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 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.

Fig. 1

Variation of species-level composition in healthy controls depends on the sample type. Multi-dimensional scaling plot using the whole-genome UniFrac metric. Each point corresponds to a single metagenome; sample type is shown by the shape, while the color shows whether the sample was collected from a CD patient or a subject from an external control group. The external control group included 385 stool metagenomes from healthy Russian, American, Danish and Chinese populations

Fig. 2

Taxonomic composition of gut metagenomes in Crohn’s disease patients is characterized by the pronounced presence of Escherichia/Shigella. The heatmap shows relative abundance of microbial genera (columns) in microbiota samples (rows). The genus levels are provided in percentages of the total bacterial abundance. The blue lines connect pairs of stool and ileal metagenomes from the same patients. Hierarchical clustering is performed using whole-genome UniFrac metric for rows and (1 - Spearman correlation) - for columns; linkage was performed by Ward’s method. Only the major genera (> 3% of the total abundance in at least one sample) are shown

Fig. 3

Variability of E. coli accessory gene presence profile across different groups of metagenomes. The boxplots show the distributions of pairwise dissimilarity of accessory genome (AG) profiles of E. coli calculated for all possible pairs from the following groups of samples: stool and ileal samples from the same Russian CD patient; all Russian CD patients; Spanish CD patients; USA treatment-naive CD patients; as well as the pairs between all unrelated samples. The scatterplots reflect the same information as the boxplots in a more detailed way

Fig. 4

Clustering of the metagenomes and E. coli genomes based on a unified representation of the accessory gene presence profile. Clustering is performed by the accessory OG profiles (binary metric, average linkage). Colour legend: black - genomes of pathogenic strains, green - commensal, red - Russian CD, blue - USA treatment-naive CD, orange - Spanish CD (remission), grey - healthy populations and other known E. coli genomes (details are in Additional file 1: Table S9)