{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,20]],"date-time":"2026-07-20T08:02:09Z","timestamp":1784534529401,"version":"3.55.0"},"reference-count":70,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2026,6,11]],"date-time":"2026-06-11T00:00:00Z","timestamp":1781136000000},"content-version":"vor","delay-in-days":161,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003593","name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","doi-asserted-by":"publisher","award":["141039\/2024-8 and 125060\/2024-6"],"award-info":[{"award-number":["141039\/2024-8 and 125060\/2024-6"]}],"id":[{"id":"10.13039\/501100003593","id-type":"DOI","asserted-by":"publisher"}]},{"name":"The Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior Brasil\u2014(CAPES)\u2014Finance Code 001, Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo","award":["2024\/16026-3"],"award-info":[{"award-number":["2024\/16026-3"]}]},{"name":"The Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior Brasil\u2014(CAPES)\u2014Finance Code 001, Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo","award":["2024\/22254-9"],"award-info":[{"award-number":["2024\/22254-9"]}]},{"name":"The Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior Brasil\u2014(CAPES)\u2014Finance Code 001, Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo","award":["2022\/14260-3"],"award-info":[{"award-number":["2022\/14260-3"]}]}],"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 rumen microbiome represents a complex, phage-rich ecosystem where microbial survival depends on both metabolic cooperation and antiviral defense. However, global and breed-associated variations in rumen prokaryotic immune systems remain poorly understood. Here, we performed the most comprehensive profile to date of antiviral defense systems (DS) in the rumen, analyzing 6530 microbial genomes and metagenome-assembled genomes (MAGs) from diverse cattle breeds and geographic regions. In this global dataset, we identified &amp;gt;90\u2009000 DS, the most abundant of which were restriction-modification, PDC-S01, deoxyribonucleic acid modification systems (DMS_other), AbiE and SoFic, with variations influenced by both host the lineage and geographic region. A more in-depth analysis was performed using two complementary antiviral annotation frameworks for Nellore cattle (Bos indicus) from Brazil. Data exhibited a remarkably enriched antiviral defense repertoire, with over 15\u2009632 DS encoded across 547 high-quality MAGs. These systems were densely clustered in dominant rumen lineages, such as Prevotella, and positively correlated with prophage abundance, consistent with virus\u2013host coevolution. Notably, we also detected viral contigs encoding both antiviral defense and anti-defense genes, underscoring the arms race between the phages and their microbial hosts. Metatranscriptomic data from North America and Oceania revealed high expression levels of toxin-antitoxin modules, clustered regularly interspaced short palindromic repeats components, and restriction enzymes, suggesting a basal level of antiviral activity. These findings reveal the rumen as an antiviral innovation hotspot, highlighting microbiome resilience with implications for ecology, adaptation, and phage-based interventions.<\/jats:p>","DOI":"10.1093\/ismeco\/ycag162","type":"journal-article","created":{"date-parts":[[2026,6,11]],"date-time":"2026-06-11T11:48:43Z","timestamp":1781178523000},"source":"Crossref","is-referenced-by-count":0,"title":["Host breed and geography shape the antiviral defense landscape of the bovine rumen microbiome"],"prefix":"10.1093","volume":"6","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1851-7254","authenticated-orcid":false,"given":"Camila A","family":"Faleiros","sequence":"first","affiliation":[{"name":"Department of Veterinary Medicine, School of Animal Science and Food Engineering (FZEA), University of S\u00e3o Paulo , Avenida Duque de Caxias Norte, 225\u2014Jardim Elite, Pirassununga, SP 13635-900 ,","place":["Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6311-799X","authenticated-orcid":false,"given":"Osiel S","family":"Gon\u00e7alves","sequence":"additional","affiliation":[{"name":"Department of Veterinary Medicine, School of Animal Science and Food Engineering (FZEA), University of S\u00e3o Paulo , Avenida Duque de Caxias Norte, 225\u2014Jardim Elite, Pirassununga, SP 13635-900 ,","place":["Brazil"]},{"name":"Department of Biological Science, Microbial Eco-Evolutionary Genomics Group, Midwestern Parana State University (UNICENTRO). Campus CEDETEG , Alameda \u00c9lio Ant\u00f4nio Dalla Vecchia, 838\u2014Vila Carli, Guarapuava, PR 85040-167 ,","place":["Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alanne T","family":"Nunes","sequence":"additional","affiliation":[{"name":"Department of Veterinary Medicine, School of Animal Science and Food Engineering (FZEA), University of S\u00e3o Paulo , Avenida Duque de Caxias Norte, 225\u2014Jardim Elite, Pirassununga, SP 13635-900 ,","place":["Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Crislaine S","family":"Pires","sequence":"additional","affiliation":[{"name":"Department of Veterinary Medicine, School of Animal Science and Food Engineering (FZEA), University of S\u00e3o Paulo , Avenida Duque de Caxias Norte, 225\u2014Jardim Elite, Pirassununga, SP 13635-900 ,","place":["Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mirele D","family":"Poleti","sequence":"additional","affiliation":[{"name":"Department of Veterinary Medicine, School of Animal Science and Food Engineering (FZEA), University of S\u00e3o Paulo , Avenida Duque de Caxias Norte, 225\u2014Jardim Elite, Pirassununga, SP 13635-900 ,","place":["Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3265-5090","authenticated-orcid":false,"given":"Heidge","family":"Fukumasu","sequence":"additional","affiliation":[{"name":"Department of Veterinary Medicine, School of Animal Science and Food Engineering (FZEA), University of S\u00e3o Paulo , Avenida Duque de Caxias Norte, 225\u2014Jardim Elite, Pirassununga, SP 13635-900 ,","place":["Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,6,11]]},"reference":[{"key":"2026072003065471500_ref1","doi-asserted-by":"publisher","first-page":"463","DOI":"10.1126\/science.1200387","article-title":"Metagenomic discovery of biomass-degrading genes and genomes from cow rumen","volume":"331","author":"Hess","year":"2011","journal-title":"Science (1979)"},{"key":"2026072003065471500_ref2","doi-asserted-by":"publisher","first-page":"553","DOI":"10.1038\/s41579-021-00543-6","article-title":"The rumen microbiome: balancing food security and environmental impacts","volume":"19","author":"Mizrahi","year":"2021","journal-title":"Nat Rev Microbiol"},{"key":"2026072003065471500_ref3","doi-asserted-by":"publisher","first-page":"115925","DOI":"10.1016\/J.ENVRES.2023.115925","article-title":"Lignocellulose degradation by rumen bacterial communities: new insights from metagenome 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