","doi-asserted-by":"publisher","first-page":"4863","DOI":"10.1007\/s11033-010-0627-8","volume":"38","author":"J Leng","year":"2011","unstructured":"Leng, J. et al. Dominant bacterial communities in the rumen of Gayals (Bos frontalis), Yaks (Bos grunniens) and Yunnan Yellow Cattle (Bos taurs) revealed by denaturing gradient gel electrophoresis. Mol. Biol. Rep. 38, 4863\u20134872 (2011).","journal-title":"Mol. Biol. Rep."},{"key":"1095_CR24","doi-asserted-by":"publisher","first-page":"900","DOI":"10.5713\/ajas.2007.900","volume":"20","author":"W Deng","year":"2007","unstructured":"Deng, W. et al. Comparison of Gayal (Bos frontalis) and Yunnan Yellow Cattle (Bos taurus): rumen function, digestibilities and nitrogen balance during feeding of pelleted Lucerne (Medicago sativum). Asian-Australas. J. Anim. Sci. 20, 900\u2013907 (2007).","journal-title":"Asian-Australas. J. Anim. Sci."},{"key":"1095_CR25","doi-asserted-by":"publisher","first-page":"1098","DOI":"10.3390\/microorganisms11051098","volume":"11","author":"H Gao","year":"2023","unstructured":"Gao, H. et al. Metagenomic sequencing reveals the taxonomic and functional characteristics of rumen micro-organisms in Gayals. Microorganisms 11, 1098 (2023).","journal-title":"Microorganisms"},{"key":"1095_CR26","first-page":"121","volume":"58","author":"K Rohde","year":"2008","unstructured":"Rohde, K. & Rohde, P. P. How to measure ecological host specificity. Vie et. Milieu 58, 121\u2013124 (2008).","journal-title":"Vie et. Milieu"},{"key":"1095_CR27","doi-asserted-by":"publisher","first-page":"627","DOI":"10.1086\/283303","volume":"112","author":"M Westoby","year":"1978","unstructured":"Westoby, M. What are the biological bases of varied diets? Am. Nat. 112, 627\u2013631 (1978).","journal-title":"Am. Nat."},{"key":"1095_CR28","doi-asserted-by":"publisher","first-page":"276","DOI":"10.1016\/S0034-5288(18)31947-7","volume":"36","author":"H Winter","year":"1984","unstructured":"Winter, H. et al. Karyotyping, red blood cell and haemoglobin typing of the mithun (Bos frontalis), its wild ancestor and its hybrids. Res. Vet. Sci. 36, 276\u2013283 (1984).","journal-title":"Res. Vet. Sci."},{"key":"1095_CR29","doi-asserted-by":"publisher","first-page":"789","DOI":"10.1101\/gr.231159.117","volume":"28","author":"SG Nergadze","year":"2018","unstructured":"Nergadze, S. G. et al. Birth, evolution, and transmission of satellite-free mammalian centromeric domains. Genome Res. 28, 789\u2013799 (2018).","journal-title":"Genome Res."},{"key":"1095_CR30","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1016\/S0378-1127(03)00124-5","volume":"181","author":"IJ Gordon","year":"2003","unstructured":"Gordon, I. J. Browsing and grazing ruminants: are they different beasts? For. Ecol. Manag. 181, 13\u201321 (2003).","journal-title":"For. Ecol. Manag."},{"key":"1095_CR31","doi-asserted-by":"crossref","unstructured":"Garc\u00eda-Yuste, S. & P\u00e9rez-Barber\u00eda, F. J. The ruminant: life history and digestive physiology of a symbiotic animal 19\u201345 (Springer International Publishing, 2020).","DOI":"10.1007\/978-3-030-46060-0_2"},{"key":"1095_CR32","doi-asserted-by":"publisher","first-page":"425","DOI":"10.3390\/ani16030425","volume":"16","author":"H Priyashantha","year":"2026","unstructured":"Priyashantha, H. et al. Phytochemicals in ruminant diets: mechanistic insights, product quality enhancement, and pathways to sustainable milk and meat production\u2014invited review. Animals 16, 425 (2026).","journal-title":"Animals"},{"key":"1095_CR33","unstructured":"Matabane, D. M., Ng\u2019ambi, J. W., Mabelebele, M., Gunya, B. & Manyelo, T. G. The role of secondary metabolites on methane reduction in small ruminants. in Latest Scientific Findings in Ruminant Nutrition - Research for Practical Implementation (IntechOpen, 2024)."