{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,4]],"date-time":"2026-08-04T14:49:37Z","timestamp":1785854977183,"version":"3.56.0"},"reference-count":73,"publisher":"Oxford University Press (OUP)","funder":[{"name":"USDA-National Institute of Food and Agriculture","award":["2022-33522-38219"],"award-info":[{"award-number":["2022-33522-38219"]}]},{"name":"USDA-National Institute of Food and Agriculture","award":["2023-68015-40015"],"award-info":[{"award-number":["2023-68015-40015"]}]},{"name":"USDA-National Institute of Food and Agriculture","award":["2024-33522-43699"],"award-info":[{"award-number":["2024-33522-43699"]}]},{"name":"USDA-National Institute of Food and Agriculture","award":["2018-67015-27496"],"award-info":[{"award-number":["2018-67015-27496"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,8]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Cattle rely on the microorganisms in their rumen to break down plant matter into useable nutrients. Studies have demonstrated that the rumen microbiome plays a critical role in economically important traits. One factor that impacts rumen microbial community assembly is the host genome. Previous studies have demonstrated host genetics affect rumen microbial community composition and the association of microbiome features with production traits. However, gaps exist relative to the underlying host genetic influence on functional features of the rumen metagenome. Here we elucidated the relationship between host genetics and functional composition of the rumen metagenome while identifying metagenomic features which may provide targets for genetic selection. Rumen samples were collected via esophageal tubing from 717 beef cattle on four diets and were subjected to shotgun sequencing from which open reading frames (ORFs) were predicted. Animal genotypes were generated from imputation based on low-pass sequencing and array data. The log-transformed relative abundance of 16,350 ORFs were used as phenotypes in linear mixed models with the random effect of host genotype. In this population of 717 animals, approximately 4% of the ORFs had heritability estimates larger than twice their standard error and more than 10% of the ORFs had estimates greater than 0.20. Functions of highly heritable ORFs included aromatic amino acid biosynthesis and genome regulation. Additionally, some ORFs were genetically correlated with production traits. Eleven host genes were associated with more than one ORF. The functionality of these candidate host genes can be generally classified as either immune-related, metabolism-related, or possibly involved in host-microbiome crosstalk. Host genetics influence the rumen microbiome function making genetic selection of the host an avenue to alter rumen microbiome functionality. Associations between host genes and rumen metagenome composition indicate multiple potential biological mechanisms underlie these associations. Moreover, a portion of the highly heritable ORFs are genetically correlated with feed efficiency traits making them potential selection targets to increase productivity. The functions of the candidate host genes show the rumen metagenome is influenced by multiple complex biological systems of the host.<\/jats:p>","DOI":"10.1093\/jas\/skag224","type":"journal-article","created":{"date-parts":[[2026,7,18]],"date-time":"2026-07-18T11:40:20Z","timestamp":1784374820000},"source":"Crossref","is-referenced-by-count":0,"title":["Influence of host genetics on the functional composition of the rumen metagenome in beef cattle"],"prefix":"10.1093","volume":"104","author":[{"given":"Andrew D","family":"Lakamp","sequence":"first","affiliation":[{"name":"Department of Animal Sciences, University of Nebraska-Lincoln , Lincoln, NE 68583,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Seidu","family":"Adams","sequence":"additional","affiliation":[{"name":"Department of Animal Sciences, University of Nebraska-Lincoln , Lincoln, NE 