Abstract
The human gut microbiome plays an important role both in health and disease. The use of antibiotics can alter gut microbiota composition, which can cause complications of various kinds. Here we report a whole-genome sequencing metagenomic study of the intestinal microbiota changes caused by Helicobacter pylori eradication therapy. We have found the significant decrease in taxonomic alpha-diversity due to the therapy. The changes observed were more extensive for patients with duodenal ulcer and female ones. We also observed perturbations in intraspecies structures (“strains”), which were significantly higher in group of patients under the therapy than in control group of people without treatment. As well across the patients under the H. pylory eradication therapy we have detected the shifts in the metabolic potentials and resistome. Metabolic pathways associated with the metabolism of carbohydrates and chorismate decreased. Changes in the resistome profile have also been identified: antibiotic resistance genes (ARGs) to macrolides were increased and to tetracyclines-decreased. We also isolated and sequenced Enterococcus faecium strains from two patients. After the therapy this bacterium increased antibiotic resistance in vitro, it had higher ARGs to macrolides and tetracyclines, and this bacterium relative abundance in metagenome was at higher level in comparison with strains before therapy.