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Glycans affect DNA extraction and induce substantial differences in gut metagenomic studies.
- Source :
-
Scientific reports [Sci Rep] 2016 May 18; Vol. 6, pp. 26276. Date of Electronic Publication: 2016 May 18. - Publication Year :
- 2016
-
Abstract
- 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.
- Subjects :
- Bacteria genetics
DNA, Bacterial genetics
Feces microbiology
Female
High-Throughput Nucleotide Sequencing
Humans
Kwashiorkor microbiology
Obesity microbiology
Polysaccharides, Bacterial chemistry
Protein-Energy Malnutrition microbiology
DNA, Bacterial isolation & purification
Gastrointestinal Microbiome genetics
Metagenomics
Polysaccharides chemistry
Subjects
Details
- Language :
- English
- ISSN :
- 2045-2322
- Volume :
- 6
- Database :
- MEDLINE
- Journal :
- Scientific reports
- Publication Type :
- Academic Journal
- Accession number :
- 27188959
- Full Text :
- https://doi.org/10.1038/srep26276