{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T05:02:35Z","timestamp":1789448555388,"version":"build-2803163510"},"reference-count":53,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2026,7,12]],"date-time":"2026-07-12T00:00:00Z","timestamp":1783814400000},"content-version":"vor","delay-in-days":192,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/**","name":"HoloRuminant","doi-asserted-by":"publisher","id":[{"id":"10.13039\/**","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/**","name":"Irish Department of Agriculture Food and the Marine (DAFM) Research Stimulus Fund","doi-asserted-by":"publisher","award":["2023RP904 2023\u20132027"],"award-info":[{"award-number":["2023RP904 2023\u20132027"]}],"id":[{"id":"10.13039\/**","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/**","name":"RuminOmics","doi-asserted-by":"publisher","award":["289319"],"award-info":[{"award-number":["289319"]}],"id":[{"id":"10.13039\/**","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/**","name":"APIS-GENE","doi-asserted-by":"publisher","id":[{"id":"10.13039\/**","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/**","name":"Agence Nationale de la Recherche","doi-asserted-by":"publisher","award":["ANR-15-CE20-0014"],"award-info":[{"award-number":["ANR-15-CE20-0014"]}],"id":[{"id":"10.13039\/**","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,14]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The cattle rumen microbiota represents a complex and dynamic ecosystem whose organization and relationship to host phenotypes are important for food security and environmental sustainability. We analyzed rumen microbiota profiles from 2496 cattle representing five breeds and production systems across five countries, identifying microbial co-abundance groups termed Ruminosignatures. We detected 14 distinct Ruminosignatures, including 2 observed across all populations dominated by Prevotella and UBA2810. Additional Ruminosignatures showed breed- and diet-specific patterns and collectively explained 96%\u201399% of variance in rumen microbial composition. Integrative cross-country analysis confirmed 10 out of 14 Ruminosignatures identified in cohort-specific analyses. Several Ruminosignatures were associated with methane emissions and feed efficiency traits and were partially under host genetic control, with heritability estimates ranging from 0.09 to 0.58. Structural equation modeling revealed consistent negative genetic and phenotypic correlations between the UBA2810-dominated Ruminosignature (RS_UBA2) and methane emissions across cohorts (rg\u2009=\u2009\u22120.40 to \u22120.65), with structural coefficients concordant in sign across all populations, supporting the expected direction of phenotypic response to selection on RS_UBA2. Meta-analysis confirmed positive associations of RS_UBA2 with average daily gain and negative associations with methane-related traits and feed conversion ratio. Functional genome-based predictions suggested RS_UBA2 may reduce methanogenesis through alternative hydrogen utilization pathways competing with methanogenic archaea. Production system type influenced both Ruminosignature occurrence and relationships with host phenotypes, emphasizing the relevance of context-specific strategies for microbiome modulation. Our findings highlight the potential of the Ruminosignatures framework for microbiome-informed breeding programs aimed at improving feed efficiency while reducing the environmental impact of cattle production.<\/jats:p>","DOI":"10.1093\/ismejo\/wrag185","type":"journal-article","created":{"date-parts":[[2026,7,11]],"date-time":"2026-07-11T11:55:35Z","timestamp":1783770935000},"source":"Crossref","is-referenced-by-count":0,"title":["Ruminosignatures associated with methane emissions and feed efficiency across geographies and cattle breeds"],"prefix":"10.1093","volume":"20","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3381-5287","authenticated-orcid":false,"given":"Ioanna-Theoni","family":"Vourlaki","sequence":"first","affiliation":[{"name":"Animal Breeding and Genetics Program, IRTA, Torre Marimon , 08140 Caldes de Montbui ,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ori","family":"Furman","sequence":"additional","affiliation":[{"name":"Department of Life Sciences, Ben-Gurion University of the Negev , Beer-Sheva 84105 ,","place":["Israel"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ilma","family":"Tapio","sequence":"additional","affiliation":[{"name":"Genomics and Breeding, Natural Resources Finland (Luke) , Jokioinen 31600 ,","place":["Finland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8420-4371","authenticated-orcid":false,"given":"Le Luo","family":"Guan","sequence":"additional","affiliation":[{"name":"Faculty of Land and Food Systems, The University of British Columbia , V6T 1Z4 Vancouver ,","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sin\u00e9ad M","family":"Waters","sequence":"additional","affiliation":[{"name":"School of Biological and Chemical Sciences and Ryan Institute, University of Galway , Galway H91 TK33 ,","place":["Ireland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Kenny","sequence":"additional","affiliation":[{"name":"Animal and Bioscience Department, Teagasc Grange , Dunsany, Co. Meath C15 PW93 ,","place":["Ireland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6663-0422","authenticated-orcid":false,"given":"Paul","family":"Smith","sequence":"additional","affiliation":[{"name":"Animal and Bioscience Department, Teagasc Grange , Dunsany, Co. Meath C15 PW93 ,","place":["Ireland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stuart F","family":"Kirwan","sequence":"additional","affiliation":[{"name":"Department of Animal Science, University of California , Davis, CA 95616 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4776-3577","authenticated-orcid":false,"given":"David","family":"Kelly","sequence":"additional","affiliation":[{"name":"Irish Cattle Breeding Federation , Link Road, Ballincolling, Co. 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Cork, P31 D452 ,","place":["Ireland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Raquel","family":"Quintanilla","sequence":"additional","affiliation":[{"name":"Animal Breeding and Genetics Program, IRTA, Torre Marimon , 08140 Caldes de Montbui ,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Miriam","family":"Piles","sequence":"additional","affiliation":[{"name":"Animal Breeding and Genetics Program, IRTA, Torre Marimon , 08140 Caldes de Montbui ,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Antonio","family":"Reverter","sequence":"additional","affiliation":[{"name":"CSIRO Agriculture and Food, St. Lucia , Brisbane, QLD 4067 ,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"P\u00e2mela A","family":"Alexandre","sequence":"additional","affiliation":[{"name":"CSIRO Agriculture and Food, St. Lucia , Brisbane, QLD 4067 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