Genetic diversity of Escherichia coli in gut microbiota of patients with Crohn's disease discovered using metagenomic and genomic analyses.

Autor: Tyakht AV; Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia. a.tyakht@gmail.com.; Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, Russian Federation, 141700. a.tyakht@gmail.com.; ITMO University, 49 Kronverkskiy pr, Saint-Petersburg, Russian Federation, 197101. a.tyakht@gmail.com., Manolov AI; Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia., Kanygina AV; Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, Russian Federation, 141700., Ischenko DS; Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia.; Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, Russian Federation, 141700., Kovarsky BA; Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia., Popenko AS; Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia., Pavlenko AV; Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia., Elizarova AV; Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, Russian Federation, 141700., Rakitina DV; Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia., Baikova JP; Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia., Ladygina VG; Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia., Kostryukova ES; Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia.; Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, Russian Federation, 141700., Karpova IY; Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia., Semashko TA; Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia.; Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, Russian Federation, 141700., Larin AK; Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia., Grigoryeva TV; Kazan Federal University, 18 Kremlyovskaya St., Kazan, Russian Federation, 420008., Sinyagina MN; Kazan Federal University, 18 Kremlyovskaya St., Kazan, Russian Federation, 420008., Malanin SY; Kazan Federal University, 18 Kremlyovskaya St., Kazan, Russian Federation, 420008., Shcherbakov PL; Moscow Clinical Scientific Center, 86 Shosse Entuziastov St., Moscow, Russian Federation, 111123., Kharitonova AY; Clinical and Research Institute of Emergency Children's Surgery and Trauma, 22 Bolshaya Polyanka St., Moscow, Russian Federation, 119180., Khalif IL; State Scientific Center of Coloproctology, 2 Salam Adil St., Moscow, Russian Federation, 123423., Shapina MV; State Scientific Center of Coloproctology, 2 Salam Adil St., Moscow, Russian Federation, 123423., Maev IV; Moscow State University of Medicine and Dentistry, Build. 6, 20 Delegatskaya St., Moscow, Russian Federation, 127473., Andreev DN; Moscow State University of Medicine and Dentistry, Build. 6, 20 Delegatskaya St., Moscow, Russian Federation, 127473., Belousova EA; Moscow Regional Research and Clinical Institute, 61/2 Shchepkina str, Moscow, Russian Federation, 129110., Buzunova YM; Moscow Regional Research and Clinical Institute, 61/2 Shchepkina str, Moscow, Russian Federation, 129110., Alexeev DG; Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia.; Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, Russian Federation, 141700., Govorun VM; Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia.; Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, Russian Federation, 141700.; M.M. Shemyakin - Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 16/10 Miklukho-Maklaya St., Moscow, Russian Federation, 117997.
Jazyk: angličtina
Zdroj: BMC genomics [BMC Genomics] 2018 Dec 27; Vol. 19 (1), pp. 968. Date of Electronic Publication: 2018 Dec 27.
DOI: 10.1186/s12864-018-5306-5
Abstrakt: Background: Crohn's disease is associated with gut dysbiosis. Independent studies have shown an increase in the abundance of certain bacterial species, particularly Escherichia coli with the adherent-invasive pathotype, in the gut. The role of these species in this disease needs to be elucidated.
Methods: We performed a metagenomic study investigating the gut microbiota of patients with Crohn's disease. A metagenomic reconstruction of the consensus genome content of the species was used to assess the genetic variability.
Results: The abnormal shifts in the microbial community structures in Crohn's disease were heterogeneous among the patients. The metagenomic data suggested the existence of multiple E. coli strains within individual patients. We discovered that the genetic diversity of the species was high and that only a few samples manifested similarity to the adherent-invasive varieties. The other species demonstrated genetic diversity comparable to that observed in the healthy subjects. Our results were supported by a comparison of the sequenced genomes of isolates from the same microbiota samples and a meta-analysis of published gut metagenomes.
Conclusions: The genomic diversity of Crohn's disease-associated E. coli within and among the patients paves the way towards an understanding of the microbial mechanisms underlying the onset and progression of the Crohn's disease and the development of new strategies for the prevention and treatment of this disease.
Databáze: MEDLINE
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