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The pathogen has a battery of virulence factors which it uses to colonise and persist within the host. The host microbiota may play a role in resistance to, and may also be indirectly responsible from some of the consequences of, <jats:italic>Salmonella<\/jats:italic> infection. To investigate this, we used 16S rRNA metagenomic sequencing to determine the changes in the gut microbiota of pigs in response to infection by <jats:italic>Salmonella<\/jats:italic> Typhimurium at three locations: ileum mucosa, ileum content and faeces. Early infection (2 days post-infection) impacted on the microbiome diversity at the mucosa, reflected in a decrease in representatives of the generally regarded as desirable genera (i.e., <jats:italic>Bifidobacterium<\/jats:italic> and <jats:italic>Lactobacillu<\/jats:italic>s). Severe damage in the epithelium of the ileum mucosa correlated with an increase in synergistic (with respect to <jats:italic>Salmonella<\/jats:italic> infection; <jats:italic>Akkermansia<\/jats:italic>) or opportunistically pathogenic bacteria (<jats:italic>Citrobacter<\/jats:italic>) and a depletion in anaerobic bacteria (<jats:italic>Clostridium spp<\/jats:italic>., <jats:italic>Ruminococcus<\/jats:italic>, <jats:italic>or Dialliser<\/jats:italic>). Predictive functional analysis, together with metabolomic analysis revealed changes in glucose and lipid metabolism in infected pigs. The observed changes in commensal healthy microbiota, including the growth of synergistic or potentially pathogenic bacteria and depletion of beneficial or competing bacteria, could contribute to the pathogen\u2019s ability to colonize the gut successfully. The findings from this study could be used to form the basis for further research aimed at creating intervention strategies to mitigate the effects of <jats:italic>Salmonella<\/jats:italic> infection.<\/jats:p>","DOI":"10.1038\/s41598-018-26083-3","type":"journal-article","created":{"date-parts":[[2018,5,11]],"date-time":"2018-05-11T13:52:21Z","timestamp":1526046741000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":79,"title":["Early Salmonella Typhimurium infection in pigs disrupts Microbiome composition and functionality principally at the ileum mucosa"],"prefix":"10.1038","volume":"8","author":[{"given":"H\u00e9ctor","family":"Arg\u00fcello","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jordi","family":"Estell\u00e9","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5084-8999","authenticated-orcid":false,"given":"Sara","family":"Zald\u00edvar-L\u00f3pez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"\u00c1ngeles","family":"Jim\u00e9nez-Mar\u00edn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ana","family":"Carvajal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M\u00aa Asunci\u00f3n","family":"L\u00f3pez-Basc\u00f3n","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fiona","family":"Crispie","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4332-1109","authenticated-orcid":false,"given":"Orla","family":"O\u2019Sullivan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5465-9068","authenticated-orcid":false,"given":"Paul D.","family":"Cotter","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Feliciano","family":"Priego-Capote","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luis","family":"Morera","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juan J.","family":"Garrido","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2018,5,17]]},"reference":[{"key":"26083_CR1","unstructured":"EFSA (European Food Safety Authority) and ECDC (European Centre for Disease Prevention and Control) The European Union summary report on trends and sources of zoonoses, zoonotic agents and food-borne outbreaks in 2015. 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