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.

Keywords: 16S rRNA gene analysis; CagA; Helicobacter pylori; gastric microbiota; multicenter study.

Figure 1

Box plot of the median relative abundances of the most dominant phyla in the three sample groups (Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Fusobacteria). The phylum Proteobacteria (with the genus Helicobacter) increased in its relative abundance from the H.p.- over the H.p.+/CagA− to the H.p.+/CagA+ group. Significant differences were only found between the H.p.− vs the H.p.+/CagA− and the H.p.− vs H.p.+/CagA+ groups, respectively.

Figure 2

Principal Component Analysis (PCA) ordination plots of relative abundance of genera (A) and OTUs (B). Statistically significant differences were found between H.p.− and the H.p.+/CagA− (adj. p-value OTU = 0.000001, adj. p-value genera = 0.000001) as well as between the H.p.− and the H.p.+/CagA+ groups (adj. p-value OTU = 0.000009, adj. p-value genera = 0.000023). No statistically significant differences were found between H.p.+/CagA− vs. H.p.+/CagA+ sample groups (adj. p-value OTU = 0.236619, adj. p-value genera = 0.095089). Ellipses denote the 95% confidence.

Figure 3

(A) Chao1, (B) PD-wholetree, and (C) observed species rarefied alpha diversity of the three sample groups (H.p.−, H.p.+/CagA−, H.p.+/CagA+). A significant difference was found between the H.p. negative and the H.p.+/CagA+ groups with a not significant intermediate phenotype of the H.p.+/CagA− group. Error bars denote standard error.

Figure 4

Venn diagram visualizing the number of group specific genera (A) and OTUs (B).

Figure 5

Linear discriminant Effect Size analysis (LefSe) analysis revealed over 40 taxa (H.p.− vs. H.p.+/CagA+ 45, H.p.− vs. H.p.+/CagA− 41) significantly different in their relative abundances between the sample groups in the pairwise comparisons H.p.− vs. H.p.+/CagA+, H.p.− vs. H.p.+/CagA− and H.p.+/CagA− vs. H.p.+/CagA+. Only taxa with a relative abundance of at least 1% in at least 50% of all samples out of one sample group were considered.