Genetic diversity of Escherichia coli in gut microbiota of patients with Crohn’s disease discovered using metagenomic and genomic analyses
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 elucid...
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BMC
2018-12-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-018-5306-5 |
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| author | Alexander V. Tyakht Alexander I. Manolov Alexandra V. Kanygina Dmitry S. Ischenko Boris A. Kovarsky Anna S. Popenko Alexander V. Pavlenko Anna V. Elizarova Daria V. Rakitina Julia P. Baikova Valentina G. Ladygina Elena S. Kostryukova Irina Y. Karpova Tatyana A. Semashko Andrei K. Larin Tatyana V. Grigoryeva Mariya N. Sinyagina Sergei Y. Malanin Petr L. Shcherbakov Anastasiya Y. Kharitonova Igor L. Khalif Marina V. Shapina Igor V. Maev Dmitriy N. Andreev Elena A. Belousova Yulia M. Buzunova Dmitry G. Alexeev Vadim M. Govorun |
| author_facet | Alexander V. Tyakht Alexander I. Manolov Alexandra V. Kanygina Dmitry S. Ischenko Boris A. Kovarsky Anna S. Popenko Alexander V. Pavlenko Anna V. Elizarova Daria V. Rakitina Julia P. Baikova Valentina G. Ladygina Elena S. Kostryukova Irina Y. Karpova Tatyana A. Semashko Andrei K. Larin Tatyana V. Grigoryeva Mariya N. Sinyagina Sergei Y. Malanin Petr L. Shcherbakov Anastasiya Y. Kharitonova Igor L. Khalif Marina V. Shapina Igor V. Maev Dmitriy N. Andreev Elena A. Belousova Yulia M. Buzunova Dmitry G. Alexeev Vadim M. Govorun |
| author_sort | Alexander V. Tyakht |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-12T12:52:30Z |
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| issn | 1471-2164 |
| language | English |
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| spelling | doaj.art-057ec1baa63d4208b083a47d6d16685d2022-12-22T00:23:57ZengBMCBMC Genomics1471-21642018-12-0119111410.1186/s12864-018-5306-5Genetic diversity of Escherichia coli in gut microbiota of patients with Crohn’s disease discovered using metagenomic and genomic analysesAlexander V. Tyakht0Alexander I. Manolov1Alexandra V. Kanygina2Dmitry S. Ischenko3Boris A. Kovarsky4Anna S. Popenko5Alexander V. Pavlenko6Anna V. Elizarova7Daria V. Rakitina8Julia P. Baikova9Valentina G. Ladygina10Elena S. Kostryukova11Irina Y. Karpova12Tatyana A. Semashko13Andrei K. Larin14Tatyana V. Grigoryeva15Mariya N. Sinyagina16Sergei Y. Malanin17Petr L. Shcherbakov18Anastasiya Y. Kharitonova19Igor L. Khalif20Marina V. Shapina21Igor V. Maev22Dmitriy N. Andreev23Elena A. Belousova24Yulia M. Buzunova25Dmitry G. Alexeev26Vadim M. Govorun27Federal Research and Clinical Centre of Physical-Chemical MedicineFederal Research and Clinical Centre of Physical-Chemical MedicineMoscow Institute of Physics and Technology, 9 Institutskiy per., DolgoprudnyFederal Research and Clinical Centre of Physical-Chemical MedicineFederal Research and Clinical Centre of Physical-Chemical MedicineFederal Research and Clinical Centre of Physical-Chemical MedicineFederal Research and Clinical Centre of Physical-Chemical MedicineMoscow Institute of Physics and Technology, 9 Institutskiy per., DolgoprudnyFederal Research and Clinical Centre of Physical-Chemical MedicineFederal Research and Clinical Centre of Physical-Chemical MedicineFederal Research and Clinical Centre of Physical-Chemical MedicineFederal Research and Clinical Centre of Physical-Chemical MedicineFederal Research and Clinical Centre of Physical-Chemical MedicineFederal Research and Clinical Centre of Physical-Chemical MedicineFederal Research and Clinical Centre of Physical-Chemical MedicineKazan Federal University, 18 Kremlyovskaya St.Kazan Federal University, 18 Kremlyovskaya St.Kazan Federal University, 18 Kremlyovskaya St.Moscow Clinical Scientific Center, 86 Shosse Entuziastov St.Clinical and Research Institute of Emergency Children’s Surgery and Trauma, 22 Bolshaya Polyanka St.State Scientific Center of Coloproctology, 2 Salam Adil St.State Scientific Center of Coloproctology, 2 Salam Adil St.Moscow State University of Medicine and Dentistry, Build. 6, 20 Delegatskaya St.Moscow State University of Medicine and Dentistry, Build. 6, 20 Delegatskaya St.Moscow Regional Research and Clinical Institute, 61/2 Shchepkina strMoscow Regional Research and Clinical Institute, 61/2 Shchepkina strFederal Research and Clinical Centre of Physical-Chemical MedicineFederal Research and Clinical Centre of Physical-Chemical MedicineAbstract 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.http://link.springer.com/article/10.1186/s12864-018-5306-5Gut microbiotaCrohn’s diseaseEscherichia coliGene contentInflammatory bowel diseasesMetagenomics |
| spellingShingle | Alexander V. Tyakht Alexander I. Manolov Alexandra V. Kanygina Dmitry S. Ischenko Boris A. Kovarsky Anna S. Popenko Alexander V. Pavlenko Anna V. Elizarova Daria V. Rakitina Julia P. Baikova Valentina G. Ladygina Elena S. Kostryukova Irina Y. Karpova Tatyana A. Semashko Andrei K. Larin Tatyana V. Grigoryeva Mariya N. Sinyagina Sergei Y. Malanin Petr L. Shcherbakov Anastasiya Y. Kharitonova Igor L. Khalif Marina V. Shapina Igor V. Maev Dmitriy N. Andreev Elena A. Belousova Yulia M. Buzunova Dmitry G. Alexeev Vadim M. Govorun Genetic diversity of Escherichia coli in gut microbiota of patients with Crohn’s disease discovered using metagenomic and genomic analyses BMC Genomics Gut microbiota Crohn’s disease Escherichia coli Gene content Inflammatory bowel diseases Metagenomics |
| title | Genetic diversity of Escherichia coli in gut microbiota of patients with Crohn’s disease discovered using metagenomic and genomic analyses |
| title_full | Genetic diversity of Escherichia coli in gut microbiota of patients with Crohn’s disease discovered using metagenomic and genomic analyses |
| title_fullStr | Genetic diversity of Escherichia coli in gut microbiota of patients with Crohn’s disease discovered using metagenomic and genomic analyses |
| title_full_unstemmed | Genetic diversity of Escherichia coli in gut microbiota of patients with Crohn’s disease discovered using metagenomic and genomic analyses |
| title_short | Genetic diversity of Escherichia coli in gut microbiota of patients with Crohn’s disease discovered using metagenomic and genomic analyses |
| title_sort | genetic diversity of escherichia coli in gut microbiota of patients with crohn s disease discovered using metagenomic and genomic analyses |
| topic | Gut microbiota Crohn’s disease Escherichia coli Gene content Inflammatory bowel diseases Metagenomics |
| url | http://link.springer.com/article/10.1186/s12864-018-5306-5 |
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