Publications des scientifiques de l'IRD

Angelakis E., Bachar D., Henrissat B., Armougom Fabrice, Audoly G., Lagier J. C., Robert C., Raoult Didier. (2016). Glycans affect DNA extraction and induce substantial differences in gut metagenomic studies. Scientific Reports - Nature, 6, p. art. 26276 [8 p.]. ISSN 2045-2322.

Titre du document
Glycans affect DNA extraction and induce substantial differences in gut metagenomic studies
Année de publication
2016
Type de document
Article référencé dans le Web of Science WOS:000375997300001
Auteurs
Angelakis E., Bachar D., Henrissat B., Armougom Fabrice, Audoly G., Lagier J. C., Robert C., Raoult Didier
Source
Scientific Reports - Nature, 2016, 6, p. art. 26276 [8 p.] ISSN 2045-2322
Exopolysaccharides produced by bacterial species and present in feces are extremely inhibitory to DNA restriction and can cause discrepancies in metagenomic studies. We determined the effects of different DNA extraction methods on the apparent composition of the gut microbiota using Illumina MiSeq deep sequencing technology. DNA was extracted from the stool from an obese female using 10 different methods and the choice of DNA extraction method affected the proportional abundance at the phylum level, species richness (Chao index, 227 to 2,714) and diversity (non parametric Shannon, 1.37 to 4.4). Moreover DNA was extracted from stools obtained from 83 different individuals by the fastest extraction assay and by an extraction assay that degradated exopolysaccharides. The fastest extraction method was able to detect 68% to 100% genera and 42% to 95% species whereas the glycan degradation extraction method was able to detect 56% to 93% genera and 25% to 87% species. To allow a good liberation of DNA from exopolysaccharides commonly presented in stools, we recommend the mechanical lysis of stools plus glycan degradation, used here for the first time. Caution must be taken in the interpretation of current metagenomic studies, as the efficiency of DNA extraction varies widely among stool samples.
Plan de classement
Sciences fondamentales / Techniques d'analyse et de recherche [020] ; Nutrition, alimentation [054] ; Biotechnologies [084]
Localisation
Fonds IRD [F B010066904]
Identifiant IRD
fdi:010066904
Contact