Shifts in the gut microbiota structure caused byHelicobacter pylorieradication therapy
Authors: Olekhnovich Evgenii I. , Manolov Alexander I. , Prianichniikov Nikita A. , Samoilov Andrei E. , Malakhova Maja V. , Pavlenko Alexander V. , Babenko Vlad V. , Larin Andrei K. , Babin Yuriy Y. , Starikova Elizaveta V. , Chuvelev Dmitry I. , Kovarsky Boris A. , Tregubova Maria A. , Safina Dilyara D. , Markelova Maria I. , Grigoryeva Tatiana V. , Boulygina Eugenia A. , Malanin Sergey Yu. , Abdulkhakov Rustam A. , Abdulkhakov Sayar R. , Kostryukova Elena S. , Ilina Elena N. , Govorun Vadim M. 
Published: April 2018

AbstractThe 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 byHelicobacter pylorieradication 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. TheEubacterium rectalepangenome extracted from metagenomic data were changed. We also isolated and sequencedEnterococcus faeciumstrains 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.ImportanceThe 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. pylorieradication 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.