The Effect of Helicobacter pylori Eradication on Human Microbiota: Metagenome Analysis of the Human Gut Microbiome

D.R. Khusnutdinova^a*, M.I. Markelova^a**, E.A. Boulygina^a, M.N. Siniagina^a, S.Yu. Malanin^a, T.V. Grigoryeva^a, R.K. Ismagilova^a, D.D. Safina^a, S.R. Abdulkhakov^a, R.A. Abdulkhakov^b, V.M. Chernov^a,c, O.A. Chernova^a,c

^aKazan Federal University, Kazan, 420008 Russia

^bKazan State Medical University, Kazan, 420012 Russia

^cKazan Institute of Biochemistry and Biophysics, Kazan Scientific Center,

Russian Academy of Sciences, Kazan, 420111 Russia

E-mail: ^*dilyahusn@gmail.com, ^**mimarkelova@gmail.com

Received February 14, 2017

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Abstract

A total of 152 stool samples from 76 patients with symptoms of gastrointestinal diseases have been analyzed using metagenomic shotgun sequencing technology to assess the effect of Helicobacter pylori eradication therapy on Bifidobacterium, Lactobacillus, Escherichia, and Clostridium genera. The relative abundance of bacteria representing these genera in the intestinal microflora of patients before and after antibiotic therapy has been evaluated. It has been shown that the therapy did not have any critical effect in the majority of cases on the number of Lactobacillus, Escherichia and Clostridium genera in the microbial community. Their abundance varied within 0.5% in 76.5%, 51.3%, and 55.2% of patients, respectively. The Bifidobacterium genus has been found to be more susceptible to antibiotics (their number decreased significantly in 60.5% of cases). However, 9.2% of patients have shown the opposite effect. Thus, the obtained data demonstrate that Helicobacter pylori eradication therapy does not have uniform effects on the key members of human intestinal microbiota. This fact should be taken into account when predicting the risks of side effects of antibiotics.

Keywords: human intestinal microbiome, Helicobacter pylori, eradication therapy, antibiotics, shotgun sequencing, metagenome analysis

Acknowledgments. The study was supported by the Ministry of Education and Science of the Russian Federation as part of the federal target program “Investigations and developments on priority areas of scientific-technological complex of Russia for 2014–2020” (Agreement no. 14.575.21.0076 of August 22, 2014, ID RFMEFI575I4X0076).

Figure Captions

Fig. 1. The distribution of 15 bacterial genera dominating in the intestinal metagenome of the control group, %.

Fig. 2. The distribution of 15 bacterial genera dominating in the intestinal metagenome of patients before H. pylori eradication therapy, %.

Fig. 3. The distribution of 15 bacterial genera dominating in the intestinal metagenome of patients after H. pylori eradication therapy, %.

Fig. 4. Changes in the number of Bifidobacterium, Lactobacillus, Escherichia, and Clostridium in the intestinal microbiome of patients after antibiotic therapy.

Fig. 5. The main variants of changes in the relative abundance of Bifidobacterium, Lactobacillus, Escherichia, and Clostridium in the intestinal microbiome of patients after antibiotic therapy in the descending order of percentage of cases.

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For citation: Khusnutdinova D.R., Markelova M.I., Boulygina E.A., Siniagina M.N., Malanin S.Yu., Grigoryeva T.V., Ismagilova R.K., Safina D.D., Abdulkhakova S.R., Abdulkhakov R.A., Chernov V.M., Chernova O.A. The effect of Helicobacter pylori eradication on human microbiota: Metagenome analysis of the human gut microbiome. Uchenye Zapiski Kazanskogo Universiteta. Seriya Estestvennye Nauki, 2017, vol. 159, no. 2, pp. 217–231. (In Russian)

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