Y 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 phageS CBS1 andRetroviridaefamily 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 ofRetroviridaeviruses 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. *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: andres.moya@uv.es or moya_and@gva.es Received 30 November 2012; accepted 6 May 2013 published online 13 June 2013 © 2013 The Author(s). Published by Wolters Kluwer Health, Inc. on behalf of The American College of Gastroenterology...