68583,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7573-5365","authenticated-orcid":false,"given":"Larry A","family":"Kuehn","sequence":"additional","affiliation":[{"name":"USDA-ARS, U.S. Meat Animal Research Center , Clay Center, NE 68933,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6282-9728","authenticated-orcid":false,"given":"Warren M","family":"Snelling","sequence":"additional","affiliation":[{"name":"USDA-ARS, U.S. Meat Animal Research Center , Clay Center, NE 68933,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James","family":"Wells","sequence":"additional","affiliation":[{"name":"USDA-ARS, U.S. Meat Animal Research Center , Clay Center, NE 68933,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kristin","family":"Hales","sequence":"additional","affiliation":[{"name":"USDA-ARS, U.S. Meat Animal Research Center , Clay Center, NE 68933,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bryan","family":"Neville","sequence":"additional","affiliation":[{"name":"USDA-ARS, U.S. Meat Animal Research Center , Clay Center, NE 68933,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samodha C","family":"Fernando","sequence":"additional","affiliation":[{"name":"Department of Animal Sciences, University of Nebraska-Lincoln , Lincoln, NE 68583,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5184-501X","authenticated-orcid":false,"given":"Matthew L","family":"Spangler","sequence":"additional","affiliation":[{"name":"Department of Animal Sciences, University of Nebraska-Lincoln , Lincoln, NE 68583,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,7,20]]},"reference":[{"key":"2026080409562302400_skag224-B1","doi-asserted-by":"publisher","first-page":"15101","DOI":"10.1038\/s41598-020-72011-9","article-title":"Influence of host genetics in shaping the rumen bacterial community in beef cattle","volume":"10","author":"Abbas","year":"2020","journal-title":"Sci Rep"},{"key":"2026080409562302400_skag224-B2","doi-asserted-by":"publisher","first-page":"baw093","DOI":"10.1093\/database\/baw093","article-title":"The Ensembl gene annotation system","volume":"2016","author":"Aken","year":"2016","journal-title":"Database."},{"key":"2026080409562302400_skag224-B3","doi-asserted-by":"publisher","first-page":"112","DOI":"10.1021\/jf60173a051","article-title":"Proline utilization during cellulose fermentation by rumen microorganisms","volume":"19","author":"Amos","year":"1971","journal-title":"J Agric Food Chem"},{"key":"2026080409562302400_skag224-B4","doi-asserted-by":"publisher","first-page":"1282767","DOI":"10.3389\/fmicb.2023.1282767","article-title":"Comparison of the effects of rumen-protected and unprotected L-leucine on fermentation parameters, bacterial composition, and amino acids metabolism in in vitro rumen batch cultures","volume":"14","author":"An","year":"2023","journal-title":"Front. Microbiol"},{"key":"2026080409562302400_skag224-B5","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1186\/s40168-017-0374-3","article-title":"Dietary energy drives the dynamic response of bovine rumen viral communities","volume":"5","author":"Anderson","year":"2017","journal-title":"Microbiome"},{"key":"2026080409562302400_skag224-B6","author":"Aroney","year":"2024"},{"key":"2026080409562302400_skag224-B7","first-page":"251","volume-title":"Methods in enzymology","author":"Astashkin","year":"2015"},{"key":"2026080409562302400_skag224-B8","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1016\/j.jare.2024.11.012","article-title":"Host genetic regulation of specific functional groups in the rumen microbiome of dairy cows: implications for lactation trait","volume":"75","author":"Bai","year":"2025","journal-title":"J Adv Res"},{"key":"2026080409562302400_skag224-B9","doi-asserted-by":"publisher","first-page":"1482","DOI":"10.3390\/ijms20061482","article-title":"Glutamatergic signaling along the microbiota-gut-brain axis","volume":"20","author":"Baj","year":"2019","journal-title":"Int J