Diversity of adhered microbial communities in colon mucosal biopsies of Crohn patients by 16S rRNA gene pyrosequencing, evidences for two main distinct groups.

The mucosal adhered microbiota of 13 patients suffering from Crohn disease (CD) and 7 control cases (HC) had been studied by means of a high quality deep-sequencing of 16S rRNA gene amplicons, followed with the identification by means of phylogenetic inference instead of identity matches. The results confirm the important role of Faecalibacterium prausnitzii in healthy mucosa, but also a predominance of members of the clade Bacteroides vulgatus – B. dorei as saprophytic microbiota. Four main groups of CD patients with different mirobiomes could be discriminated. Two of them (CD1 and CD2) were most informative and presented a common trend mainly exhibited as depletion in members of the class Clostridia. CD1 showed enhanced presence of co-colonizing Bacteroidetes as a result of the disappearance of Firmicutes. CD2 seemed to exhibit an opportunistic colonization of the mucosa by members of Proteobacteria. The results point to the fact that Crohn disease may at least include two different pathological disorders with a similar inflammatory end processes.