E-GEOD-51760 - Development and validation of a microarray for the investigation of the CAZymes encoded by the human gut microbiome

Status
Released on 28 October 2013, last updated on 13 May 2014
Organism
human gut metagenome
Samples (8)
Array (1)
Protocols (5)
Description
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 high density 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. Fecal samples were collected from eight female subjects. Three were obese subjects of BMI kg m-2: 35, 46.8 and 51.3, respectively; age: 42, 21 and 65 years old, respectively. Three were anorexic women of BMI kg m-2: 9.8, 10 and 13.7, respectively; age: 19, 23 and 49 years old, respectively. Finally, two fecal samples from lean women of BMI kg m-2: 18.6 and 23.42 were analyzed.
Experiment type
comparative genomic hybridization by array 
Contacts
Abdessamad EL KAOUTARI <samad.elk@gmail.com>, Abdessamad El Kaoutari, Bernard Henrissat, Bernard Vialettes, Didier Raoult, Fabrice Armougom, Matthieu Million, Quentin Leroy
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-51760.idf.txt
Sample and data relationshipE-GEOD-51760.sdrf.txt
Raw data (1)E-GEOD-51760.raw.1.zip
Processed data (1)E-GEOD-51760.processed.1.zip
Array designA-GEOD-17807.adf.txt
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