{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T03:42:37Z","timestamp":1790826157302,"version":"4.1.0"},"reference-count":45,"publisher":"American Dairy Science Association","issue":"5","license":[{"start":{"date-parts":[[2023,5,1]],"date-time":"2023-05-01T00:00:00Z","timestamp":1682899200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2023,3,3]],"date-time":"2023-03-03T00:00:00Z","timestamp":1677801600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["journalofdairyscience.org","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Journal of Dairy Science"],"published-print":{"date-parts":[[2023,5]]},"DOI":"10.3168\/jds.2022-22573","type":"journal-article","created":{"date-parts":[[2023,3,7]],"date-time":"2023-03-07T22:14:47Z","timestamp":1678227287000},"page":"3176-3191","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":15,"title":["Associations among the genome, rumen metabolome, ruminal bacteria, and milk production in early-lactation Holsteins"],"prefix":"10.3168","volume":"106","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1298-3107","authenticated-orcid":false,"given":"H.M.","family":"Golder","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1921-0975","authenticated-orcid":false,"given":"J.","family":"Thomson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J.","family":"Rehberger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4108-5613","authenticated-orcid":false,"given":"A.H.","family":"Smith","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2588-3236","authenticated-orcid":false,"given":"E.","family":"Block","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1045-7907","authenticated-orcid":false,"given":"I.J.","family":"Lean","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1747","reference":[{"key":"10.3168\/jds.2022-22573_bib1","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1016\/j.femsle.2005.05.023","article-title":"The genetic diversity of lactic acid producing bacteria in the equine gastrointestinal tract","volume":"248","author":"Al Jassim","year":"2005","journal-title":"FEMS Microbiol. Lett."},{"key":"10.3168\/jds.2022-22573_bib2","doi-asserted-by":"crossref","first-page":"18933","DOI":"10.1073\/pnas.1007028107","article-title":"Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors","volume":"107","author":"Benson","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.3168\/jds.2022-22573_bib3","series-title":"Bergey's Manual of Systematic Bacteriology: Volume 3: The Firmicutes","author":"Bergey","year":"2011"},{"key":"10.3168\/jds.2022-22573_bib4","doi-asserted-by":"crossref","first-page":"852","DOI":"10.1038\/s41587-019-0209-9","article-title":"Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2","volume":"37","author":"Bolyen","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"10.3168\/jds.2022-22573_bib5","doi-asserted-by":"crossref","first-page":"308","DOI":"10.3168\/jds.2006-601","article-title":"The definition of acidosis in dairy herds predominantly fed on pasture and concentrates","volume":"91","author":"Bramley","year":"2008","journal-title":"J. Dairy Sci."},{"key":"10.3168\/jds.2022-22573_bib6","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0056976","article-title":"Linear regression in genetic association studies","volume":"8","author":"B\u016f\u017ekov\u00e1","year":"2013","journal-title":"PLoS One"},{"key":"10.3168\/jds.2022-22573_bib7","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1007\/s00248-018-1234-9","article-title":"Altering the gut microbiome of cattle: Considerations of host-microbiome interactions for persistent microbiome manipulation","volume":"77","author":"Clemmons","year":"2019","journal-title":"Microb. Ecol."},{"key":"10.3168\/jds.2022-22573_bib8","doi-asserted-by":"crossref","first-page":"5111","DOI":"10.3168\/jds.2020-19777","article-title":"Invited review: The future of selection decisions and breeding programs: What are we breeding for, and who decides?","volume":"104","author":"Cole","year":"2021","journal-title":"J. Dairy Sci."