},{"key":"1095_CR34","doi-asserted-by":"publisher","DOI":"10.3389\/fvets.2021.628445","volume":"8","author":"LO Tedeschi","year":"2021","unstructured":"Tedeschi, L. O. et al. Nutritional aspects of ecologically relevant phytochemicals in ruminant production. Front. Vet. Sci. 8, 628445 (2021).","journal-title":"Front. Vet. Sci."},{"key":"1095_CR35","doi-asserted-by":"publisher","unstructured":"Okaiyeto, S. A. et al. Anti-nutrients of plant-based food: physicochemical properties, effects on health and degradation techniques- a comprehensive review. J. Future Foods https:\/\/doi.org\/10.1016\/j.jfutfo.2025.06.022 (2025).","DOI":"10.1016\/j.jfutfo.2025.06.022"},{"key":"1095_CR36","doi-asserted-by":"publisher","first-page":"1516","DOI":"10.2527\/1995.7351516x","volume":"73","author":"JD Reed","year":"1995","unstructured":"Reed, J. D. Nutritional toxicology of tannins and related polyphenols in forage legumes. J. Anim. Sci. 73, 1516\u20131528 (1995).","journal-title":"J. Anim. Sci."},{"key":"1095_CR37","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3389\/fmicb.2025.1554271","volume":"16","author":"R Fu","year":"2025","unstructured":"Fu, R. et al. Studies on the concerted interaction of microbes in the gastrointestinal tract of ruminants on lignocellulose and its degradation mechanism. Front. Microbiol. 16, 1\u201319 (2025).","journal-title":"Front. Microbiol."},{"key":"1095_CR38","doi-asserted-by":"publisher","first-page":"279","DOI":"10.1146\/annurev-micro-092412-155618","volume":"68","author":"BA White","year":"2014","unstructured":"White, B. A., Lamed, R., Bayer, E. A. & Flint, H. J. Biomass utilization by gut microbiomes. Annu Rev. Microbiol. 68, 279\u2013296 (2014).","journal-title":"Annu Rev. Microbiol."},{"key":"1095_CR39","doi-asserted-by":"publisher","first-page":"79","DOI":"10.1186\/s40104-021-00599-7","volume":"12","author":"DRG Lopes","year":"2021","unstructured":"Lopes, D. R. G. et al. Assessing the relationship between the rumen microbiota and feed efficiency in Nellore steers. J. Anim. Sci. Biotechnol. 12, 79 (2021).","journal-title":"J. Anim. Sci. Biotechnol."},{"key":"1095_CR40","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-019-0699-1","volume":"7","author":"F Li","year":"2019","unstructured":"Li, F. et al. Host genetics influence the rumen microbiota and heritable rumen microbial features associate with feed efficiency in cattle. Microbiome 7, 92 (2019).","journal-title":"Microbiome"},{"key":"1095_CR41","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1038\/s41559-025-02904-3","volume":"10","author":"OE Tovar-Herrera","year":"2026","unstructured":"Tovar-Herrera, O. E. et al. Core rumen microbes are functional generalists that sustain host metabolism and gut ecosystem function. Nat. Ecol. Evol. 10, 44\u201358 (2026).","journal-title":"Nat. Ecol. Evol."},{"key":"1095_CR42","doi-asserted-by":"publisher","first-page":"916","DOI":"10.1111\/1749-4877.12830","volume":"20","author":"H Liu","year":"2025","unstructured":"Liu, H. et al. Multi-omics reveal the gut microbiota-mediated severe foraging environment adaption of small wild ruminants in the Three-River-Source National Park, China. Integr. Zool. 20, 916\u2013935 (2025).","journal-title":"Integr. Zool."