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BMC Genomics. 2018 Dec 27;19(1):968. doi: 10.1186/s12864-018-5306-5.

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

Author information

1
Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia. a.tyakht@gmail.com.
2
Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, Russian Federation, 141700. a.tyakht@gmail.com.
3
ITMO University, 49 Kronverkskiy pr, Saint-Petersburg, Russian Federation, 197101. a.tyakht@gmail.com.
4
Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia.
5
Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, Russian Federation, 141700.
6
Kazan Federal University, 18 Kremlyovskaya St., Kazan, Russian Federation, 420008.
7
Moscow Clinical Scientific Center, 86 Shosse Entuziastov St., Moscow, Russian Federation, 111123.
8
Clinical and Research Institute of Emergency Children's Surgery and Trauma, 22 Bolshaya Polyanka St., Moscow, Russian Federation, 119180.
9
State Scientific Center of Coloproctology, 2 Salam Adil St., Moscow, Russian Federation, 123423.
10
Moscow State University of Medicine and Dentistry, Build. 6, 20 Delegatskaya St., Moscow, Russian Federation, 127473.
11
Moscow Regional Research and Clinical Institute, 61/2 Shchepkina str, Moscow, Russian Federation, 129110.
12
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.

Abstract

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.

KEYWORDS:

Crohn’s disease; Escherichia coli; Gene content; Gut microbiota; Inflammatory bowel diseases; Metagenomics; Pangenome

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