title: The active bacterial assemblages of the upper GI tract in individuals with and withoutHelicobacterinfection.
abstract: Patients infected withHelicobacter pyloridevelop chronic gastritis with a subgroup progressing to further complications. The role of microbiota from the oral cavity swallowed with saliva and either transiting the stomach or persisting in the gastric mucosa is uncertain. It is also not known whether the bacterial community differs in luminal and mucosal niches. A key question is whetherH. pyloriinfluences the bacterial communities of gastroduodenal niches.
  
  
  
  Saliva, gastric and duodenal aspirates as well as gastric and duodenal biopsies were collected during oesophagogastroduodenoscopy from 24 patients (m:9, f:15, mean age 52.2±SD 14.5 years). RNA was extracted and the V1-V2 region of the retrotranscribed bacterial 16S rRNA amplified and sequenced on the Illumina MiSeq platform.
  
  
  
  Overall, 687 bacterial phylotypes that belonged to 95 genera and 11 phyla were observed. Each individual comprised a unique microbiota composition that was consistent across the different niches. However, the stomach fluid enriched for specific microbiota components.Helicobacterspp were shown to dominate the mucosa-associated community in the stomach, and to significantly influence duodenal and oral communities.
  
  
  
  The detailed analysis of the active global bacterial communities from the five distinct sites of the upper GI tract allowed for the first time the differentiation between host effects and the influence of sampling region on the bacterial community. The influence ofHelicobacterspp on the global community structures is striking.
authors.affiliation: Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany.|Microbial Interactions and Processes (MINP) Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany.
authors.forename: Christian
authors.initials: C
authors.lastname: Schulz
authors.affiliation: Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany.|Department of Internal Medicine and Gastroenterology, Niels-Stensen-Kliniken, Marienhospital, Osnabrück, Germany.
authors.forename: Kerstin
authors.initials: K
authors.lastname: Schütte
authors.affiliation: Microbial Interactions and Processes (MINP) Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany.
authors.forename: Nadine
authors.initials: N
authors.lastname: Koch
authors.affiliation: Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany.
authors.forename: Ramiro
authors.initials: R
authors.lastname: Vilchez-Vargas
authors.affiliation: Microbial Interactions and Processes (MINP) Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany.
authors.forename: Melissa L
authors.initials: ML
authors.lastname: Wos-Oxley
authors.affiliation: Microbial Interactions and Processes (MINP) Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany.|Molecular Sciences Laboratory, SARDI Aquatic Sciences, West Beach, South Australia, Australia.
authors.forename: Andrew P A
authors.initials: APA
authors.lastname: Oxley
authors.affiliation: Microbial Interactions and Processes (MINP) Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany.
authors.forename: Marius
authors.initials: M
authors.lastname: Vital
authors.affiliation: Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany.
authors.forename: Peter
authors.initials: P
authors.lastname: Malfertheiner
authors.affiliation: Microbial Interactions and Processes (MINP) Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany.
authors.forename: Dietmar H
authors.initials: DH
authors.lastname: Pieper
mesh_terms: D000328:Adult; D000368:Aged; D001706:Biopsy; D002908:Chronic Disease; D004386:Duodenum / Q000382:microbiology* / Q000473:pathology; D016099:Endoscopy, Gastrointestinal; D005260:Female; D005750:Gastric Juice / Q000382:microbiology; D005753:Gastric Mucosa / Q000382:microbiology* / Q000473:pathology; D005756:Gastritis / Q000382:microbiology / Q000473:pathology; D000069196:Gastrointestinal Microbiome; D016481:Helicobacter Infections / Q000382:microbiology* / Q000473:pathology; D016480:Helicobacter pylori; D006801:Humans; D007413:Intestinal Mucosa / Q000382:microbiology* / Q000473:pathology; D008297:Male; D008875:Middle Aged; D009055:Mouth / Q000382:microbiology; D012336:RNA, Ribosomal, 16S / Q000032:analysis; D012463:Saliva / Q000382:microbiology*
chemical_list: D012336:RNA, Ribosomal, 16S
keywords: BACTERIAL INTERACTIONS; HELICOBACTER PYLORI