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We investigated the role of <jats:italic>Helicobacter pylori<\/jats:italic> infection in extra-gastroduodenal diseases by determining the impact of <jats:italic>H. pylori<\/jats:italic> infection on the duodenal microbiota. We sequenced 16\u00a0S rRNA genes in samples aspirated from the descending duodenum of 47 (male, 20; female, 27) individuals who were screened for gastric cancer. Samples were analysed using 16\u00a0S rRNA gene amplicon sequencing, and the LEFSe and Kyoto Encyclopaedia of Genes and Genomes methods were used to determine whether the duodenal microflora and microbial biofunctions were affected using <jats:italic>H. pylori<\/jats:italic> infection.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>Thirteen and 34 participants tested positive and negative for <jats:italic>H. pylori<\/jats:italic>, respectively. We identified 1,404 bacterial operational taxonomic units from 23 phyla and 253 genera. <jats:italic>H. pylori infection changed the relative mean abundance of three phyla (Proteobacteria, Actinobacteria, and TM7) and ten genera (Neisseria, Rothia, TM7-3, Leptotrichia, Lachnospiraceae, Megasphaera, F16, Moryella, Filifactor, and Paludibacter).<\/jats:italic> Microbiota features were significantly influenced in <jats:italic>H. pylori<\/jats:italic>-positive participants by 12 taxa mostly classified as <jats:italic>Gammaproteobacteria<\/jats:italic>. Microbial functional annotation revealed that <jats:italic>H. pylori<\/jats:italic> significantly affected 12 microbial metabolic pathways.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p><jats:italic>H. pylori<\/jats:italic> disrupted normal bacterial communities in the duodenum and changed the biofunctions of commensal microbiota primarily by upregulating specific metabolic pathways. Such upregulation may be involved in the onset of diseases associated with <jats:italic>H. pylori<\/jats:italic> infection.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12866-022-02437-w","type":"journal-article","created":{"date-parts":[[2022,1,15]],"date-time":"2022-01-15T07:03:09Z","timestamp":1642230189000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":14,"title":["Impact of Helicobacter pylori infection on fluid duodenal microbial community structure and microbial metabolic pathways"],"prefix":"10.1186","volume":"22","author":[{"given":"Tadashi","family":"Maeda","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hiroaki","family":"Zai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuto","family":"Fukui","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yoshifumi","family":"Kato","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eri","family":"Kumade","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Toshiyasu","family":"Watanabe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Norihiro","family":"Furusyo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hitoshi","family":"Nakajima","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kazuho","family":"Arai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yoshikazu","family":"Ishii","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kazuhiro","family":"Tateda","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yoshihisa","family":"Urita","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2022,1,15]]},"reference":[{"key":"2437_CR1","doi-asserted-by":"publisher","first-page":"135","DOI":"10.1111\/j.1574-6968.2007.00648.x","volume":"268","author":"M Clyne","year":"2007","unstructured":"Clyne M, Dolan B, Reeves EP. 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