Gastric microbes associated with gastric inflammation, atrophy and intestinal metaplasia 1 year after Helicobacter pylori eradication

Abstract

Objective: Helicobacter pylori is associated with gastric inflammation, precancerous gastric atrophy (GA) and intestinal metaplasia (IM). We aimed to identify microbes that are associated with progressive inflammation, GA and IM 1 year after H. pylori eradication.

Design: A total of 587 H. pylori-positive patients were randomised to receive H. pylori eradication therapy (295 patients) or placebo (292 patients). Bacterial taxonomy was analysed on 404 gastric biopsy samples comprising 102 pairs before and after 1 year H. pylori eradication and 100 pairs before and after 1 year placebo by 16S rRNA sequencing.

Results: Analysis of microbial sequences confirmed the eradication of H. pylori in treated group after 1 year. Principal component analysis revealed distinct microbial clusters reflected by increase in bacterial diversity (p<0.00001) after H. pylori eradication. While microbial interactions remained largely unchanged after placebo treatment, microbial co-occurrence was less in treated group. Acinetobacter lwoffii, Streptococcus anginosus and Ralstonia were enriched while Roseburia and Sphingomonas were depleted in patients with persistent inflammation 1 year after H. pylori eradication. A distinct cluster of oral bacteria comprising Peptostreptococcus, Streptococcus, Parvimonas, Prevotella, Rothia and Granulicatella were associated with emergence and persistence of GA and IM. Probiotic Faecalibacterium praustznii was depleted in subjects who developed GA following H. pylori eradication. Functional pathways including amino acid metabolism and inositol phosphate metabolism were enriched while folate biosynthesis and NOD-like receptor signalling decreased in atrophy/IM-associated gastric microbiota.

Conclusion: This study identified that gastric microbes contribute to the progression of gastric carcinogenesis after H. pylori eradication.

Keywords: H. pylorieradication; atrophy; gastric inflammation; gastric microbes; intestinal metaplasia.

Figure 1

Eradication of Helicobacter pylori with omeprazole, amoxicillin and clarithromycin (OAC) treatment. (A) Relative abundance of H. pylori in Pre_placebo, Post_placebo, Pre_OAC treatment and Post_OAC treatment groups. (B) Principal component analysis plot showing a distinct cluster for Post_OAC treatment group. (C) Bacterial diversity estimated by Shannon index for Pre_OAC treatment and Post_OAC treatment groups. (D) Top 20 bacterial genera before and after 1 year of OAC treatment. (B) Relative abundance of Neisseria, Haemophilus and Actinobacillus 1 year after OAC treatment. *Adjusted p<0.05, **adjusted p<0.01, ***adjusted p<0.001.

Figure 2

Microbiota ecology is altered after Helicobacter pylori eradication. Ecological co-occurrence network in (A) Pre_placebo, (B) Post_placebo, (C) Pre_OAC treatment and (D) Post_OAC treatment groups. Significant (Q>0.05) SparCC algorithm was used to infer co-occurrence among top (0.1% relative abundance) bacterial genera and with Helicobacter.

Figure 3

Bacteria associated with inflammation after Helicobacter pylori eradication. Linear discriminant analysis (LDA) with effect size (Lefse) showing (A) bacterial genera and (B) bacterial OTU associated with inflammation 1 year after H. pylori. OTU, operational taxonomic unit.

Figure 4

Bacteria associated with atrophy before and after Helicobacter pylori eradication. (A) Linear discriminant analysis (LDA) with effect size (Lefse) showing bacterial genera enriched in patients with atrophy before H. pylori eradication. (B) Spearman correlation of bacterial genera with atrophy scores after H. pylori eradication. (C) LDA with effect size (Lefse) showing bacterial genera enriched or depleted in patients with emerged atrophy 1 year after H. pylori eradication.

Figure 5

Bacteria associated with intestinal metaplasia (IM) before and after Helicobacter pylori eradication. (A) Linear discriminant analysis (LDA) with effect size (Lefse) showing bacterial genera enriched or depleted in patients with IM before H. pylori eradication. (B) Spearman correlation of bacterial genera with IM scores after H. pylori eradication. (C) Linear discriminant analysis (LDA) with effect size (Lefse) showing bacterial genera enriched or depleted in patients with persistent IM or (C) emerged IM 1 year after H. pylori eradication.

Figure 6

Functional features of gastric microbiota associated with inflammation, atrophy and IM after H. pylori eradication. (A) Predicted microbiota functional changes and (B) corresponding KEGG ontologies in persistent inflammation-associated gastric microbiota. (C) Predicted microbiota functional changes and (D) corresponding KEGG ontologies in GA-associated gastric microbiota. (E) Predicted microbiota functional changes and (F) corresponding KEGG ontologies in persistent IM-associated gastric microbiota. GA, gastric atrophy; IM, intestinal metaplasia; KEGG, Kyoto Encyclopedia of Genes and Genomes.