Mol Sci"},{"key":"2026080409562302400_skag224-B10","doi-asserted-by":"publisher","first-page":"393","DOI":"10.1146\/annurev-genet-102209-163602","article-title":"The RecQ DNA helicases in DNA Repair","volume":"44","author":"Bernstein","year":"2010","journal-title":"Annu Rev Genet"},{"key":"2026080409562302400_skag224-B11","doi-asserted-by":"publisher","first-page":"4949","DOI":"10.1128\/AEM.07759-11","article-title":"Effect of phenotypic residual feed intake and dietary forage content on the rumen microbial community of beef cattle","volume":"78","author":"Carberry","year":"2012","journal-title":"Appl Environ Microbiol"},{"key":"2026080409562302400_skag224-B12","doi-asserted-by":"publisher","first-page":"795717","DOI":"10.3389\/fgene.2022.795717","article-title":"Host genome\u2013metagenome analyses using combinatorial network methods reveal key metagenomic and host genetic features for methane emission and feed efficiency in cattle","volume":"13","author":"Cardinale","year":"2022","journal-title":"Front Genet"},{"key":"2026080409562302400_skag224-B13","doi-asserted-by":"publisher","first-page":"1925","DOI":"10.1093\/bioinformatics\/btz848","article-title":"GTDB-Tk: a toolkit to classify genomes with the genome taxonomy database","volume":"36","author":"Chaumeil","year":"2020","journal-title":"Bioinformatics"},{"key":"2026080409562302400_skag224-B14","volume-title":"The ruminant animal: Digestive physiology and nutrition","author":"Church","year":"1993"},{"key":"2026080409562302400_skag224-B15","doi-asserted-by":"publisher","first-page":"80","DOI":"10.4161\/fly.19695","article-title":"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w 1118; iso-2; iso-3","volume":"6","author":"Cingolani","year":"2012","journal-title":"Fly (Austin)"},{"key":"2026080409562302400_skag224-B16","doi-asserted-by":"publisher","first-page":"D691","DOI":"10.1093\/nar\/gkq1018","article-title":"Reactome: a database of reactions, pathways and biological processes","volume":"39","author":"Croft","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"2026080409562302400_skag224-B17","doi-asserted-by":"publisher","first-page":"e1007580","DOI":"10.1371\/journal.pgen.1007580","article-title":"Host genetics and the rumen microbiome jointly associate with methane emissions in dairy cows","volume":"14","author":"Difford","year":"2018","journal-title":"PLOS Genet"},{"key":"2026080409562302400_skag224-B18","doi-asserted-by":"publisher","first-page":"e0015821","DOI":"10.1128\/msystems.00158-21","article-title":"Association between human genetic variants and the vaginal bacteriome of pregnant women. H. Bik, editor","volume":"6","author":"Fan","year":"2021","journal-title":"mSystems"},{"key":"2026080409562302400_skag224-B19","doi-asserted-by":"publisher","first-page":"7576","DOI":"10.3168\/jds.2024-25797","article-title":"International symposium on ruminant physiology: stochastic and deterministic factors that shape the rumen microbiome*","volume":"108","author":"Fernando","year":"2025","journal-title":"J Dairy Sci"},{"key":"2026080409562302400_skag224-B20","doi-asserted-by":"publisher","first-page":"7482","DOI":"10.1128\/AEM.00388-10","article-title":"Rumen microbial population dynamics during adaptation to a high-grain diet","volume":"76","author":"Fernando","year":"2010","journal-title":"Appl Environ Microbiol"},{"key":"2026080409562302400_skag224-B21","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1016\/s0065-2164(04)56003-3","article-title":"Polysaccharide breakdown by anaerobic microorganisms inhabiting the mammalian gut","volume":"56","author":"Flint","year":"2004","journal-title":"Adv Appl Microbiol"},{"key":"2026080409562302400_skag224-B22","doi-asserted-by":"publisher","first-page":"giaa149","DOI":"10.1093\/gigascience\/giaa149","article-title":"GALLO: an R package for genomic annotation and integration of multiple data sources in livestock for positional candidate