Distinctive features of microbiota from patients with Crohn`s disease

The ultimate etiology of Crohnu0027s disease (CD) still remains unknown [1]. The goal of our work was to investigate the  distinctive features of microbiota associated with CD.  We sequenced 24 metagenomes from 19 patients with CD and 28 genomes of E. coli (EC) isolated for ten of these patients. Both stool and ileal samples were obtained. We also included available metadata to perform phylogenetic and functional analysis and to determine genes under selection.An increased presence of various opportunists in each patient was observed along with the increased fraction of E. coli in comparison with the healthy population (2.4% ± 16.5% vs. 0.2% ± 7.7%). Using ad hoc metagenomic SNP profiling algorithm we revealed two cases of CD patients hosting multiple strains of E. coli. EC from the stool and ileal samples were highly similar.We found that propanediol utilization genes were significantly overrepresented in CD-associated E. coli. Interestingly, the microbial species  containing these genes varied between the patients ( E. coli, K. pneumoniae, P. putida). Other overrepresented genes were involved in carbohydrate and iron uptake, intestinal colonization. We also observed signs of negative selection in the genes associated with the response to oxidative stress.