Probiotics modulate the interactions between gastric and intestinal microbiota after Helicobacter pylori eradication

Abstract

Standard eradication therapy for Helicobacter pylori ( H. pylori ) induces substantial gastrointestinal dysbiosis. Here, we investigated whether probiotic supplementation mitigates these spatial microbial perturbations and facilitates ecological recovery post-eradication. C57BL/6 mice were assigned to five groups: uninfected controls, H. pylori PMSS1-infected mice, infected mice receiving two weeks of triple therapy (omeprazole, clarithromycin and metronidazole), and infected mice undergoing either four-week spontaneous recovery or probiotic supplementation ( Enterococcus faecium R0026 and Bacillus subtilis R0179 ) after eradication. Paired gastric and fecal 16 S rRNA sequencing was utilized to assess microbial composition, cross-compartment co-occurrence networks and predicted functional profiles. H. pylori infection reshapes both the gastric and intestinal microbiota, with more pronounced perturbation on the stomach. However, eradication therapy triggered severe compartment specific dysbiosis that predominantly disrupted the intestine, characterized by near complete depletion of Bacteroidota and expansion of Escherichia-Shigella and Klebsiella . Spontaneous recovery remained incomplete four weeks post eradication. Interestingly, probiotic administration significantly accelerated gastrointestinal restoration and preferentially shaped the intestinal microbiota. It replenished depleted gastric dominant taxa such as Pseudomonas , norank_f_Muribaculaceae , and Ligilactobacillus and rescued the gut microbiota by enriching Bacteroidota and short chain fatty acid (SCFA) producers including Lachnospiraceae_FCS020_group and Ligilactobacillus . Paired analysis revealed that eradication severely disrupted the shared ASVs between the stomach and intestine, a trans-compartment connectivity that was effectively restored by probiotics. Notably, this microbial restoration coincided with enhanced cross-compartment network stability, enrichment of predicted SCFA metabolism and immune modulation pathways and improved intestinal barrier integrity. We delineate the distinct spatial ecological disruptions driven by H. pylori infection and eradication therapy. Probiotic intervention actively orchestrates the synergistic recovery of the gastrointestinal microbiome, providing compelling preclinical evidence for this adjunctive strategy to counter eradication induced dysbiosis.