loci","volume":"9","author":"Fonseca","year":"2020","journal-title":"GigaScience"},{"key":"2026080409562302400_skag224-B23","doi-asserted-by":"publisher","first-page":"1835","DOI":"10.1099\/00221287-133-7-1835","article-title":"Establishment of the microflora and anaerobic fungi in the rumen of LAMBS","volume":"133","author":"Fonty","year":"1987","journal-title":"Microbiology (N Y)"},{"key":"2026080409562302400_skag224-B24","author":"Gilmour","year":"2021"},{"key":"2026080409562302400_skag224-B25","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1111\/j.1574-6968.2008.01343.x","article-title":"Linkage of microbial ecology to phenotype: correlation of rumen microbial ecology to cattle\u2019s feed efficiency","volume":"288","author":"Guan","year":"2008","journal-title":"FEMS Microbiol. Lett"},{"key":"2026080409562302400_skag224-B26","doi-asserted-by":"publisher","first-page":"907","DOI":"10.2307\/3870046","article-title":"The Shikimate pathway: early steps in the biosynthesis of aromatic compounds","volume":"7","author":"Herrmann","year":"1995","journal-title":"Plant Cell"},{"key":"2026080409562302400_skag224-B27","doi-asserted-by":"publisher","first-page":"53","DOI":"10.1186\/s12711-023-00822-1","article-title":"Combining host and rumen metagenome profiling for selection in sheep: prediction of methane, feed efficiency, production, and health traits","volume":"55","author":"Hess","year":"2023","journal-title":"Genet Sel Evol"},{"key":"2026080409562302400_skag224-B28","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1186\/1471-2105-11-119","article-title":"Prodigal: prokaryotic gene recognition and translation initiation site identification","volume":"11","author":"Hyatt","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2026080409562302400_skag224-B29","doi-asserted-by":"publisher","first-page":"1184","DOI":"10.3390\/ani11041184","article-title":"Seasonal influence on rumen microbiota, rumen fermentation, and enteric methane emissions of Holstein and jersey steers under the same total mixed ration","volume":"11","author":"Islam","year":"2021","journal-title":"Animals"},{"key":"2026080409562302400_skag224-B30","doi-asserted-by":"publisher","first-page":"1069","DOI":"10.1038\/ismej.2013.2","article-title":"Exploring the bovine rumen bacterial community from birth to adulthood","volume":"7","author":"Jami","year":"2013","journal-title":"Isme J"},{"key":"2026080409562302400_skag224-B31","doi-asserted-by":"publisher","first-page":"726","DOI":"10.1016\/j.jmb.2015.11.006","article-title":"BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences","volume":"428","author":"Kanehisa","year":"2016","journal-title":"J Mol Biol"},{"key":"2026080409562302400_skag224-B32","doi-asserted-by":"publisher","first-page":"1674","DOI":"10.1093\/bioinformatics\/btv033","article-title":"MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph","volume":"31","author":"Li","year":"2015","journal-title":"Bioinformatics"},{"key":"2026080409562302400_skag224-B33","doi-asserted-by":"publisher","first-page":"92","DOI":"10.1186\/s40168-019-0699-1","article-title":"Host genetics influence the rumen microbiota and heritable rumen microbial features associate with feed efficiency in cattle","volume":"7","author":"Li","year":"2019","journal-title":"Microbiome"},{"key":"2026080409562302400_skag224-B34","author":"Li","year":"2013"},{"key":"2026080409562302400_skag224-B35","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2026080409562302400_skag224-B36","doi-asserted-by":"publisher","first-page":"1789","DOI":"10.1016\/j.cellsig.2015.05.013","article-title":"Phosphatidylinositol (3,4) bisphosphate-specific phosphatases and effector proteins: a distinct branch of PI3K signaling","volume":"27","author":"Li","year":"2015","journal-title":"Cell Signal"},{"key":"2026080409562302400_skag224-B37","doi-asserted-by":"publisher","first-page":"1658","DOI":"10.1093\/bioinformatics\/btl158","article-title":"Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences","volume":"22","author":"Li","year":"2006","journal-title":"Bioinformatics"},{"key":"2026080409562302400_skag224-B38","doi-asserted-by":"publisher","first-page":"skaa070","DOI":"10.1093\/jas\/skaa070","article-title":"Combined