Study of the Viral and Microbial Communities Associated... : Clinical and Translational Gastroenterology (original) (raw)

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Study of the Viral and Microbial Communities Associated With Crohn's Disease: A Metagenomic Approach

Pérez-Brocal, Vicente PhD1,2,3; García-López, Rodrigo MSc1,3; Vázquez-Castellanos, Jorge F MSc1,3; Nos, Pilar MD4; Beltrán, Belén MD4; Latorre, Amparo PhD1,2,3; Moya, Andrés PhD1,2,3

1Área de Genómica y Salud, Centro Superior de Investigación en Salud Pública—Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (CSISP-FISABIO), Valencia, Spain

2CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain

3Departamento de Genética, Cavanilles Institute on Biodiversity and Evolutionary Biology, University of València, Valencia, Spain

4Unidad de Gastroenterología, Hospital Universitario La Fe, Valencia, Valencia, Spain

*Correspondence: Andrés Moya, PhD, Departamento de Genética, Cavanilles Institute on Biodiversity and Evolutionary Biology, University of València, c/ José Beltrán 2, 46980 Paterna, Valencia, Spain or Genomics and Health Area, Centro Superior de Investigación en Salud Pública—Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (CSISP-FISABIO), Avenida de Cataluña 21, 46020 Valencia, Spain. E-mail: [email protected] or [email protected]

Received 30 November 2012; accepted 6 May 2013

published online 13 June 2013

Clinical and Translational Gastroenterology 4(6):p e36, June 2013. | DOI: 10.1038/ctg.2013.9

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Abstract

OBJECTIVES:

This study aimed to analyze and compare the diversity and structure of the viral and microbial communities in fecal samples from a control group of healthy volunteers and from patients affected by Crohn's disease (CD).

METHODS:

Healthy adult controls ( n= 8) and patients affected by ileocolic CD ( n= 11) were examined for the viral and microbial communities in their feces and, in one additional case, in the intestinal tissue. Using two different approaches, we compared the viral and microbial communities in several ways: by group (patients vs. controls), entity (viruses vs. bacteria), read assembly (unassembled vs. assembled reads), and methodology (our approach vs. an existing pipeline). Differences in the viral and microbial composition, and abundance between the two groups were analyzed to identify taxa that are under- or over-represented.

RESULTS:

A lower diversity but more variability between the CD samples in both virome and microbiome was found, with a clear distinction between groups based on the microbiome. Only ≈5% of the differential viral biomarkers are more represented in the CD group ( Synechococcus phage S CBS1 and Retroviridae family viruses), compared with 95% in the control group. Unrelated patterns of bacteria and bacteriophages were observed.

CONCLUSIONS:

Our use of an extensive database is critical to retrieve more viral hits than in previous approaches. Unrelated patterns of bacteria and bacteriophages may be due to uneven representation of certain viruses in databases, among other factors. Further characterization of Retroviridae viruses in the CD group could be of interest, given their links with immunodeficiency and the immune responses. To conclude, some methodological considerations underlying the analysis of the viral community composition and abundance are discussed.