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In this study, the comparison of transcriptomes of intestinal tissues between super-shedders (SS) and cattle negative for <jats:italic>E. coli<\/jats:italic> O157 (NS) was performed, aiming to identify genes that are potentially associated with super-shedding. In total, 16,846\u2009\u00b1\u2009639 (cecum) to 18,137\u2009\u00b1\u2009696 (distal jejunum) were expressed throughout the intestine, with the expressed genes associated with immune functions more pronounced in the small intestine. In total, 351 differentially expressed (DE) genes were identified throughout the intestine between SS and NS, with 101 being up-regulated and 250 down-regulated in SS. Functional analysis revealed DE genes were involved in increased T-cell responses and cholesterol absorption in the distal jejunum and descending colon, and decreased B-cell maturation in the distal jejunum of SS. RNA-Seq based SNP discovery revealed that the mutations in seven DE genes involved in leukocyte activation and cholesterol transportation were associated with <jats:italic>E. coli<\/jats:italic> O157 shedding. Our findings suggest that T-cell responses and cholesterol metabolism in the intestinal tract may be associated with super-shedding phenomenon, and the SNPs in the DE genes are possibly associated with the observed gene expression difference between SS and NS.<\/jats:p>","DOI":"10.1038\/s41598-017-06737-4","type":"journal-article","created":{"date-parts":[[2017,8,3]],"date-time":"2017-08-03T07:07:03Z","timestamp":1501744023000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":19,"title":["Host mechanisms involved in cattle Escherichia coli O157 shedding: a fundamental understanding for reducing foodborne pathogen in food animal production"],"prefix":"10.1038","volume":"7","author":[{"given":"Ou","family":"Wang","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tim A.","family":"McAllister","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Graham","family":"Plastow","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kim","family":"Stanford","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Brent","family":"Selinger","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Le Luo","family":"Guan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2017,8,9]]},"reference":[{"key":"6737_CR1","doi-asserted-by":"publisher","first-page":"7","DOI":"10.3201\/eid1701.P11101","volume":"17","author":"E Scallan","year":"2011","unstructured":"Scallan, E. et al. 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