signature of rumen microbiome and metabolome in dairy cows with different feed intake levels","volume":"98","author":"Li","year":"2020","journal-title":"J Anim Sci"},{"key":"2026080409562302400_skag224-B39","doi-asserted-by":"publisher","first-page":"709","DOI":"10.3390\/brainsci12060709","article-title":"ATP11B deletion affects the gut microbiota and accelerates brain aging in mice","volume":"12","author":"Liu","year":"2022","journal-title":"Brain Sci"},{"key":"2026080409562302400_skag224-B40","doi-asserted-by":"publisher","first-page":"782","DOI":"10.1002\/iid3.335","article-title":"The pivotal roles of neddylation pathway in immunoregulation","volume":"8","author":"Lu","year":"2020","journal-title":"Immun Inflamm Dis"},{"key":"2026080409562302400_skag224-B41","doi-asserted-by":"publisher","first-page":"350","DOI":"10.1038\/s42003-022-03293-0","article-title":"Bovine host genome acts on rumen microbiome function linked to methane emissions","volume":"5","author":"Mart\u00ednez-\u00c1lvaro","year":"2022","journal-title":"Commun Biol"},{"key":"2026080409562302400_skag224-B42","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1186\/s40168-022-01352-6","article-title":"Microbiome-driven breeding strategy potentially improves beef fatty acid profile benefiting human health and reduces methane emissions","volume":"10","author":"Mart\u00ednez-\u00c1lvaro","year":"2022","journal-title":"Microbiome"},{"key":"2026080409562302400_skag224-B43","doi-asserted-by":"publisher","first-page":"26060","DOI":"10.1038\/s41598-024-77782-z","article-title":"Revealing host genome\u2013microbiome networks underlying feed efficiency in dairy cows","volume":"14","author":"Martinez-Boggio","year":"2024","journal-title":"Sci Rep"},{"key":"2026080409562302400_skag224-B44","doi-asserted-by":"publisher","first-page":"D412","DOI":"10.1093\/nar\/gkaa913","article-title":"Pfam: the protein families database in 2021","volume":"49","author":"Mistry","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2026080409562302400_skag224-B45","doi-asserted-by":"publisher","first-page":"10869","DOI":"10.3168\/jds.2025-26894","article-title":"Genetic and physiological influences on the rumen microbiome and metabolic status in Holstein cows","volume":"108","author":"Motyka","year":"2025","journal-title":"J Dairy Sci"},{"key":"2026080409562302400_skag224-B46","doi-asserted-by":"publisher","first-page":"1139611","DOI":"10.3389\/fbioe.2023.1139611","article-title":"Pullulanase: unleashing the power of enzyme with a promising future in the food industry","volume":"11","author":"Naik","year":"2023","journal-title":"Front Bioeng Biotechnol"},{"key":"2026080409562302400_skag224-B47","doi-asserted-by":"publisher","first-page":"211","DOI":"10.3390\/ani8110211","article-title":"Monensin alters the functional and metabolomic profile of rumen microbiota in beef cattle","volume":"8","author":"Ogunade","year":"2018","journal-title":"Animals"},{"key":"2026080409562302400_skag224-B48","doi-asserted-by":"publisher","first-page":"2864","DOI":"10.1038\/ismej.2017.126","article-title":"dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication","volume":"11","author":"Olm","year":"2017","journal-title":"Isme J"},{"key":"2026080409562302400_skag224-B49","doi-asserted-by":"publisher","first-page":"1720","DOI":"10.3390\/genes14091720","article-title":"Genomic Instability of G-Quadruplex sequences in Escherichia coli: roles of DinG, RecG, and RecQ Helicases","volume":"14","author":"Parekh","year":"2023","journal-title":"Genes (Basel)"},{"key":"2026080409562302400_skag224-B50","doi-asserted-by":"publisher","first-page":"1206","DOI":"10.3389\/fmicb.2016.01206","article-title":"Rumen bacterial community composition in Holstein and Jersey cows is different under same dietary