In an Analysis published in Nature Biotechnology, Costea et al. examined the effects of technical variation in metagenomic analysis. The researchers examined the extent to which DNA extraction processes influence the quantification of microbial composition, with shotgun metagenomic sequencing as the readout. Twenty-one representative DNA extraction protocols were tested on the same faecal samples by laboratories across 11 countries, with differences in the observed microbial communities quantified. DNA extraction had the largest effect on the outcome of metagenomic analysis. The authors ultimately recommended a standardized protocol for DNA extraction from human stool samples that, if accepted by the research community, could improve comparability of findings across metagenomic studies.
Costea, P. I. et al. Towards standards for human fecal sample processing in metagenomic studies. Nat. Biotechnol. http://dx.doi.org/10.1038/nbt.3960 (2017)
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Ray, K. Human faecal sample processing in metagenomic studies: striving for standards. Nat Rev Gastroenterol Hepatol 14, 631 (2017). https://doi.org/10.1038/nrgastro.2017.143