Most Cited Extraction Methods Substantially Skew Microbial Profiles

“Different DNA extraction protocols result in substantial technical variation , both in taxonomic and in functional space”

Costea, et al. (Nature Biotechnology, 2017)

Is the difference technical or biological?

The two best-known human microbiome profiling efforts, the Human Microbiome Project (HMP) and Metagenomics of Human Intestinal Tract (MetaHIT) agree that Bacteroidetes and Firmicutes are in dominance, but the HMP profile indicates higher abundance of Bacteroidetes. Is the difference observed capturing a biological change? When these DNA extraction methods were replicated on the same samples, researchers found the HMP protocol yields a higher relative abundance of Bacteroidetes as compared to the MetaHIT DNA extraction protocol (Wesolowska-Andersen et al., 2014). This indicates the differences are at least in part technical and highlights the difficulty in comparing data generated using different, nonstandardized extraction methods.

“The interlab comparability of measurements on microbiomes is generally poor. Biases exist along every step of the measurement process, from sample collection, extraction techniques, measurement technology employed (e.g. NGS, mass spec, NMR), and, finally, to data analysis and interpretation. There is a need for the adoption of reference materials, reference data, and reference protocols in order to identify and eliminate measurement bias.”

Stulberg, et al. (Nature Microbiology, 2016)

“Unfortunately, variations at each step in the pipeline is enormous from physical sample collection and processing to computational quantification of microbial communities.”

Sinha, et al. (Genomie Biology, 2016)