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The composition of the lung microbiota has been shown to be predictive of clinical outcome in critically ill patients. However, the dynamics of the lung and gut microbiota composition over time during severe pneumonia remains ill defined. We used a mouse model of pneumonia-derived sepsis caused by <jats:italic>Klebsiella pneumoniae<\/jats:italic> in order to follow the pathogen burden as well as the composition of the lung, tongue and fecal microbiota from local infection towards systemic spread.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>Already at 6\u00a0h post-inoculation with <jats:italic>K. pneumoniae<\/jats:italic>, marked changes in the lung microbiota were seen. The alpha diversity of the lung microbiota did not change throughout the infection, whereas the beta diversity did. A shift between the prominent lung microbiota members of <jats:italic>Streptococcus<\/jats:italic> and <jats:italic>Klebsiella<\/jats:italic> was seen from 12\u00a0h onwards and was most pronounced at 18\u00a0h post-inoculation (PI) which was also reflected in the release of pro-inflammatory cytokines indicating severe pulmonary inflammation. Around 18\u00a0h PI, <jats:italic>K. pneumoniae<\/jats:italic> bacteremia was observed together with a systemic inflammatory response. The composition of the tongue microbiota was not affected during infection, even at 18\u201330\u00a0h PI when <jats:italic>K. pneumoniae<\/jats:italic> had become the dominant bacterium in the lung. Moreover, we observed differences in the gut microbiota during pulmonary infection. The gut microbiota contributed to the lung microbiota at 12\u00a0h PI, however, this decreased at a later stage of the infection.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>At 18\u00a0h PI, <jats:italic>K. pneumoniae<\/jats:italic> was the dominant member in the lung microbiota. The lung microbiota profiles were significantly explained by the lung <jats:italic>K. pneumoniae<\/jats:italic> bacterial counts and <jats:italic>Klebsiella<\/jats:italic> and <jats:italic>Streptococcus<\/jats:italic> were correlating with the measured cytokine levels in the lung and\/or blood. The oral microbiota in mice, however, was not influenced by the severity of murine pneumonia, whereas the gut microbiota was affected. This study is of significance for future studies investigating the role of the lung microbiota during pneumonia and sepsis.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s40635-021-00398-4","type":"journal-article","created":{"date-parts":[[2021,7,11]],"date-time":"2021-07-11T23:03:28Z","timestamp":1626044608000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":21,"title":["Pulmonary and intestinal microbiota dynamics during Gram-negative pneumonia-derived sepsis"],"prefix":"10.1186","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4495-2292","authenticated-orcid":false,"given":"Nora S.","family":"Wolff","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Max C.","family":"Jacobs","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"W. 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