2018
DOI: 10.1186/s12864-018-5306-5
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Genetic diversity of Escherichia coli in gut microbiota of patients with Crohn’s disease discovered using metagenomic and genomic analyses

Abstract: BackgroundCrohn’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.MethodsWe 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 variab… Show more

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Cited by 26 publications
(19 citation statements)
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“…Conversely, the symptoms of diabetes and inflammation were also shown to be ameliorated upon the administration of Faecalibacterium prausnitzii to such patients [53], suggesting an important diagnostic and therapeutic relevance of these microorganisms. Additionally, reduced Faecalibacterium prausnitzii levels in the gut have also been observed during the prevalence of ulcerative colitis and Crohn's disease [54][55][56]. Furthermore, in patients with Parkinson's disease, the gut levels of Prevotella copri, Faecalibacterium prausnitzii, and Coprococcus eutactus were also observed to be relatively decreased [57].…”
Section: Discussionmentioning
confidence: 87%
“…Conversely, the symptoms of diabetes and inflammation were also shown to be ameliorated upon the administration of Faecalibacterium prausnitzii to such patients [53], suggesting an important diagnostic and therapeutic relevance of these microorganisms. Additionally, reduced Faecalibacterium prausnitzii levels in the gut have also been observed during the prevalence of ulcerative colitis and Crohn's disease [54][55][56]. Furthermore, in patients with Parkinson's disease, the gut levels of Prevotella copri, Faecalibacterium prausnitzii, and Coprococcus eutactus were also observed to be relatively decreased [57].…”
Section: Discussionmentioning
confidence: 87%
“…While our method is cultivation-independent and allows to capture a variety of taxa undetected during a classic stool test, its taxonomic detection accuracy is limited by the level of genus. A single genus can include species and strains with a highly variable gene content resulting in dramatically different phenotypes -from probiotic to human pathogen like in the case of Escherichia coli [6] -or correlating to opposing dietary patterns as shown for Prevotella copri [56]. Despite this limitation, a general-level profile of the gut microbiome composition provided by the proposed platform can be useful for assessing the general degree of dysbiosis.…”
Section: Discussionmentioning
confidence: 99%
“…The gut is colonized with 10 13 of microbes belonging to thousands of species. Alterations of microbiome composition are linked to lifestyle changes, short-and long-term diet [1], probiotics intake [1,2], medications including antibiotics [3] and diseases including obesity, type 2 diabetes [4], colorectal cancer [5], Crohn's disease [6] and others. Based on the discovered associations, a number of microbial taxa have been proposed as potential biomarkers.…”
Section: Introductionmentioning
confidence: 99%
“…As an alternative to generating a simple consensus sequence of a reference genome, or profiling of marker genes, some tools attempt to reconstruct the haplotypes of all strains co-existing in a sample based on the frequencies of the observed polymorphisms (haplotype reconstruction-based tools, [22,[26][27][28][29][30][31][32]). To achieve best performances, these approaches rely on a simultaneous analysis of a cohort of samples (as, e.g., human fecal sample series from healthy or diseased individuals [26][27][28]33], environmental sample series [29,34] and anaerobic digester metagenome time series [28]). If such a cohort is not available, the performance will depend strongly on the differences between relative abundances of the strains, as well as the coverage of the species of interest (e.g., >30× for Evorha [30]).…”
Section: Introductionmentioning
confidence: 99%