{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T03:22:54Z","timestamp":1792725774378,"version":"4.5.0"},"reference-count":32,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2025,1,1]],"date-time":"2025-01-01T00:00:00Z","timestamp":1735689600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,1,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Infectious bovine keratoconjunctivitis (IBK), commonly known as bovine pinkeye, is a disease that infects the ocular surface and surrounding tissue which is a concern to animal health and welfare as well as producer economics. Vaccinations have been shown to have variable efficacy, while limited genetics studies using either ulcer scores or binary health phenotypes have suggested that direct genetic selection for resistance would be slow. Therefore, an investigation into the host genetic component of the ocular microbiome was conducted. Animals were genotyped using either a 50K or 100K commercial genotyping array. After filtering for common markers, there were 35,374 markers available for analysis. Ocular microbiome samples were taken on approximately 600 preweaned beef calves at four time points. From these, amplicon sequence variants (ASV) were extracted and taxonomy assigned using the V4 region of the 16S rRNA gene. Four metrics of alpha diversity (observed richness, Chao1 index, Simpson index, and Shannon index) and the log-transformed relative abundance (RA) of each ASV at each sampling time point were used as phenotypes in a univariate animal model. The observed richness and Chao1 index had heritability estimates of approximately 0.15 at sample times 1 and 3 with estimates of 0 at sample times 2 and 4. Conversely, the Simpson and Shannon indices had heritability estimates ranging from approximately 0.12 to 0.03 at sample times 1 and 4, with estimates near zero for sample times 2 and 3. The RAs of 59% of ocular bacterial community were influenced by host genetics at various sampling times. Estimates of heritability ranged from 0 to 0.60, depending on time and level of taxonomic classification. A small collection of microbes previously associated with IBK (specifically Moraxella bovis, Moraxella bovoculi, and Mycoplasma bovoculi) had moderate to high heritability estimates at multiple sampling time points. This indicates selection for reduced pathogen load is possible.<\/jats:p>","DOI":"10.1093\/jas\/skaf153","type":"journal-article","created":{"date-parts":[[2025,5,4]],"date-time":"2025-05-04T08:21:31Z","timestamp":1746346891000},"source":"Crossref","is-referenced-by-count":1,"title":["Genetic influence on the composition of the ocular microbiome in preweaned beef calves"],"prefix":"10.1093","volume":"103","author":[{"given":"Andrew D","family":"Lakamp","sequence":"first","affiliation":[{"name":"Department of Animal Science, University of Nebraska-Lincoln , Lincoln, NE ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alison C","family":"Neujahr","sequence":"additional","affiliation":[{"name":"Department of Animal Science, University of Nebraska-Lincoln , Lincoln, NE ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew M","family":"Hille","sequence":"additional","affiliation":[{"name":"School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln , Lincoln, NE ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John D","family":"Loy","sequence":"additional","affiliation":[{"name":"School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln , Lincoln, NE ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samodha C","family":"Fernando","sequence":"additional","affiliation":[{"name":"Department of Animal Science, University of Nebraska-Lincoln , Lincoln, NE ,","place":["USA"]}],"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 Science, University of Nebraska-Lincoln , Lincoln, NE ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,5,4]]},"reference":[{"key":"2025053012065198800_CIT0001","doi-asserted-by":"publisher","first-page":"487","DOI":"10.1016\/j.cvfa.2010.09.006","article-title":"Infectious bovine keratoconjunctivitis: a review of cases in clinical practice","volume":"26","author":"Alexander","year":"2010","journal-title":"Vet. Clin. North Am. Food Anim. Pract"},{"key":"2025053012065198800_CIT0002","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1186\/1297-9686-44-22","article-title":"Genetic parameters of infectious bovine keratoconjunctivitis and its relationship with weight and parasite infestations in Australian tropical Bos taurus cattle","volume":"44","author":"Ali","year":"2012","journal-title":"Genet. Sel. Evol"},{"key":"2025053012065198800_CIT0003","doi-asserted-by":"publisher","first-page":"btad445","DOI":"10.1093\/bioinformatics\/btad445","article-title":"AGHmatrix: genetic relationship matrices in R. Bioinforma","volume":"39","author":"Amadeu","year":"2023","journal-title":"Bioinformatics (Oxford, England)"},{"key":"2025053012065198800_CIT0004","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1016\/j.cvfa.2014.11.006","article-title":"Infectious bovine keratoconjunctivitis (Pinkeye)","volume":"31","author":"Angelos","year":"2015","journal-title":"Vet. Clin. North Am. Food Anim. Pract"},{"key":"2025053012065198800_CIT0005","doi-asserted-by":"publisher","first-page":"109752","DOI":"10.1016\/j.vetmic.2023.109752","article-title":"Investigation of the pathogens contributing to naturally occurring outbreaks of infectious bovine keratoconjunctivitis (pinkeye) using next generation sequencing","volume":"282","author":"Anis","year":"2023","journal-title":"Vet. Microbiol"},{"key":"2025053012065198800_CIT0006","doi-asserted-by":"publisher","first-page":"16","DOI":"10.1186\/s42523-021-00079-3","article-title":"Longitudinal assessment of the bovine ocular bacterial community dynamics in calves","volume":"3","author":"Bartenslager","year":"2021","journal-title":"Anim. Microbiome"},{"key":"2025053012065198800_CIT0007","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1038\/nmeth.3869","article-title":"DADA2: high-resolution sample inference from Illumina amplicon data","volume":"13","author":"Callahan","year":"2016","journal-title":"Nat. Methods"},{"key":"2025053012065198800_CIT0008","first-page":"265","article-title":"Nonparametric estimation of the number of classes in a population","volume":"11","author":"Chao","year":"1984","journal-title":"Scand. J. Stat"},{"key":"2025053012065198800_CIT0009","doi-asserted-by":"publisher","first-page":"267","DOI":"10.1016\/j.vetmic.2017.07.003","article-title":"Microbial community sequencing analysis of the calf eye microbiota and relationship to infectious bovine keratoconjunctivitis","volume":"207","author":"Cullen","year":"2017","journal-title":"Vet. Microbiol"},{"key":"2025053012065198800_CIT0010","doi-asserted-by":"publisher","first-page":"355","DOI":"10.1016\/j.cvfa.2021.03.010","article-title":"A review of global prevalence and economic impacts of infectious bovine keratoconjunctivitis","volume":"37","author":"Dennis","year":"2021","journal-title":"Vet. Clin. North Am. Food Anim. Pract"},{"key":"2025053012065198800_CIT0011","doi-asserted-by":"publisher","first-page":"60","DOI":"10.1186\/s42523-023-00282-4","article-title":"Alterations to the bovine bacterial ocular surface microbiome in the context of infectious bovine keratoconjunctivitis","volume":"5","author":"Gafen","year":"2023","journal-title":"Anim. Microbiome"},{"key":"2025053012065198800_CIT0012","volume-title":"ASReml-SA user guide release 4.2 functional specification","author":"Gilmour","year":"2021"},{"key":"2025053012065198800_CIT0013","doi-asserted-by":"publisher","first-page":"916","DOI":"10.3390\/vaccines10060916","article-title":"A five year randomized controlled trial to assess the efficacy and antibody responses to a commercial and autogenous vaccine for the prevention of infectious bovine keratoconjunctivitis","volume":"10","author":"Hille","year":"2022","journal-title":"Vaccines"},{"key":"2025053012065198800_CIT0014","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1186\/1471-2156-14-23","article-title":"Genome-wide association study of infectious bovine keratoconjunctivitis in Angus cattle","volume":"14","author":"Kizilkaya","year":"2013","journal-title":"BMC Genet"},{"key":"2025053012065198800_CIT0015","doi-asserted-by":"publisher","first-page":"5112","DOI":"10.1128\/AEM.01043-13","article-title":"Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq illumina sequencing platform","volume":"79","author":"Kozich","year":"2013","journal-title":"Appl. Environ. Microbiol"},{"key":"2025053012065198800_CIT0016","doi-asserted-by":"publisher","first-page":"579","DOI":"10.1177\/104063870401600615","article-title":"Diagnosis of a mixed mycoplasma infection associated with a severe outbreak of bovine pinkeye in young calves","volume":"16","author":"Levisohn","year":"2004","journal-title":"J. Vet. Diagn. Invest"},{"key":"2025053012065198800_CIT0017","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":"2025053012065198800_CIT0018","doi-asserted-by":"publisher","first-page":"295","DOI":"10.1016\/j.cvfa.2021.03.005","article-title":"Component causes of infectious bovine keratoconjunctivitis\u2014non-Moraxella organisms in the epidemiology of infectious bovine keratoconjunctivitis","volume":"37","author":"Loy","year":"2021","journal-title":"Vet. Clin. North Am. Food Anim. Pract"},{"key":"2025053012065198800_CIT0019","doi-asserted-by":"publisher","first-page":"279","DOI":"10.1016\/j.cvfa.2021.03.004","article-title":"Component