},{"key":"1095_CR43","doi-asserted-by":"crossref","unstructured":"Pinnell, L. J. et al. Bacteroidetes and firmicutes drive differing microbial diversity and community composition among micro-environments in the bovine rumen. Front. Vet. Sci. 9, 897996 (2022).","DOI":"10.3389\/fvets.2022.897996"},{"key":"1095_CR44","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.00563-25","volume":"13","author":"AM Buckner","year":"2025","unstructured":"Buckner, A. M. et al. The selective culture and enrichment of major rumen bacteria on three distinct anaerobic culture media. Microbiol. Spectr. 13, e0056325 (2025).","journal-title":"Microbiol. Spectr."},{"key":"1095_CR45","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2025.1709019","volume":"16","author":"J Ru","year":"2025","unstructured":"Ru, J. et al. Screening of microbial consortium with high efficiency of lignin-degrading and its synergistic metabolic mechanism. Front. Microbiol. 16, 1709019 (2025).","journal-title":"Front. Microbiol."},{"key":"1095_CR46","doi-asserted-by":"publisher","first-page":"a040592","DOI":"10.1101\/cshperspect.a040592","volume":"13","author":"NS Chandel","year":"2021","unstructured":"Chandel, N. S. Nucleotide Metabolism. Cold Spring Harb. Perspect. Biol. 13, a040592 (2021).","journal-title":"Cold Spring Harb. Perspect. Biol."},{"key":"1095_CR47","doi-asserted-by":"publisher","first-page":"495","DOI":"10.3168\/jds.2012-5810","volume":"96","author":"EA Elwakeel","year":"2013","unstructured":"Elwakeel, E. A. et al. In vitro degradation of lysine by ruminal fluid-based fermentations and by Fusobacterium necrophorum. J. Dairy Sci. 96, 495\u2013505 (2013).","journal-title":"J. Dairy Sci."},{"key":"1095_CR48","doi-asserted-by":"publisher","first-page":"325","DOI":"10.1038\/mi.2010.71","volume":"4","author":"CU Duerr","year":"2011","unstructured":"Duerr, C. U. et al. Control of intestinal Nod2-mediated peptidoglycan recognition by epithelium-associated lymphocytes. Mucosal Immunol. 4, 325\u2013334 (2011).","journal-title":"Mucosal Immunol."},{"key":"1095_CR49","doi-asserted-by":"publisher","first-page":"261","DOI":"10.1038\/85330","volume":"2","author":"Y Latchman","year":"2001","unstructured":"Latchman, Y. et al. PD-L2 is a second ligand for PD-1 and inhibits T cell activation. Nat. Immunol. 2, 261\u2013268 (2001).","journal-title":"Nat. Immunol."},{"key":"1095_CR50","doi-asserted-by":"publisher","first-page":"1623","DOI":"10.1126\/science.1255904","volume":"345","author":"HS Kuehn","year":"2014","unstructured":"Kuehn, H. S. et al. Immune dysregulation in human subjects with heterozygous germline mutations in CTLA4. Science 345, 1623\u20131627 (2014).","journal-title":"Science"},{"key":"1095_CR51","doi-asserted-by":"publisher","first-page":"3520","DOI":"10.4049\/jimmunol.180.5.3520","volume":"180","author":"K Dower","year":"2008","unstructured":"Dower, K., Ellis, D. K., Saraf, K., Jelinsky, S. A. & Lin, L.-L. Innate immune responses to TREM-1 activation: overlap, divergence, and positive and negative cross-talk with bacterial lipopolysaccharide. J. Immunol. 180, 3520\u20133534 (2008).","journal-title":"J. Immunol."},{"key":"1095_CR52","doi-asserted-by":"publisher","first-page":"776","DOI":"10.1016\/j.immuni.2014.10.007","volume":"41","author":"N Satoh-Takayama","year":"2014","unstructured":"Satoh-Takayama, N. et al. The chemokine receptor CXCR6 controls the functional topography of interleukin-22 producing intestinal innate lymphoid cells. Immunity 41, 776\u2013788 (2014).","journal-title":"Immunity"},{"key":"1095_CR53","doi-asserted-by":"publisher","first-page":"562","DOI":"10.1016\/j.immuni.2017.04.008","volume":"46","author":"Y Belkaid","year":"2017","unstructured":"Belkaid, Y. & Harrison, O. J. Homeostatic immunity and the microbiota. Immunity 46, 562\u2013576 (2017).","journal-title":"Immunity"},{"key":"1095_CR54","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1007\/s12026-012-8308-4","volume":"54","author":"L Steele","year":"2012","unstructured":"Steele, L., Mayer, L. & Berin, M. C. Mucosal immunology of tolerance and allergy in the gastrointestinal tract. Immunol. Res. 54, 75\u201382 (2012).","journal-title":"Immunol. Res."