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In particular, oral-origin bacteria may dominate the gastric niche in the absence of\n                      <jats:italic>H. pylori<\/jats:italic>\n                      , yet their specific roles in different gastroduodenal disorders remain unclear. This study aimed to profile and compare the gastric microbiota composition in Turkish patients with non-ulcer dyspepsia (NUD) and peptic ulcer disease (PUD), in order to better understand microbial profiles potentially associated with gastroduodenal disease.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      Ninety-eight patients underwent endoscopic evaluation and were divided into two groups according to the presence or absence of ulcers. Group 1 (\n                      <jats:italic>n<\/jats:italic>\n                      \u2009=\u200952) included individuals with NUD, while Group 2 (\n                      <jats:italic>n<\/jats:italic>\n                      \u2009=\u200946) comprised patients with PUD. Gastric biopsy samples from both groups were analyzed for the relative abundance of\n                      <jats:italic>H. pylori<\/jats:italic>\n                      using quantitative real-time PCR (qPCR), and next-generation sequencing was employed for a comprehensive analysis of the gastric microbiota.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      In total,\n                      <jats:italic>H. pylori<\/jats:italic>\n                      DNA was detected in 71.4% (70\/98) of the samples, with a significantly higher prevalence in PUD patients (82.6%) compared to NUD patients (61.5%) (\n                      <jats:italic>p<\/jats:italic>\n                      \u2009=\u20090.02). Distinct microbial profiles were observed based on\n                      <jats:italic>H. pylori<\/jats:italic>\n                      status. In NUD patients,\n                      <jats:italic>Alloprevotella<\/jats:italic>\n                      showed significantly higher relative abundance in\n                      <jats:italic>H. pylori<\/jats:italic>\n                      -negative samples (\n                      <jats:italic>p<\/jats:italic>\n                      \u2009&lt;\u20090.05). Among PUD patients, the absence of\n                      <jats:italic>H. pylori<\/jats:italic>\n                      was associated with increased levels of\n                      <jats:italic>Porphyromonas<\/jats:italic>\n                      and\n                      <jats:italic>Neisseria<\/jats:italic>\n                      compared to NUD patients without\n                      <jats:italic>H. pylori<\/jats:italic>\n                      (\n                      <jats:italic>p<\/jats:italic>\n                      \u2009&lt;\u20090.05). These genera, typically associated with the oral cavity, appeared to expand opportunistically when\n                      <jats:italic>H. pylori<\/jats:italic>\n                      was absent.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>\n                      The absence of\n                      <jats:italic>H. pylori<\/jats:italic>\n                      in gastric disorders was linked to a notable shift in microbiota composition, with increased representation of oral-origin bacteria such as\n                      <jats:italic>Alloprevotella<\/jats:italic>\n                      ,\n                      <jats:italic>Porphyromonas<\/jats:italic>\n                      , and\n                      <jats:italic>Neisseria<\/jats:italic>\n                      . These findings, observed in a Turkish patient cohort, may reflect a potentially compensatory or opportunistic microbial shift in\n                      <jats:italic>H. pylori<\/jats:italic>\n                      -negative gastroduodenal disease. As exploratory findings, this study represents the first analysis from T\u00fcrkiye comparing gastric microbiota profiles in NUD and PUD patients and provides novel regional insight into gastric microbial ecology.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12866-025-04607-y","type":"journal-article","created":{"date-parts":[[2025,12,15]],"date-time":"2025-12-15T05:34:44Z","timestamp":1765776884000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Comparative gastric microbiota profiles in non-ulcer dyspepsia and peptic ulcer patients"],"prefix":"10.1186","volume":"26","author":[{"given":"Silva Polat","family":"Sari","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aliye","family":"Soylu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kivanc Derya","family":"Peker","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gokhan","family":"Adas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ozer","family":"Akgul","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Burcu","family":"Sapmaz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yasar Ali","family":"Oner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pelin Yuksel","family":"Mayda","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2764-1823","authenticated-orcid":false,"given":"Reyhan","family":"Caliskan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,12,15]]},"reference":[{"key":"4607_CR1","unstructured":"Demiryas S, Caliskan R, Saribas S, Akkus S, Gareayaghi N, Kirmusaoglu S, Kepil N, Dinc H, Dag H, Dagdeviren E, Tokman HB, Kalayci F, Demirci M, Tasci I, Erzin Y, Bal K, Kocazeybek B. 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