title: Mucosa-associated Faecalibacterium prausnitzii phylotype richness is reduced in patients with inflammatory bowel disease.
abstract: Faecalibacterium prausnitzii depletion in intestinal diseases has been extensively reported, but little is known about intraspecies variability. This work aims to determine if subjects with gastrointestinal disease host mucosa-associated F. prausnitzii populations different from those hosted by healthy individuals. A new species-specific PCR-denaturing gradient gel electrophoresis (PCR-DGGE) method targeting the 16S rRNA gene was developed to fingerprint F. prausnitzii populations in biopsy specimens from 31 healthy control (H) subjects and 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 (OTUs) consisted of four phylotypes (OTUs with a 99% 16S rRNA gene sequence similarity [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 the populations in IBD and CRC patients from that in H subjects. At the level of a minimum similarity of 97% (OTU97), two phylogroups accounted for 98% of the sequences. Phylogroup I was found in 87% of H subjects but in under 50% of IBD patients (P = 0.003). In contrast, phylogroup II was detected in >75% of IBD patients and in only 52% of H subjects (P = 0.005). This study reveals that even though the main members of the F. prausnitzii population are present in both H subjects 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 F. prausnitzii phylotypes to be quantified as a putative biomarker of disease and depicting the importance of the loss of these subtypes in disease pathogenesis.
authors: Laboratory of Molecular Microbiology, Biology Department, Universitat de Girona, Girona, Spain.
authors: Mireia
authors: M
authors: Lopez-Siles
authors: Laboratory of Molecular Microbiology, Biology Department, Universitat de Girona, Girona, Spain.
authors: Margarita
authors: M
authors: Martinez-Medina
authors: Laboratory of Molecular Microbiology, Biology Department, Universitat de Girona, Girona, Spain.
authors: Carles
authors: C
authors: Abellà
authors: Department of Gastroenterology, Hospital Universitari Dr. Josep Trueta, Girona, Spain.
authors: David
authors: D
authors: Busquets
authors: Department of Gastroenterology, Hospital Santa Caterina, Salt, Girona, Spain.
authors: Miriam
authors: M
authors: Sabat-Mir
authors: Microbial Ecology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom.
authors: Sylvia H
authors: SH
authors: Duncan
authors: Department of Gastroenterology, Hospital Universitari Dr. Josep Trueta, Girona, Spain.
authors: Xavier
authors: X
authors: Aldeguer
authors: Microbial Ecology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom.
authors: Harry J
authors: HJ
authors: Flint
authors: Laboratory of Molecular Microbiology, Biology Department, Universitat de Girona, Girona, Spain jesus.garcia@udg.edu.
authors: L Jesús
authors: LJ
authors: Garcia-Gil
mesh_terms: D001706:Biopsy; D000068016:Eubacteriales / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D058645:Denaturing Gradient Gel Electrophoresis; D014644:Genetic Variation; D005838:Genotype; D006801:Humans; D015212:Inflammatory Bowel Diseases / Q000382:microbiology*; D007413:Intestinal Mucosa / Q000382:microbiology*; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S