},{"key":"10.3168\/jds.2022-22573_bib9","doi-asserted-by":"crossref","first-page":"7625","DOI":"10.3168\/jds.2018-14529","article-title":"Characterization of best linear unbiased estimates generated from national genetic evaluations of reproductive performance, survival, and milk yield in dairy cows","volume":"101","author":"Dunne","year":"2018","journal-title":"J. Dairy Sci."},{"key":"10.3168\/jds.2022-22573_bib10","doi-asserted-by":"crossref","first-page":"12627","DOI":"10.1074\/jbc.M116.720953","article-title":"The anti-inflammatory protein TSG-6 regulates chemokine function by inhibiting chemokine\/glycosaminoglycan interactions","volume":"291","author":"Dyer","year":"2016","journal-title":"J. Biol. Chem."},{"key":"10.3168\/jds.2022-22573_bib11","first-page":"793","article-title":"Netrin-4 promotes differentiation and migration of osteoblasts","volume":"31","author":"Enoki","year":"2017","journal-title":"In Vivo"},{"key":"10.3168\/jds.2022-22573_bib12","doi-asserted-by":"crossref","first-page":"1450","DOI":"10.2527\/jas.2014-8754","article-title":"Ruminant nutrition symposium: How to use data on the rumen microbiome to improve our understanding of ruminant nutrition","volume":"93","author":"Firkins","year":"2015","journal-title":"J. Anim. Sci."},{"key":"10.3168\/jds.2022-22573_bib13","series-title":"Proc. Dairy Research Foundation, Camden, NSW, Australia","first-page":"118","article-title":"Validation of an acidosis model","author":"Golder","year":"2012"},{"key":"10.3168\/jds.2022-22573_bib14","doi-asserted-by":"crossref","first-page":"985","DOI":"10.3168\/jds.2013-7166","article-title":"Effects of feed additives on rumen and blood profiles during a starch and fructose challenge","volume":"97","author":"Golder","year":"2014","journal-title":"J. Dairy Sci."},{"key":"10.3168\/jds.2022-22573_bib15","doi-asserted-by":"crossref","DOI":"10.3168\/jds.2022-22571","article-title":"Characterizing ruminal acidosis risk: A multiherd, multicountry study","volume":"106","author":"Golder","year":"2023","journal-title":"J. Dairy Sci."},{"key":"10.3168\/jds.2022-22573_bib16","doi-asserted-by":"crossref","first-page":"62","DOI":"10.3389\/fgene.2018.00062","article-title":"Genetic markers are associated with the ruminal microbiome and metabolome in grain and sugar challenged dairy heifers","volume":"9","author":"Golder","year":"2018","journal-title":"Front. Genet."},{"key":"10.3168\/jds.2022-22573_bib17","doi-asserted-by":"crossref","DOI":"10.1038\/srep14567","article-title":"Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range","volume":"5","author":"Henderson","year":"2015","journal-title":"Sci. Rep."},{"key":"10.3168\/jds.2022-22573_bib18","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1016\/j.anaerobe.2012.04.003","article-title":"Similarity of the ruminal bacteria across individual lactating cows","volume":"18","author":"Jami","year":"2012","journal-title":"Anaerobe"},{"key":"10.3168\/jds.2022-22573_bib19","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0085423","article-title":"Potential role of the bovine rumen microbiome in modulating milk composition and feed efficiency","volume":"9","author":"Jami","year":"2014","journal-title":"PLoS One"},{"key":"10.3168\/jds.2022-22573_bib20","doi-asserted-by":"crossref","first-page":"412","DOI":"10.3389\/fgene.2019.00412","article-title":"A large-scale genome-wide association study in U.S. Holstein cattle","volume":"10","author":"Jiang","year":"2019","journal-title":"Front. Genet."},{"key":"10.3168\/jds.2022-22573_bib21","doi-asserted-by":"crossref","first-page":"1075","DOI":"10.1038\/s12276-020-0465-2","article-title":"Deacetylation by SIRT1 promotes the tumor-suppressive activity of HINT1 by enhancing its binding capacity for \u03b2-catenin or MITF in colon cancer and melanoma cells","volume":"52","author":"Jung","year":"2020","journal-title":"Exp. Mol. Med."