},{"key":"1095_CR55","doi-asserted-by":"publisher","first-page":"451","DOI":"10.1097\/FJC.0b013e31821c0220","volume":"58","author":"GK Carnegie","year":"2011","unstructured":"Carnegie, G. K. & Burmeister, B. T. A-kinase anchoring proteins that regulate cardiac remodeling. J. Cardiovasc. Pharm. 58, 451\u2013458 (2011).","journal-title":"J. Cardiovasc. Pharm."},{"key":"1095_CR56","doi-asserted-by":"publisher","first-page":"105","DOI":"10.1085\/jgp.201511507","volume":"147","author":"E Bocksteins","year":"2016","unstructured":"Bocksteins, E. Kv5, Kv6, Kv8, and Kv9 subunits: no simple silent bystanders. J. Gen. Physiol. 147, 105\u2013125 (2016).","journal-title":"J. Gen. Physiol."},{"key":"1095_CR57","first-page":"1","volume":"12","author":"L Zhu","year":"2021","unstructured":"Zhu, L., Wang, J. & Bahrndorff, S. Editorial: the wildlife gut microbiome and its implication for conservation biology. Front. Microbiol. 12, 1\u20134 (2021).","journal-title":"Front. Microbiol."},{"key":"1095_CR58","doi-asserted-by":"publisher","first-page":"e3000410","DOI":"10.1371\/journal.pbio.3000410","volume":"18","author":"N Percie du Sert","year":"2020","unstructured":"Percie du Sert, N. et al. The ARRIVE guidelines 2.0: Updated guidelines for reporting animal research. PLoS Biol. 18, e3000410 (2020).","journal-title":"PLoS Biol."},{"key":"1095_CR59","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-021-01078-x","volume":"9","author":"F Xie","year":"2021","unstructured":"Xie, F. et al. An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants. Microbiome 9, 137 (2021).","journal-title":"Microbiome"},{"key":"1095_CR60","doi-asserted-by":"publisher","first-page":"790","DOI":"10.1101\/gr.250704.119","volume":"30","author":"L Fang","year":"2020","unstructured":"Fang, L. et al. Comprehensive analyses of 723 transcriptomes enhance genetic and biological interpretations for complex traits in cattle. Genome Res. 30, 790\u2013801 (2020).","journal-title":"Genome Res."},{"key":"1095_CR61","doi-asserted-by":"publisher","first-page":"302","DOI":"10.1186\/s12866-020-01993-3","volume":"20","author":"G Gong","year":"2020","unstructured":"Gong, G., Zhou, S., Luo, R., Gesang, Z. & Suolang, S. Metagenomic insights into the diversity of carbohydrate-degrading enzymes in the yak fecal microbial community. BMC Microbiol. 20, 302 (2020).","journal-title":"BMC Microbiol."},{"key":"1095_CR62","doi-asserted-by":"crossref","unstructured":"Fu, H. et al. Domestication shapes the community structure and functional metagenomic content of the yak fecal microbiota. Front. Microbiol. 12, 594075 (2021).","DOI":"10.3389\/fmicb.2021.594075"},{"key":"1095_CR63","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-28402-9","volume":"13","author":"F Tong","year":"2022","unstructured":"Tong, F. et al. The microbiome of the buffalo digestive tract. Nat. Commun. 13, 823 (2022).","journal-title":"Nat. Commun."