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

Mireia Lopez-Siles, Margarita Martinez-Medina, Carles Abellà, David Busquets, Miriam Sabat-Mir, Sylvia H Duncan, Xavier Aldeguer, Harry J Flint, L Jesús Garcia-Gil

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78 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)7582-7592
Number of pages11
JournalApplied and Environmental Microbiology
Issue number21
Early online date21 Aug 2015
Publication statusPublished - Nov 2015

Bibliographical note

Date of Acceptance: 18/8/15

Copyright © 2015, American Society for Microbiology. All Rights Reserved.

This work was partially funded by the Spanish Ministry of Education and Science through project SAF2010-15896. Mireia Lopez-Siles was the recipient of an FI grant from the Generalitat de Catalunya (2010FI_B2 00135), which receives support from the European Union Commission. Harry J. Flint and Sylvia H. Duncan acknowledge support from the Food, Land, and People program of the Scottish government. We thank Teresa Mas-de-Xaxars for assistance with recruitment of samples from CRC patients, Natàlia Adell from the Serveis Tècnics de Recerca for statistical assistance, Pau Boher for assistance with heat map analysis, and Marc Llirós and Carla Camprubí-Font for critically revising
the manuscript. We appreciate the generosity of the patients who freely gave their time and samples to make this study possible and the surgical theater staff of all centers for their dedication and careful sample collection.


  • Inflammatory Bowel Disease
  • Faecalibacterium prausnitzii


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