causes of infectious bovine keratoconjunctivitis \u2013 the role of Moraxella species in the epidemiology of infectious bovine keratoconjunctivitis","volume":"37","author":"Loy","year":"2021","journal-title":"Vet. Clin. North Am. Food Anim. Pract"},{"key":"2025053012065198800_CIT0020","doi-asserted-by":"publisher","first-page":"e61217","DOI":"10.1371\/journal.pone.0061217","article-title":"phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data","volume":"8","author":"McMurdie","year":"2013","journal-title":"PLoS One"},{"key":"2025053012065198800_CIT0021","doi-asserted-by":"publisher","first-page":"7188","DOI":"10.1093\/nar\/gkm864","article-title":"SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB","volume":"35","author":"Pruesse","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"2025053012065198800_CIT0022","volume-title":"R: A language and environment for statistical computing","author":"R Core Team","year":"2019"},{"key":"2025053012065198800_CIT0023","doi-asserted-by":"publisher","first-page":"847","DOI":"10.3390\/microorganisms10050847","article-title":"Impact of climate and slope aspects on the composition of soil bacterial communities involved in pedogenetic processes along the chilean coastal cordillera","volume":"10","author":"Rodriguez","year":"2022","journal-title":"Microorganisms"},{"key":"2025053012065198800_CIT0024","doi-asserted-by":"publisher","first-page":"203","DOI":"10.1146\/annurev-animal-020420-032054","article-title":"Host genetic determinants of the microbiome across animals: from Caenorhabditis elegans to cattle","volume":"10","author":"Ryu","year":"2022","journal-title":"Annu. Rev. Anim. Biosci"},{"key":"2025053012065198800_CIT0025","doi-asserted-by":"publisher","first-page":"92","DOI":"10.1016\/j.tvjl.2014.11.009","article-title":"Point prevalence of infection with Mycoplasma bovoculi and Moraxella spp. in cattle at different stages of infectious bovine keratoconjunctivitis","volume":"203","author":"Schnee","year":"2015","journal-title":"Vet. J"},{"key":"2025053012065198800_CIT0026","doi-asserted-by":"publisher","first-page":"379","DOI":"10.1002\/j.1538-7305.1948.tb01338.x","article-title":"A mathematical theory of communication","volume":"27","author":"Shannon","year":"1948","journal-title":"Bell Syst. Tech. J"},{"key":"2025053012065198800_CIT0027","doi-asserted-by":"publisher","first-page":"688","DOI":"10.1038\/163688a0","article-title":"Measurement of diversity","volume":"163","author":"Simpson","year":"1949","journal-title":"Nature"},{"key":"2025053012065198800_CIT0028","doi-asserted-by":"publisher","first-page":"507","DOI":"10.2527\/2005.833507x","article-title":"Genetic and environmental factors associated with incidence of infectious bovine keratoconjunctivitis in preweaned beef calves1","volume":"83","author":"Snowder","year":"2005","journal-title":"J. Anim. Sci"},{"key":"2025053012065198800_CIT0029","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":"2025053012065198800_CIT0030","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":"2025053012065198800_CIT0031","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2019.02209","article-title":"Variation in actinobacterial community composition and potential function in different soil ecosystems belonging to the Arid Heihe River Basin of Northwest China","volume":"10","author":"Zhang","year":"2019","journal-title":"Front. Microbiol"},{"key":"2025053012065198800_CIT0032","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1186\/s13073-014-0099-x","article-title":"The conjunctival microbiome in health and trachomatous disease: a case control study","volume":"6","author":"Zhou","year":"2014","journal-title":"Genome Med"}],"container-title":["Journal of Animal Science"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/jas\/advance-article-pdf\/doi\/10.1093\/jas\/skaf153\/63051902\/skaf153.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/jas\/article-pdf\/doi\/10.1093\/jas\/skaf153\/63051902\/skaf153.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/jas\/article-pdf\/doi\/10.1093\/jas\/skaf153\/63051902\/skaf153.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,5,30]],"date-time":"2025-05-30T16:07:00Z","timestamp":1748621220000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/jas\/article\/doi\/10.1093\/jas\/skaf153\/8124715"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025]]},"references-count":32,"URL":"https:\/\/doi.org\/10.1093\/jas\/skaf153","relation":{},"ISSN":["0021-8812","1525-3163"],"issn-type":[{"value":"0021-8812","type":"print"},{"value":"1525-3163","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025]]},"published":{"date-parts":[[2025]]},"article-number":"skaf153"}}