},{"key":"1095_CR64","doi-asserted-by":"publisher","DOI":"10.1128\/msphere.00738-24","volume":"10","author":"J Kwon","year":"2025","unstructured":"Kwon, J. et al. Prospective comparison of the digestive tract resistome and microbiota in cattle raised in grass-fed versus grain-fed production systems. mSphere 10, e0073824 (2025).","journal-title":"mSphere"},{"key":"1095_CR65","doi-asserted-by":"publisher","DOI":"10.1038\/s41597-025-04919-8","volume":"12","author":"TPRA Legrand","year":"2025","unstructured":"Legrand, T. P. R. A. et al. Genome-centric metagenomics reveals uncharacterised microbiomes in Angus cattle. Sci. Data 12, 547 (2025).","journal-title":"Sci. Data"},{"key":"1095_CR66","doi-asserted-by":"crossref","unstructured":"Chen, Z. et al. Differences in meat quality between Angus cattle and Xinjiang brown cattle in association with gut microbiota and its lipid metabolism. Front. Microbiol. 13, 988984 (2022).","DOI":"10.3389\/fmicb.2022.988984"},{"key":"1095_CR67","doi-asserted-by":"crossref","unstructured":"Conteville, L. C. et al. Rumen and fecal microbiomes are related to diet and production traits in Bos indicus beef cattle. Front. Microbiol. 14, 1282851 (2023).","DOI":"10.3389\/fmicb.2023.1282851"},{"key":"1095_CR68","doi-asserted-by":"publisher","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","volume":"34","author":"S Chen","year":"2018","unstructured":"Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884\u2013i890 (2018).","journal-title":"Bioinformatics"},{"key":"1095_CR69","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","volume":"30","author":"AM Bolger","year":"2014","unstructured":"Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114\u20132120 (2014).","journal-title":"Bioinformatics"},{"key":"1095_CR70","doi-asserted-by":"publisher","first-page":"8019","DOI":"10.1073\/pnas.1503283112","volume":"112","author":"TR Kartzinel","year":"2015","unstructured":"Kartzinel, T. R. et al. DNA metabarcoding illuminates dietary niche partitioning by African large herbivores. Proc. Natl. Acad. Sci. USA 112, 8019\u20138024 (2015).","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"1095_CR71","doi-asserted-by":"publisher","first-page":"333","DOI":"10.1111\/j.2041-210X.2011.00092.x","volume":"2","author":"KS Burgess","year":"2011","unstructured":"Burgess, K. S. et al. Discriminating plant species in a local temperate flora using the rbcL+matK DNA barcode. Methods Ecol. Evol. 2, 333\u2013340 (2011).","journal-title":"Methods Ecol. Evol."},{"key":"1095_CR72","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1093\/nar\/gkl938","volume":"35","author":"P Taberlet","year":"2007","unstructured":"Taberlet, P. et al. Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding. Nucleic Acids Res. 35, 1\u20138 (2007).","journal-title":"Nucleic Acids Res."},{"key":"1095_CR73","doi-asserted-by":"publisher","first-page":"782663","DOI":"10.3389\/fpls.2021.782663","volume":"12","author":"L Matiz-Ceron","year":"2021","unstructured":"Matiz-Ceron, L., Reyes, A. & Anzola, J. Taxonomical evaluation of plant chloroplastic markers by Bayesian classifier. Front. Plant Sci. 12, 782663 (2021).","journal-title":"Front. Plant Sci."},{"key":"1095_CR74","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","volume":"215","author":"SF Altschul","year":"1990","unstructured":"Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403\u2013410 (1990).","journal-title":"J. Mol. Biol."