Microbial composition of gastric lesions: differences based on Helicobacter pylori virulence profile

Abstract

Helicobacter pylori infection is a major risk factor for gastric adenocarcinomas. In the case of the intestinal subtype, chronic gastritis and intestinal metaplasia are well-known sequential steps in carcinogenesis. H. pylori has high genetic diversity that can modulate virulence and pathogenicity in the human host as a cag Pathogenicity Island (cagPAI). However, bacterial gene combinations do not always explain the clinical presentation of the disease, indicating that other factors associated with H. pylori may play a role in the development of gastric disease. In this context, we characterized the microbial composition of patients with chronic gastritis (inactive and active), intestinal metaplasia, and gastric cancer as well as their potential association with H. pylori. To this end, 16 S rRNA metagenomic analysis was performed on gastric mucosa samples from patients with different types of lesions and normal gastric tissues. Our main finding was that H. pylori virulence status can contribute to significant differences in the constitution of the gastric microbiota between the sequential steps of the carcinogenesis cascade. Differential microbiota was observed in inactive and active gastritis dependent of the H. pylori presence and status (p = 0.000575). Pseudomonades, the most abundant order in the gastritis, was associated the presence of non-virulent H. pylori in the active gastritis. Notably, there are indicator genera according to H. pylori status that are poorly associated with diseases and provide additional evidence that the microbiota, in addition to H. pylori, is relevant to gastric carcinogenesis.

Keywords: Gastric cancer; Helicobacter pylori; Metagenomics.

Fig. 1

Alpha Diversity by Observed, Chao1, Shannon and Simpson analysis. The samples were separated by type of lesion (Control, Cancer, Gastritis and Metaplasia).

Fig. 2

Distribution of files with an abundance above 5%, separated by lesion (Gastritis, Metaplasia and Cancer). Control refers to patients without gastric lesions. The different colors in the vertical bars indicate the main phyla observed in each sample. Lowercase letters show the statistical importance of that phylum in the sample group.

Fig. 3

Distribution of phyla with abundance above 5% for Metaplasia and Cancer. Control refers to patients without gastric lesions. Samples derived from patients with metaplasia are separated into “HP Pos” and “HP Neg” and, referring to the presence or absence of H. pylori. Samples derived from cancer patients are separated into “Non-virulent” and “Virulent”, referring to the virulence profile of the H. pylori.

Fig. 4

Distribution of orders with abundance above 5% separated by lesion. Control refers to patients without gastric lesions.

Fig. 5

Distribution of orders with abundance above 5% for Gastritis. Control refers to patients without gastric lesions. Gastritis samples are separated according to the presence and virulence of H. pylori as well as active or inactive gastritis status.

Fig. 6

Distribution of orders with abundance above 5% for Metaplasia. Control refers to patients without gastric lesions. Samples derived from patients with metaplasia are separated into “HP Pos” and “HP Neg”, referring to the presence or absence of H. pylori.

Fig. 7

Distribution of genus with abundance above 20%, separated by lesion. Control refers to patients without gastric lesions.

Fig. 8

Distribution of genera with abundance above 20% for the Gastritis group. Control refers to patients without gastric lesions. Samples derived from patients with gastritis are separated according to the presence and virulence of H. pylori as well as the active or inactive state of the gastritis.

Fig. 9

Distribution of genera with abundance above 20% for Metaplasia. Control refers to patients without gastric lesions. Samples derived from patients with metaplasia are separated into “HPneg” and “HPpos”, referring to the absence or presence of H. pylori, respectively.

Fig. 10

Genus’s distribution with abundance above 20% for Cancer. Control refers to patients without gastric lesions. Samples derived from cancer patients are separated into “Non-virulent” and “Virulent”, referring to the virulence profile of the H. pylori.

Fig. 11

Main genera involved in each group of gastric lesions, classified in families.

Fig. 12

Most abundant genera in each group of gastric lesions.