condition and is not affected by sampling method","volume":"7","author":"Paz","year":"2016","journal-title":"Front Microbiol"},{"key":"2026080409562302400_skag224-B51","doi-asserted-by":"publisher","first-page":"1045","DOI":"10.1093\/jas\/skx081","article-title":"Rumen bacterial community structure impacts feed efficiency in beef cattle","volume":"96","author":"Paz","year":"2018","journal-title":"J Anim Sci"},{"key":"2026080409562302400_skag224-B52","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1016\/j.livsci.2014.05.007","article-title":"Linkage disequilibrium levels in Bos indicus and Bos taurus cattle using medium and high density SNP chip data and different minor allele frequency distributions","volume":"166","author":"P\u00e9rez O\u2019Brien","year":"2014","journal-title":"Livest Sci"},{"key":"2026080409562302400_skag224-B53","author":"R Core Team","year":"2024"},{"key":"2026080409562302400_skag224-B54","doi-asserted-by":"publisher","first-page":"e1005846","DOI":"10.1371\/journal.pgen.1005846","article-title":"Bovine host genetic variation influences rumen micorbial methane production with best selection criterion for low methane emitting and efficiently feed converting hosts based on metagenomic gene abundance","volume":"12","author":"Roehe","year":"2016","journal-title":"PLOS Genet"},{"key":"2026080409562302400_skag224-B55","doi-asserted-by":"publisher","first-page":"3452","DOI":"10.2527\/jas.2011-3961","article-title":"Genetic and phenotypic parameter estimates for feed intake and other traits in growing beef cattle, and opportunities for selection","volume":"89","author":"Rolfe","year":"2011","journal-title":"J Anim Sci"},{"key":"2026080409562302400_skag224-B56","doi-asserted-by":"publisher","first-page":"giaa021","DOI":"10.1093\/gigascience\/giaa021","article-title":"De novo assembly of the cattle reference genome with single-molecule sequencing","volume":"9","author":"Rosen","year":"2020","journal-title":"GigaScience"},{"key":"2026080409562302400_skag224-B57","doi-asserted-by":"publisher","first-page":"78","DOI":"10.1186\/s40168-018-0457-9","article-title":"The hologenome concept of evolution after 10 years","volume":"6","author":"Rosenberg","year":"2018","journal-title":"Microbiome"},{"key":"2026080409562302400_skag224-B58","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1007\/978-981-16-5812-9_2","volume-title":"Practical guide to life science databases","author":"Safran","year":"2021"},{"key":"2026080409562302400_skag224-B59","author":"Schnabel","year":"2018"},{"key":"2026080409562302400_skag224-B60","doi-asserted-by":"publisher","first-page":"2958","DOI":"10.1038\/ismej.2016.62","article-title":"Specific microbiome-dependent mechanisms underlie the energy harvest efficiency of ruminants","volume":"10","author":"Shabat","year":"2016","journal-title":"Isme J"},{"key":"2026080409562302400_skag224-B61","doi-asserted-by":"publisher","first-page":"1123","DOI":"10.3390\/biomedicines11041123","article-title":"N-carbamoylputrescine amidohydrolase of Bacteroides thetaiotaomicron, a dominant species of the human gut microbiota","volume":"11","author":"Shimokawa","year":"2023","journal-title":"Biomedicines"},{"key":"2026080409562302400_skag224-B62","doi-asserted-by":"publisher","first-page":"1312","DOI":"10.3390\/genes11111312","article-title":"Assessment of imputation from low-pass sequencing to predict merit of beef steers","volume":"11","author":"Snelling","year":"2020","journal-title":"Genes"},{"key":"2026080409562302400_skag224-B63","doi-asserted-by":"publisher","first-page":"158","DOI":"10.1186\/s40168-018-0541-1","article-title":"MetaWRAP\u2014a flexible pipeline for genome-resolved metagenomic data analysis","volume":"6","author":"Uritskiy","year":"2018","journal-title":"Microbiome"},{"key":"2026080409562302400_skag224-B64","doi-asserted-by":"publisher","first-page":"4414","DOI":"10.3168\/jds.2007-0980","article-title":"Efficient methods to compute genomic