},{"key":"1095_CR75","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","volume":"9","author":"B Langmead","year":"2012","unstructured":"Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357\u2013359 (2012).","journal-title":"Nat. Methods"},{"key":"1095_CR76","doi-asserted-by":"publisher","first-page":"e2584","DOI":"10.7717\/peerj.2584","volume":"4","author":"T Rognes","year":"2016","unstructured":"Rognes, T., Flouri, T., Nichols, B., Quince, C. & Mah\u00e9, F. VSEARCH: a versatile open source tool for metagenomics. PeerJ 4, e2584 (2016).","journal-title":"PeerJ"},{"key":"1095_CR77","doi-asserted-by":"publisher","first-page":"1674","DOI":"10.1093\/bioinformatics\/btv033","volume":"31","author":"D Li","year":"2015","unstructured":"Li, D., Liu, C.-M., Luo, R., Sadakane, K. & Lam, T.-W. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 31, 1674\u20131676 (2015).","journal-title":"Bioinformatics"},{"key":"1095_CR78","doi-asserted-by":"publisher","first-page":"1088","DOI":"10.1093\/bioinformatics\/btv697","volume":"32","author":"A Mikheenko","year":"2016","unstructured":"Mikheenko, A., Saveliev, V. & Gurevich, A. MetaQUAST: evaluation of metagenome assemblies. Bioinformatics 32, 1088\u20131090 (2016).","journal-title":"Bioinformatics"},{"key":"1095_CR79","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-018-0541-1","volume":"6","author":"GV Uritskiy","year":"2018","unstructured":"Uritskiy, G. V., DiRuggiero, J. & Taylor, J. MetaWRAP\u2014a flexible pipeline for genome-resolved metagenomic data analysis. Microbiome 6, 158 (2018).","journal-title":"Microbiome"},{"key":"1095_CR80","doi-asserted-by":"publisher","first-page":"1043","DOI":"10.1101\/gr.186072.114","volume":"25","author":"DH Parks","year":"2015","unstructured":"Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P. & Tyson, G. W. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 25, 1043\u20131055 (2015).","journal-title":"Genome Res."},{"key":"1095_CR81","doi-asserted-by":"publisher","first-page":"2864","DOI":"10.1038\/ismej.2017.126","volume":"11","author":"MR Olm","year":"2017","unstructured":"Olm, M. R., Brown, C. T., Brooks, B. & Banfield, J. F. dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. ISME J. 11, 2864\u20132868 (2017).","journal-title":"ISME J."},{"key":"1095_CR82","doi-asserted-by":"publisher","first-page":"1925","DOI":"10.1093\/bioinformatics\/btz848","volume":"36","author":"P-A Chaumeil","year":"2019","unstructured":"Chaumeil, P.-A., Mussig, A. J., Hugenholtz, P. & Parks, D. H. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics 36, 1925\u20131927 (2019).","journal-title":"Bioinformatics"},{"key":"1095_CR83","doi-asserted-by":"publisher","first-page":"W78","DOI":"10.1093\/nar\/gkae268","volume":"52","author":"I Letunic","year":"2024","unstructured":"Letunic, I. & Bork, P. Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool. Nucleic Acids Res. 52, W78\u2013W82 (2024).","journal-title":"Nucleic Acids Res."},{"key":"1095_CR84","doi-asserted-by":"crossref","unstructured":"Anderson, M. J. Permutational multivariate analysis of variance (PERMANOVA). in Wiley StatsRef: Statistics Reference Online 1\u201315 (John Wiley & Sons, 2017).","DOI":"10.1002\/9781118445112.stat07841"},{"key":"1095_CR85","doi-asserted-by":"publisher","first-page":"e30126","DOI":"10.1371\/journal.pone.0030126","volume":"7","author":"I Holmes","year":"2012","unstructured":"Holmes, I., Harris, K. & Quince, C. Dirichlet multinomial mixtures: generative models for microbial metagenomics. PLoS ONE 7, e30126 (2012).","journal-title":"PLoS ONE"},{"key":"1095_CR86","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-11-119","volume":"11","author":"D Hyatt","year":"2010","unstructured":"Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform. 11, 119 (2010).","journal-title":"BMC Bioinform."},{"key":"1095_CR87","doi-asserted-by":"publisher","first-page":"366","DOI":"10.1038\/s41592-021-01101-x","volume":"18","author":"B Buchfink","year":"2021","unstructured":"Buchfink, B., Reuter, K. & Drost, H.