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The V3-V4 region of the bacterial 16S rRNA gene was examined by high throughput sequencing method.<\/jats:p>\n<\/jats:sec><jats:sec>\n<jats:title>Results<\/jats:title>\n<jats:p>The diversity of the HC duodenal microbiota was higher than that of IM patient based on the Shannon and Simpson index while the Chao indices of IM duodenal mucosal microbiota was significantly higher than that of gastric mucosal microbiota of patients with IM. There was a marked difference in the duodenal microbiota structure between patients with IM and HC (ANOSIM, R\u2009=\u20091, <jats:italic>P<\/jats:italic>\u2009=\u20090.001). We also found that the <jats:italic>Helicobacter pylori<\/jats:italic> infection in gastric mucosa did not influence the structure of duodenal mucosal microbiota. The gastric mucosal microbiota structure significantly differed between patients with IM and HC who were <jats:italic>H. pylori<\/jats:italic>-negative (ANOSIM, R\u2009=\u20090.452, <jats:italic>P<\/jats:italic>\u2009=\u20090.042) or <jats:italic>H. pylori<\/jats:italic>-positive (ANOSIM, R\u2009=\u20090.548, <jats:italic>P<\/jats:italic>\u2009=\u20090.003), respectively. For duodenal mucosal microbiota, genera <jats:italic>Lactococcus<\/jats:italic>, <jats:italic>Flavobacterium<\/jats:italic>, <jats:italic>Psychrobacter<\/jats:italic>, <jats:italic>Mysroides<\/jats:italic>, <jats:italic>Enhydrobacter<\/jats:italic>, <jats:italic>Streptococcus<\/jats:italic>, and <jats:italic>Leuconostoc<\/jats:italic> were enriched in patients with IM. In contrast, genera <jats:italic>Bacillus<\/jats:italic>, <jats:italic>Solibacillus<\/jats:italic>, <jats:italic>Lysinibacillus<\/jats:italic>, <jats:italic>Exiguobacterium<\/jats:italic>, <jats:italic>Oceanobacillus<\/jats:italic>, and <jats:italic>Paenibacillus<\/jats:italic> were enriched in HC.<\/jats:p>\n<\/jats:sec><jats:sec>\n<jats:title>Conclusion<\/jats:title>\n<jats:p>A marked dysbiosis duodenal mucosal microbiota in patients with IM was observed, and this dysbiosis might be responsible for IM pathogenesis.<\/jats:p>\n<\/jats:sec>","DOI":"10.1186\/s12866-019-1666-5","type":"journal-article","created":{"date-parts":[[2019,12,9]],"date-time":"2019-12-09T10:02:51Z","timestamp":1575885771000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":25,"title":["Change of the duodenal mucosa-associated microbiota is related to intestinal metaplasia"],"prefix":"10.1186","volume":"19","author":[{"given":"Jian","family":"Gong","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lixiang","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiuli","family":"Zuo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9325-4808","authenticated-orcid":false,"given":"Yanqing","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2019,12,9]]},"reference":[{"issue":"1","key":"1666_CR1","doi-asserted-by":"publisher","first-page":"7","DOI":"10.3322\/caac.21332","volume":"66","author":"RL Siegel","year":"2016","unstructured":"Siegel RL, Miller KD, Jemal A. 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