},{"key":"10.3168\/jds.2022-22573_bib22","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1186\/s42523-019-0013-3","article-title":"The gut microbiome of horses: Current research on equine enteral microbiota and future perspectives","volume":"1","author":"Kauter","year":"2019","journal-title":"Anim. Microbiome"},{"key":"10.3168\/jds.2022-22573_bib23","doi-asserted-by":"crossref","first-page":"716","DOI":"10.1099\/ijs.0.038075-0","article-title":"Introducing EzTaxon-e: A prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species","volume":"62","author":"Kim","year":"2012","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"10.3168\/jds.2022-22573_bib24","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1186\/s40168-019-0618-5","article-title":"Comparative metagenomic and metatranscriptomic analyses reveal the breed effect on the rumen microbiome and its associations with feed efficiency in beef cattle","volume":"7","author":"Li","year":"2019","journal-title":"Microbiome"},{"key":"10.3168\/jds.2022-22573_bib25","doi-asserted-by":"crossref","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":"10.3168\/jds.2022-22573_bib26","doi-asserted-by":"crossref","first-page":"1924","DOI":"10.1111\/j.1365-2672.2009.04376.x","article-title":"Effects of sampling location and time, and host animal on assessment of bacterial diversity and fermentation parameters in the bovine rumen","volume":"107","author":"Li","year":"2009","journal-title":"J. Appl. Microbiol."},{"key":"10.3168\/jds.2022-22573_bib27","doi-asserted-by":"crossref","first-page":"1327","DOI":"10.1128\/AEM.03138-14","article-title":"Prepartum and postpartum rumen fluid microbiomes: Characterization and correlation with production traits in dairy cows","volume":"81","author":"Lima","year":"2015","journal-title":"Appl. Environ. Microbiol."},{"key":"10.3168\/jds.2022-22573_bib28","doi-asserted-by":"crossref","first-page":"8453","DOI":"10.1096\/fj.201802456R","article-title":"Dynamic changes in rumen fermentation and bacterial community following rumen fluid transplantation in a sheep model of rumen acidosis: Implications for rumen health in ruminants","volume":"33","author":"Liu","year":"2019","journal-title":"FASEB J."},{"key":"10.3168\/jds.2022-22573_bib29","doi-asserted-by":"crossref","first-page":"E8151","DOI":"10.1073\/pnas.1614935113","article-title":"TNF\u03b1-stimulated gene-6 (TSG6) activates macrophage phenotype transition to prevent inflammatory lung injury","volume":"113","author":"Mittal","year":"2016","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.3168\/jds.2022-22573_bib30","doi-asserted-by":"crossref","first-page":"e00103","DOI":"10.1128\/mSystems.00103-19","article-title":"Bovine genome-microbiome interactions: Metagenomic frontier for the selection of efficient productivity in cattle systems","volume":"4","author":"Myer","year":"2019","journal-title":"mSystems"},{"key":"10.3168\/jds.2022-22573_bib31","doi-asserted-by":"crossref","first-page":"E17","DOI":"10.3168\/jds.2006-478","article-title":"Ruminal acidosis in beef cattle: The current microbiological and nutritional outlook","volume":"90","author":"Nagaraja","year":"2007","journal-title":"J. Dairy Sci."},{"key":"10.3168\/jds.2022-22573_bib32","series-title":"Nutrient Requirements of Dairy Cattle","author":"National Research Council (NRC)","year":"2001"},{"key":"10.3168\/jds.2022-22573_bib33","doi-asserted-by":"crossref","first-page":"904","DOI":"10.1038\/ng1847","article-title":"Principal components analysis corrects for stratification in genome-wide association studies","volume":"38","author":"Price","year":"2006","journal-title":"Nat. Genet."},{"key":"10.3168\/jds.2022-22573_bib34","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1002\/ijc.30043","article-title":"Roles of N-Myc and STAT interactor in cancer: From initiation to dissemination","volume":"139","author":"Pruitt","year":"2016","journal-title":"Int. J. Cancer"},{"key":"10.3168\/jds.2022-22573_bib35","doi-asserted-by":"crossref","DOI":"10.7717\/peerj.2584","article-title":"VSEARCH: A versatile open source tool for metagenomics","volume":"4","author":"Rognes","year":"2016","journal-title":"PeerJ"},{"key":"10.3168\/jds.2022-22573_bib36","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1016\/j.bbabio.2012.11.003","article-title":"LYRM7\/MZM1L is a UQCRFS1 chaperone involved in the last steps of mitochondrial Complex III assembly in human cells","volume":"1827","author":"S\u00e1nchez","year":"2013","journal-title":"Biochim. Biophys. Acta Bioenerg."