-G. Sensitive protein alignments at tree-of-life scale using DIAMOND. Nat. Methods 18, 366\u2013368 (2021).","journal-title":"Nat. Methods"},{"key":"1095_CR88","doi-asserted-by":"publisher","DOI":"10.1002\/imt2.83","volume":"2","author":"Y-X Liu","year":"2023","unstructured":"Liu, Y.-X. et al. EasyAmplicon: An easy-to-use, open-source, reproducible, and community-based pipeline for amplicon data analysis in microbiome research. iMeta 2, e83 (2023).","journal-title":"iMeta"},{"key":"1095_CR89","doi-asserted-by":"publisher","first-page":"bbae116","DOI":"10.1093\/bib\/bbae116","volume":"25","author":"C Peng","year":"2024","unstructured":"Peng, C., Chen, Q., Tan, S., Shen, X. & Jiang, C. Generalized reporter score-based enrichment analysis for omics data. Brief. Bioinform. 25, bbae116 (2024).","journal-title":"Brief. Bioinform."},{"key":"1095_CR90","doi-asserted-by":"publisher","first-page":"907","DOI":"10.1038\/s41587-019-0201-4","volume":"37","author":"D Kim","year":"2019","unstructured":"Kim, D., Paggi, J. M., Park, C., Bennett, C. & Salzberg, S. L. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat. Biotechnol. 37, 907\u2013915 (2019).","journal-title":"Nat. Biotechnol."},{"key":"1095_CR91","doi-asserted-by":"publisher","first-page":"e108","DOI":"10.1093\/nar\/gkt214","volume":"41","author":"Y Liao","year":"2013","unstructured":"Liao, Y., Smyth, G. K. & Shi, W. The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote. Nucleic Acids Res. 41, e108 (2013).","journal-title":"Nucleic Acids Res."},{"key":"1095_CR92","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-9-559","volume":"9","author":"P Langfelder","year":"2008","unstructured":"Langfelder, P. & Horvath, S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinform. 9, 559 (2008).","journal-title":"BMC Bioinform."},{"key":"1095_CR93","doi-asserted-by":"publisher","first-page":"5","DOI":"10.6026\/97320630002005","volume":"2","author":"L Kumar","year":"2007","unstructured":"Kumar, L. & Futschik, M. E. Mfuzz: a software package for soft clustering of microarray data. Bioinformation 2, 5\u20137 (2007).","journal-title":"Bioinformation"},{"key":"1095_CR94","doi-asserted-by":"publisher","first-page":"284","DOI":"10.1089\/omi.2011.0118","volume":"16","author":"G Yu","year":"2012","unstructured":"Yu, G., Wang, L.-G., Han, Y. & He, Q.-Y. clusterProfiler: an R Package for comparing biological themes among gene clusters. OMICS 16, 284\u2013287 (2012).","journal-title":"OMICS"}],"container-title":["npj Biofilms and Microbiomes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41522-026-01095-4","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41522-026-01095-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41522-026-01095-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,11,3]],"date-time":"2026-11-03T02:03:21Z","timestamp":1793671401000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41522-026-01095-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,11]]},"references-count":94,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["1095"],"URL":"https:\/\/doi.org\/10.1038\/s41522-026-01095-4","relation":{},"ISSN":["2055-5008"],"issn-type":[{"value":"2055-5008","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,11]]},"assertion":[{"value":"14 February 2026","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"3 July 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"11 July 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Ethics"}}],"article-number":"221"}}