THE HUMAN GASTRIC MICROBIOME IS PREDICATED UPON INFECTION WITH HELICOBACTER PYLORI

The human gastric lumen is one of the most hostile environments of the human body and was suspected to be sterile until the discovery of Helicobacter pylori (H.p.). State of the art next generation sequencing technologies multiply the knowledge on H.p. functional genomics as well as on the colonization of supposed sterile human environments like the gastric habitat. Here we studied in a prospective, clinical trial the 16s rRNA gene amplicon based bacterial microbiome in a total of 30 gastric biopsy samples. The evaluation of the samples for H.p. infection status was done by histopathology and a quantitative real time PCR assay. CagA status was determined by a CagA-specific PCR assay. Patients were grouped accordingly as H.p.-negative, H.p.-positive but CagA-negative and H.p.-positive and CagA-positive (n=10, respectively). Here we show that H.p. infection of the gastric habitat dominates the gastric microbiota in most patients and is associated with a significant decrease of the microbial alpha diversity from H.p. negative to H.p. positive with CagA as an intermittent factor. The genera Actinomyces, Granulicatella, Veillonella, Fusobacterium, Neisseria, Helicobacter, Streptococcus and Prevotella are significantly different between the H.p.-positive and H.p.-negative sample groups. In H.p. negative samples, microbiota were similar to those found in the oropharynx. Differences in microbiota found between CagA-positive and CagA-negative patients were not statistically significant and need to be re-evaluated in larger sample cohorts. In conclusion, H.p. infection dominates the gastric microbiome in a well characterized European cohort of patients with gastritis. We hypothesize that the bacterial derived nucleic acids detected in H.p. negative gastric biopsies are due to swallowed microbiota rather than an active bacterial replication and colonization.