Study of the Viral and Microbial Communities Associated With Crohn's Disease: A Metagenomic Approach
Identifieur interne : 000286 ( Main/Merge ); précédent : 000285; suivant : 000287Study of the Viral and Microbial Communities Associated With Crohn's Disease: A Metagenomic Approach
Auteurs : Vicente Pérez-Brocal [Espagne] ; Rodrigo García-L Pez [Espagne] ; Jorge F. Vázquez-Castellanos [Espagne] ; Pilar Nos [Espagne] ; Belén Beltrán [Espagne] ; Amparo Latorre [Espagne] ; Andrés Moya [Espagne]Source :
- Clinical and Translational Gastroenterology [ 2155-384X ] ; 2013.
Abstract
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).
Healthy adult controls (
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 (
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
Url:
DOI: 10.1038/ctg.2013.9
PubMed: 23760301
PubMed Central: 3696940
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sortKey="Perez Brocal, Vicente" sort="Perez Brocal, Vicente" uniqKey="Perez Brocal V" first="Vicente" last="Pérez-Brocal">Vicente Pérez-Brocal</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Área 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)</institution>, Valencia,<country>Spain</country></nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>CIBER Epidemiología y Salud Pública (CIBERESP)</institution>, Madrid,<country>Spain</country></nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff3"><institution>Departamento de Genética, Cavanilles Institute on Biodiversity and Evolutionary Biology, University of València</institution>, Valencia,<country>Spain</country></nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Garcia L Pez, Rodrigo" sort="Garcia L Pez, Rodrigo" uniqKey="Garcia L Pez R" first="Rodrigo" last="García-L Pez">Rodrigo García-L Pez</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Área 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)</institution>, Valencia,<country>Spain</country></nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff3"><institution>Departamento de Genética, Cavanilles Institute on Biodiversity and Evolutionary Biology, University of València</institution>, Valencia,<country>Spain</country></nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Vazquez Castellanos, Jorge F" sort="Vazquez Castellanos, Jorge F" uniqKey="Vazquez Castellanos J" first="Jorge F" last="Vázquez-Castellanos">Jorge F. Vázquez-Castellanos</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Área 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)</institution>, Valencia,<country>Spain</country></nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff3"><institution>Departamento de Genética, Cavanilles Institute on Biodiversity and Evolutionary Biology, University of València</institution>, Valencia,<country>Spain</country></nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Nos, Pilar" sort="Nos, Pilar" uniqKey="Nos P" first="Pilar" last="Nos">Pilar Nos</name><affiliation wicri:level="1"><nlm:aff id="aff4"><institution>Unidad de Gastroenterología, Hospital Universitario La Fe, Valencia</institution>, Valencia,<country>Spain</country></nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Beltran, Belen" sort="Beltran, Belen" uniqKey="Beltran B" first="Belén" last="Beltrán">Belén Beltrán</name><affiliation wicri:level="1"><nlm:aff id="aff4"><institution>Unidad de Gastroenterología, Hospital Universitario La Fe, Valencia</institution>, Valencia,<country>Spain</country></nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Latorre, Amparo" sort="Latorre, Amparo" uniqKey="Latorre A" first="Amparo" last="Latorre">Amparo Latorre</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Área 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)</institution>, Valencia,<country>Spain</country></nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>CIBER Epidemiología y Salud Pública (CIBERESP)</institution>, Madrid,<country>Spain</country></nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff3"><institution>Departamento de Genética, Cavanilles Institute on Biodiversity and Evolutionary Biology, University of València</institution>, Valencia,<country>Spain</country></nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Moya, Andres" sort="Moya, Andres" uniqKey="Moya A" first="Andrés" last="Moya">Andrés Moya</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Área 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)</institution>, Valencia,<country>Spain</country></nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>CIBER Epidemiología y Salud Pública (CIBERESP)</institution>, Madrid,<country>Spain</country></nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff3"><institution>Departamento de Genética, Cavanilles Institute on Biodiversity and Evolutionary Biology, University of València</institution>, Valencia,<country>Spain</country></nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author></analytic><series><title level="j">Clinical and Translational Gastroenterology</title><idno type="eISSN">2155-384X</idno><imprint><date when="2013">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>OBJECTIVES:</title><p>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).</p></sec><sec><title>METHODS:</title><p>Healthy adult controls (<italic>n=</italic>8) and patients affected by ileocolic CD (<italic>n=</italic>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.</p></sec><sec><title>RESULTS:</title><p>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 (<italic>Synechococcus phage</italic> S CBS1 and <italic>Retroviridae</italic> family viruses), compared with 95% in the control group. Unrelated patterns of bacteria and bacteriophages were observed.</p></sec><sec><title>CONCLUSIONS:</title><p>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 <italic>Retroviridae</italic> 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.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Whitman, Wb" uniqKey="Whitman W">WB Whitman</name></author><author><name sortKey="Coleman, Dc" uniqKey="Coleman D">DC Coleman</name></author><author><name sortKey="Wiebe, Wj" uniqKey="Wiebe W">WJ Wiebe</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sekirov, I" uniqKey="Sekirov I">I Sekirov</name></author><author><name sortKey="Russell, Sl" uniqKey="Russell S">SL Russell</name></author><author><name sortKey="Antunes, Lc" uniqKey="Antunes L">LC Antunes</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wegrzyn, G" uniqKey="Wegrzyn G">G Wegrzyn</name></author><author><name sortKey="Thomas, Ms" uniqKey="Thomas M">MS 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