predictions","volume":"91","author":"VanRaden","year":"2008","journal-title":"J Dairy Sci"},{"key":"2026080409562302400_skag224-B65","doi-asserted-by":"publisher","first-page":"668","DOI":"10.3168\/jds.2012-5702","article-title":"Genomic imputation and evaluation using high-density Holstein genotypes","volume":"96","author":"VanRaden","year":"2013","journal-title":"J Dairy Sci"},{"key":"2026080409562302400_skag224-B66","doi-asserted-by":"publisher","first-page":"839","DOI":"10.1186\/s12864-015-2032-0","article-title":"The rumen microbial metagenome associated with high methane production in cattle","volume":"16","author":"Wallace","year":"2015","journal-title":"BMC Genomics"},{"key":"2026080409562302400_skag224-B67","doi-asserted-by":"publisher","first-page":"eaav8391","DOI":"10.1126\/sciadv.aav8391","article-title":"A heritable subset of the core rumen microbiome dictates dairy cow productivity and emissions","volume":"5","author":"Wallace","year":"2019","journal-title":"Sci Adv"},{"key":"2026080409562302400_skag224-B68","doi-asserted-by":"publisher","first-page":"5075","DOI":"10.1080\/10495398.2023.2276974","article-title":"Differences in composition and diversity of rumen fungi in buffalo fed different diets","volume":"34","author":"Wang","year":"2023","journal-title":"Anim Biotechnol"},{"key":"2026080409562302400_skag224-B69","doi-asserted-by":"publisher","first-page":"197","DOI":"10.1186\/s12864-021-07508-2","article-title":"Comparing low-pass sequencing and genotyping for trait mapping in pharmacogenetics","volume":"22","author":"Wasik","year":"2021","journal-title":"BMC Genomics"},{"key":"2026080409562302400_skag224-B70","doi-asserted-by":"publisher","first-page":"5902","DOI":"10.3168\/jds.2010-3500","article-title":"Host specificity of the ruminal bacterial community in the dairy cow following near-total exchange of ruminal contents","volume":"93","author":"Weimer","year":"2010","journal-title":"J Dairy Sci"},{"key":"2026080409562302400_skag224-B71","doi-asserted-by":"publisher","first-page":"e225","DOI":"10.1002\/imt2.225","article-title":"Deciphering functional groups of rumen microbiome and their underlying potentially causal relationships in shaping host traits","volume":"3","author":"Xue","year":"2024","journal-title":"iMeta"},{"key":"2026080409562302400_skag224-B72","doi-asserted-by":"publisher","first-page":"3954","DOI":"10.1128\/aem.58.12.3954-3958.1992","article-title":"Resistance of proline-containing peptides to ruminal degradation in vitro","volume":"58","author":"Yang","year":"1992","journal-title":"Appl Environ Microbiol"},{"key":"2026080409562302400_skag224-B73","doi-asserted-by":"publisher","first-page":"232","DOI":"10.1186\/s40168-024-01937-3","article-title":"An integrated microbiome- and metabolome-genome-wide association study reveals the role of heritable ruminal microbial carbohydrate metabolism in lactation performance in Holstein dairy cows","volume":"12","author":"Zhang","year":"2024","journal-title":"Microbiome"}],"container-title":["Journal of Animal Science"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/jas\/advance-article-pdf\/doi\/10.1093\/jas\/skag224\/69636312\/skag224.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/jas\/article-pdf\/doi\/10.1093\/jas\/skag224\/69636312\/skag224.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/jas\/article-pdf\/doi\/10.1093\/jas\/skag224\/69636312\/skag224.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,4]],"date-time":"2026-08-04T13:56:29Z","timestamp":1785851789000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/jas\/article\/doi\/10.1093\/jas\/skag224\/8738593"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026]]},"references-count":73,"URL":"https:\/\/doi.org\/10.1093\/jas\/skag224","relation":{},"ISSN":["0021-8812","1525-3163"],"issn-type":[{"value":"0021-8812","type":"print"},{"value":"1525-3163","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026]]},"published":{"date-parts":[[2026]]},"article-number":"skag224"}}