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PLoS One. 2013 Dec 31;8(12):e84033. doi: 10.1371/journal.pone.0084033. eCollection 2013.

Development and validation of a microarray for the investigation of the CAZymes encoded by the human gut microbiome.

Author information

  • 1Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Marseille, France ; URMITE, UM63, CNRS 7278, L'Institut de Recherche pour le Développement 198, INSERM 1095, Aix-Marseille Université, Faculté de Médecine, Marseille, France.
  • 2URMITE, UM63, CNRS 7278, L'Institut de Recherche pour le Développement 198, INSERM 1095, Aix-Marseille Université, Faculté de Médecine, Marseille, France.
  • 3Service de Nutrition, Maladies Métaboliques et Endocrinologie, UMR-INRA U1260, CHU de la Timone, Marseille, France.
  • 4Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Marseille, France ; Centre National de la Recherche Scientifique, CNRS UMR 7257, Marseille, France ; Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.

Abstract

Distal gut bacteria play a pivotal role in the digestion of dietary polysaccharides by producing a large number of carbohydrate-active enzymes (CAZymes) that the host otherwise does not produce. We report here the design of a custom microarray that we used to spot non-redundant DNA probes for more than 6,500 genes encoding glycoside hydrolases and lyases selected from 174 reference genomes from distal gut bacteria. The custom microarray was tested and validated by the hybridization of bacterial DNA extracted from the stool samples of lean, obese and anorexic individuals. Our results suggest that a microarray-based study can detect genes from low-abundance bacteria better than metagenomic-based studies. A striking example was the finding that a gene encoding a GH6-family cellulase was present in all subjects examined, whereas metagenomic studies have consistently failed to detect this gene in both human and animal gut microbiomes. In addition, an examination of eight stool samples allowed the identification of a corresponding CAZome core containing 46 families of glycoside hydrolases and polysaccharide lyases, which suggests the functional stability of the gut microbiota despite large taxonomical variations between individuals.

PMID:
24391873
[PubMed - indexed for MEDLINE]
PMCID:
PMC3877134
Free PMC Article
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