The Human Gastric Microbiome Is Predicated upon Infection with Helicobacter pylori

Abstract

The human gastric lumen is one of the most hostile environments of the human body 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, multicenter, clinical trial the 16S rRNA gene amplicon based bacterial microbiome in a total of 30 homogenized and frozen gastric biopsy samples from eight geographic locations. The evaluation of the samples for H.p. infection status was done by histopathology and a specific 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 a considerable 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. 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 multicentre cohort of patients with varying diagnoses.

The eradication of Helicobacter pylori restores rather than disturbs the gastrointestinal microbiota in asymptomatic young adults

“…Recently, an accumulating number of studies have been conducted to compare the compositional differences of gastric microbiota between H pylori ‐positive and H pylori ‐negative samples. A study by Klymiuk et al reported the effect of H pylori infection on the gastric microbiota and found that the number of Lactobacillus , Streptococcus , Acinetobacter , Prevotella, and Bacteroides genera was remarkedly decreased, while Helicobacter was increased in H pylori ‐positive samples. Another study compared the active bacterial communities in the stomach with and without Helicobacter infection and found that the stomach biopsies in individuals infected with H pylori had higher abundance of Helicobacter but lower abundance of Prevotella and Streptococcus .…”

Helicobacter pylori infection alters gastric and tongue coating microbial communities

“…However, investigations of gastric fluid and biopsy samples by next‐generation sequencing (NGS) demonstrate that the human gastric microbiota is a diverse ecosystem that dominated by five phyla, including Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria, and Proteobacteria . There is a trend of gastric microbiota alterations in people with Helicobacter pylori ( H pylori ) infection; however, inconsistent results have been obtained . With a small Colombian patient cohort (n = 40), Yang et al showed that the overall gastric microbiota composition was largely independent of the H pylori infection and carriage of the cag pathogenicity island .…”

Impact of Duodeno-Jejunal Bypass Liner (EndoBarrierTM) Implantation on Insulin Sensitivity in Patients with Type 2 Diabetes Mellitus (T2DM): A Study Protocol for a Pilot Trial

“…Total DNA is isolated from frozen stool samples using the MagnaPure LC DNA Isolation Kit III (Bacteria, Fungi) (Roche Diagnostics) according to the manufacturer’s instructions, including mechanic and enzymatic lysis as described in Klymiuk et al [21]. For 16S rRNA gene analysis, hypervariable regions V1–2 are amplified in a target-specific PCR assay (primers: 27F-AGAGTTTGATCCTGGCTCAG; R357-CTGCTGCCTYCCGTA), and amplification products are sequenced after indexing and purification on an Illumina MiSeq desktop sequencer (Illumina, Eindhoven, The Netherlands) according to published procedures [21, 22] at the Core Facility for Molecular Biology at the Center for Medical Research in Graz.…”

“…For 16S rRNA gene analysis, hypervariable regions V1–2 are amplified in a target-specific PCR assay (primers: 27F-AGAGTTTGATCCTGGCTCAG; R357-CTGCTGCCTYCCGTA), and amplification products are sequenced after indexing and purification on an Illumina MiSeq desktop sequencer (Illumina, Eindhoven, The Netherlands) according to published procedures [21, 22] at the Core Facility for Molecular Biology at the Center for Medical Research in Graz.…”