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The composition and function of the microbiota in the distal part of the intestine has been mainly described, while there is limited information on the small intestine microbiota. The objective of the present study was to describe the duodenal microbiome in individuals with dyspepsia in the presence or absence of <jats:italic>Helicobacter pylori<\/jats:italic> gastric infection.<\/jats:p><\/jats:sec><jats:sec><jats:title>Materials and Methods<\/jats:title><jats:p>Thirty\u2010eight biopsies from the proximal duodenum of uninfected and 37 from <jats:italic>H\u00a0pylori<\/jats:italic>\u2010infected individuals were analyzed. Microbiota composition was assessed by PCR amplification and sequencing of 16S rRNA and ITS genes; sequences were analyzed with QIIME2.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results and Conclusions<\/jats:title><jats:p>At the phyla level, Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, and Fusobacteria were predominant in the mucosal associated duodenal microbiota (MAM); at the genera level, we observed the predominance of <jats:italic>Ralstonia<\/jats:italic>, <jats:italic>Streptococcus, Pseudomonas<\/jats:italic>, <jats:italic>Haemophilus, Herbaspirillum, Neisseria, and Veillonella<\/jats:italic>. Microbiota \u03b1\u2010diversity was higher in <jats:italic>H\u00a0pylori<\/jats:italic>\u2010infected individuals than in non\u2010infected ones. In terms of \u03b2\u2010diversity metrics, there was a statistically significant difference between groups. Also, relative abundance of <jats:italic>Haemophilus, Neisseria, Prevotella pallens, Prevotella<\/jats:italic> 7, and <jats:italic>Streptococcus<\/jats:italic> was greater in <jats:italic>H\u00a0pylori<\/jats:italic>\u2010infected patients. In infected patients, several types of <jats:italic>H\u00a0pylori<\/jats:italic> were present in duodenal MAM. Finally, the majority of duodenal samples had fungi sequences; the most common taxa observed were Recurvomyces followed by Ascomycota and Basidiomycota.<\/jats:p><\/jats:sec>","DOI":"10.1111\/hel.12753","type":"journal-article","created":{"date-parts":[[2020,9,28]],"date-time":"2020-09-28T20:00:08Z","timestamp":1601323208000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":19,"title":["Duodenal microbiome in patients with or without <i>Helicobacter pylori<\/i> infection"],"prefix":"10.1111","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1381-7701","authenticated-orcid":false,"given":"Andr\u00e9s","family":"Su\u00e1rez\u2010Jaramillo","sequence":"first","affiliation":[{"name":"Instituto de Microbiolog\u00eda COCIBA Universidad San Francisco de Quito Quito Ecuador"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manuel 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