},{"key":"10.3168\/jds.2022-22573_bib37","doi-asserted-by":"crossref","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":"10.3168\/jds.2022-22573_bib38","doi-asserted-by":"crossref","first-page":"296","DOI":"10.3389\/fmicb.2015.00296","article-title":"Redundancy, resilience, and host specificity of the ruminal microbiota: Implications for engineering improved ruminal fermentations","volume":"6","author":"Weimer","year":"2015","journal-title":"Front. Microbiol."},{"key":"10.3168\/jds.2022-22573_bib39","doi-asserted-by":"crossref","first-page":"7165","DOI":"10.3168\/jds.2017-12746","article-title":"Transient changes in milk production efficiency and bacterial community composition resulting from near-total exchange of ruminal contents between high- and low-efficiency Holstein cows","volume":"100","author":"Weimer","year":"2017","journal-title":"J. Dairy Sci."},{"key":"10.3168\/jds.2022-22573_bib40","doi-asserted-by":"crossref","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":"10.3168\/jds.2022-22573_bib41","series-title":"Genetic Data Analysis II","author":"Weir","year":"1996"},{"key":"10.3168\/jds.2022-22573_bib42","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1016\/j.anaerobe.2009.07.002","article-title":"ARISA analysis of ruminal bacterial community dynamics in lactating dairy cows during the feeding cycle","volume":"16","author":"Welkie","year":"2010","journal-title":"Anaerobe"},{"key":"10.3168\/jds.2022-22573_bib43","doi-asserted-by":"crossref","first-page":"739","DOI":"10.1093\/femsre\/fuy029","article-title":"On the maverick Planctomycetes","volume":"42","author":"Wiegand","year":"2018","journal-title":"FEMS Microbiol. Rev."},{"key":"10.3168\/jds.2022-22573_bib44","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1146\/annurev-animal-021815-111422","article-title":"Genomic selection in dairy cattle: The USDA experience","volume":"5","author":"Wiggans","year":"2017","journal-title":"Annu. Rev. Anim. Biosci."},{"key":"10.3168\/jds.2022-22573_bib45","doi-asserted-by":"crossref","first-page":"449","DOI":"10.3892\/or.2016.5239","article-title":"NTN4 is associated with breast cancer metastasis via regulation of EMT-related biomarkers","volume":"37","author":"Xu","year":"2017","journal-title":"Oncol. Rep."}],"container-title":["Journal of Dairy Science"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0022030223001108?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0022030223001108?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0022030223001108","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,11,8]],"date-time":"2024-11-08T21:35:44Z","timestamp":1731101744000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0022030223001108"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,5]]},"references-count":45,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2023,5]]}},"alternative-id":["S0022030223001108"],"URL":"https:\/\/doi.org\/10.3168\/jds.2022-22573","relation":{},"ISSN":["0022-0302"],"issn-type":[{"value":"0022-0302","type":"print"}],"subject":[],"published":{"date-parts":[[2023,5]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Associations among the genome, rumen metabolome, ruminal bacteria, and milk production in early-lactation Holsteins","name":"articletitle","label":"Article Title"},{"value":"Journal of Dairy Science","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.3168\/jds.2022-22573","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"https:\/\/doi.org\/10.3168\/jds.2022-22571","name":"associatedlink","label":"CrossRef DOI link to the associated document"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2023 The Author(s).","name":"copyright","label":"Copyright"}]}}