Maria Markelova

Shifts in the gut microbiota structure caused by Helicobacter pylori eradication therapy

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 decrease in taxonomic alpha-diversity due to the therapy. The changes observed were more extensive for patients with duodenal ulcer and female ones. As well across the patients under the therapy we have detected the shifts in the metabolic potential and resistome. Seven KEGG pathways associated with quorum sensing, genetic Information processing and environmental Information processing were increased, while metabolic pathways related with metabolism of cofactors and vitamins and glycan biosynthesis and metabolism decreased. Changes in the resistome profile have also been identified. We observed perturbations in intraspecies structures, which were higher in group of patients under the therapy than in control group of people without treatment. The Eubacterium rectale pangenome extracted from metagenomic data were changed. We also isolated and sequenced Enterococcus faecium strains from two patients before and after eradication therapy. After the therapy this bacterium increased as the antibiotic resistance in vitro, as well the number of ARGs to macrolides and tetracyclines and metagenomic relative abundance in comparison with strains before therapy. In summary, microbial community demonstrated shift to reduce metabolic potential and to increased mechanisms, which mediate more survival condition through intraspecies perturbations. Importance 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. H. pylori eradication therapy causes multiple shifts and alterations (including intraspecies changes) of the intestinal microbiota structure and leads to the accumulation of genes which determine resistance to macrolides. Since these changes are not the same for patients with various diseases, patients with duodenal ulcer may be further paid special attention for reducing side effects, such as antibiotic-induced dysbiosis. Also, study of antibiotic treatment in terms of its impact upon the human gut microbiota allows shedding light on of the complex processes that cause accumulation and spread of antibiotic resistance. An identification and understanding of these complicated processes may help to constrain antibiotic resistance spread, which is of great importance for human health care.

The Influence of Helicobacter Pylori Eradication Therapy on Intestinal Microbiota

H. pylori eradication therapy including antibiotics as well as H. pylori itself can influence the normal intestinal microbiota content. The aim of the study was to describe the gut microbiota composition in H. pylori-positive and H. pylori-negative patients as well as the influence of eradication therapy on gut microbiota. 198 stool samples were taken for analysis: 74 samples from H. pylori-positive patients before eradication therapy, 74 from the same patients after eradication, 50 from H. pylori-negative patients (control group). Total DNA was isolated from the stool samples and subjected to whole-genome sequencing on SOLiD 5500 Wildfire platform. Intestinal microbiota was evaluated based on number of species, qualitative composition, Shannon diversity index and Bray-Curtis metrics. Results. Bacterial community was quite similar in all groups: Bacteroides, Prevotella, Eubacterium, Roseburia, Faecalibacterium and Clostridium genera were predominant in all samples. The spread in variations of the prevailing Firmicutes and Bacteroides phyla was wider after the treatment than in control samples. In about half of patients eradication therapy led to the decrease of both the number of species and the Shannon index indicating a decrease in the overall bacterial diversity with a possible predominance of individual species. Eradication therapy resulted in the reduction of the relative representation of Bifidobacterium, Collinsella, Coprococcus genera, accompanied with the increase of Clostridium, Bacteroides, Coprobacillus and Flavonifractor genera. Evaluation of taxonomic diversity changes based on Shannon index and Bray-Curtis metrics allows to differentiate patients into the groups with mild, moderate and severe changes. In 82% of cases mild and moderate changes in microbial community content were found increased level of Bacteroides genus, decreasing levels of Bifidobacterium and Eubacterium genus, simultaneously. Escherichia genus had the increased abundance in the majority of patients with severe microbial shifts after eradication therapy. Changes in the composition of intestinal microbiota after H. pylori eradication therapy depend mostly on the initial content of the intestinal microbiota: the closer initial microbial state of H. pylori-positive patients to the control samples is, the milder changes could be detected after eradication therapy. Gene-centric analysis of the functional composition in paired samples taken before and after therapy showed an increase of the relative abundance of genes conferring antibiotic resistance. Conclusions. Evaluation of intestinal microflora content prior to treatment can probably predict the incidence of side effects related to changes in microbial composition. This work was financially supported by the Ministry of Education and Science of Russian Federation (agreement #14.575.21.0076, ID RFMEFI575I4X0076).

Shotgun metagenomic data on the human stool samples to characterize shifts of the gut microbial profile after the Helicobacter pylori eradication therapy

The shotgun sequencing data presented in this report are related to the research article named “Gut microbiome shotgun sequencing in assessment of microbial community changes associated with H. pylori eradication therapy” (Khusnutdinova et al., 2016) [1]. Typically, the H. pylori eradication protocol includes a prolonged two-week use of the broad-spectrum antibiotics. The presented data on the whole-genome sequencing of the total DNA from stool samples of patients before the start of the eradication, immediately after eradication and several weeks after the end of treatment could help to profile the gut microbiota both taxonomically and functionally. The presented data together with those described in Glushchenko et al. (2017) [2] allow researchers to characterize the metagenomic profiles in which the use of antibiotics could result in dramatic changes in the intestinal microbiota composition. We perform 15 gut metagenomes from 5 patients with H. pylori infection, obtained through the shotgun sequencing on the SOLiD 5500 W platform. Raw reads are deposited in the ENA under project ID PRJEB21338.