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Recent research suggests that there is potential for the commensal ocular microbiome to help mitigate IBK. Therefore, this study characterized the ocular microbiome of cattle with and without IBK using culture-based methods and shotgun metagenomic sequencing and assessed the ability of commensal bacteria to inhibit\n                      <jats:italic>Moraxella<\/jats:italic>\n                      spp. in vitro. Ocular swabs (\n                      <jats:italic>n<\/jats:italic>\n                      \u2009=\u2009143) were collected from IBK-affected (\n                      <jats:italic>n<\/jats:italic>\n                      \u2009=\u2009102) and healthy cattle (\n                      <jats:italic>n<\/jats:italic>\n                      \u2009=\u200941) before antimicrobial treatment from North Dakota herds. Bacteria were cultured aerobically and anaerobically on five different media and the isolates were identified. A subset of swabs (37 IBK-affected; 12 healthy) underwent shotgun metagenomic sequencing. The genomes of 31 isolates, including\n                      <jats:italic>Moraxella bovoculi<\/jats:italic>\n                      ,\n                      <jats:italic>Moraxella bovis<\/jats:italic>\n                      , and commensal bacteria, were also sequenced. Fifty-two commensal isolates were screened for inhibition of\n                      <jats:italic>Moraxella<\/jats:italic>\n                      spp. using an agar slab method, with five isolates further tested by qPCR for inhibition in the presence of the culturable ocular microbiome.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      The 351 bacterial isolates taxonomically identified represented 61 genera from three phyla. The majority of isolates belonged to\n                      <jats:italic>Bacillus<\/jats:italic>\n                      (25.9%),\n                      <jats:italic>Streptococcus<\/jats:italic>\n                      (11.1%),\n                      <jats:italic>Staphylococcus<\/jats:italic>\n                      (10.1%), and\n                      <jats:italic>Moraxella<\/jats:italic>\n                      (9.4%) genera. Shotgun metagenomic analysis revealed significant differences in ocular microbial species composition between IBK-affected and healthy cattle (R\u00b2 = 0.05;\n                      <jats:italic>P<\/jats:italic>\n                      \u2009=\u20090.015) based on Bray-Curtis dissimilarity. Dominant bacterial species included\n                      <jats:italic>Cutibacterium acnes<\/jats:italic>\n                      ,\n                      <jats:italic>Mannheimia pernigra<\/jats:italic>\n                      ,\n                      <jats:italic>Mesomycoplasma bovoculi<\/jats:italic>\n                      ,\n                      <jats:italic>Moraxella bovis<\/jats:italic>\n                      , and\n                      <jats:italic>Moraxella bovoculi<\/jats:italic>\n                      . Eight bacterial species, including\n                      <jats:italic>Bifidobacterium globosum<\/jats:italic>\n                      and\n                      <jats:italic>Bacillus licheniformis<\/jats:italic>\n                      , were more abundant in healthy cattle, while\n                      <jats:italic>Arthrobacter luteus<\/jats:italic>\n                      was enriched in IBK cases. Thirty-seven high-quality metagenome-assembled genomes were also recovered, with 27% classified as\n                      <jats:italic>Mesomycoplasma bovoculi<\/jats:italic>\n                      .\n                      <jats:italic>Moraxella<\/jats:italic>\n                      spp. genomes exhibited strain-specific antimicrobial resistance and virulence gene diversity. Seventeen commensal isolates inhibited\n                      <jats:italic>Moraxella<\/jats:italic>\n                      , with\n                      <jats:italic>Weizmannia coagulans<\/jats:italic>\n                      ,\n                      <jats:italic>Lentilactobacillus buchneri<\/jats:italic>\n                      , and\n                      <jats:italic>Paenibacillus polymyxa<\/jats:italic>\n                      showing strong activity. Selected isolates maintained inhibitory effects in co-culture with the ocular microbiome.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>The ocular surface of beef cattle is inhabited by a diverse microbiome that includes several bacterial strains that have the potential to be used as therapeutics to inhibit IBK pathogens.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s42523-026-00587-0","type":"journal-article","created":{"date-parts":[[2026,6,15]],"date-time":"2026-06-15T08:45:14Z","timestamp":1781513114000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["The bovine ocular microbiome: a multi-approach study of composition and antimicrobial activity"],"prefix":"10.1186","volume":"8","author":[{"given":"Samat","family":"Amat","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Devin B.","family":"Holman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah M.","family":"Luecke","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katherine E.","family":"Gzyl","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muhammad","family":"Anas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gerald","family":"Stokka","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,6,15]]},"reference":[{"issue":"2","key":"587_CR1","doi-asserted-by":"publisher","first-page":"355","DOI":"10.1016\/j.cvfa.2021.03.010","volume":"37","author":"EJ Dennis","year":"2021","unstructured":"Dennis EJ, Kneipp M. 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