Mucosa-associated Faecalibacterium prausnitzii phylotype richness is reduced in inflammatory bowel disease patients

Faecalibacterium prausnitzii depletion in intestinal diseases has been extensively reported, but little is known about intra-species variability. This work aims to determine if subjects with gastrointestinal disease host different mucosa-associated F. prausnitzii populations from healthy individuals. A new species-specific polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) targeting the 16SrRNA gene was developed to fingerprint F. prausnitzii populations in biopsies from 31 healthy controls (H), 36 Crohn's disease (CD), 23 ulcerative colitis (UC), 6 irritable bowel syndrome (IBS), and 22 colorectal cancer (CRC) patients. The richness of F. prausnitzii subtypes was lower in inflammatory bowel disease (IBD) patients than in H subjects. The most prevalent operational taxonomic units (OTU) consisted of four phylotypes (OTU99), which were shared by all groups of patients. Their distribution and the presence of some disease-specific F. prausnitzii phylotypes allowed us to differentiate IBD and CRC population from that in H. At the OTU97 level, two phylogroups accounted for of 98% the sequences. Phylogroup I was found in 87% of H but in under 50% of IBD patients (P=0.003). In contrast, phylogroup II was detected in >75% of IBD patients and only in 52% of H subjects (P=0.005). This study reveals that despite the main members of F. prausnitzii population are present in both H and individuals with gut diseases, richness is reduced in the latter, and an altered phylotype distribution exists between diseases. This approach may serve as a basis for addressing the suitability of their quantification as putative biomarkers of disease, and depicting the importance of these subtype losses in disease pathogenesis.