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We characterized the bacterial nasopharyngeal microbiota in cattle at feedlot entry (day 0) and day 60 using 454 pyrosequencing. We also identified the most frequently isolated aerobic bacteria from nasopharyngeal swabs after plating onto three types of media. The cattle nasopharyngeal microbiota was composed primarily of <jats:italic>Proteobacteria<\/jats:italic> (68.9%) and <jats:italic>Firmicutes<\/jats:italic> (19.2%). At the genus-level, there was more inter-individual variability and a total of 55 genera were identified. The genera <jats:italic>Pseudomonas<\/jats:italic> (23.7%), <jats:italic>Shewanella<\/jats:italic> (23.5%), <jats:italic>Acinetobacter<\/jats:italic> (17.5%) and <jats:italic>Carnobacterium<\/jats:italic> (12.2%) were most prevalent at entry, while after 60 days in the feedlot, <jats:italic>Staphylococcus<\/jats:italic> (20.8%), <jats:italic>Mycoplasma<\/jats:italic> (14.9%), <jats:italic>Mannheimia<\/jats:italic> (10.4%) and <jats:italic>Moraxella<\/jats:italic> (9.4%) were dominant. The nasopharyngeal microbiota also became more homogenous after 60 days in the feedlot and differed in structure at day 0 and 60. Using culture-based methods, the most frequently isolated bacteria from nasopharyngeal swabs were <jats:italic>Bacillus<\/jats:italic>, <jats:italic>Staphylococcus<\/jats:italic>, <jats:italic>Moraxella<\/jats:italic>, <jats:italic>Pasteurella<\/jats:italic> and <jats:italic>Mannheimia<\/jats:italic>. These results provide insight into the nasopharyngeal microbiota of cattle and demonstrate that specific changes take place during feedlot production.<\/jats:p>","DOI":"10.1038\/srep15557","type":"journal-article","created":{"date-parts":[[2015,10,26]],"date-time":"2015-10-26T09:08:28Z","timestamp":1445850508000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":75,"title":["The nasopharyngeal microbiota of feedlot cattle"],"prefix":"10.1038","volume":"5","author":[{"given":"Devin B.","family":"Holman","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Edouard","family":"Timsit","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Trevor W.","family":"Alexander","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2015,10,26]]},"reference":[{"key":"BFsrep15557_CR1","unstructured":"Feedlot 2011 Part IV: Health and Health Management on U.S. Feedlots with a Capacity of 1,000 or More Head (2013). 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