Standardizing Gut Microbiome Studies: Applying the use of a mock gut microbial community for DNA extraction optimization

摘要

Microbiome studies investigating the human gut microbiome and its influence on health are of significant interest and continue to grow in number and scope. However, variations in sample processing between labs can introduce artifacts and biases into data, resulting in ambiguous or even conflicting study results. While the use of mock microbial communities containing mixtures of organisms found in various environments is becoming more common to detect such biases, a mock community mimicking the human gut would provide greater confidence that data generated from fecal samples are accurate, representative, and that methods used are appropriate and performed adequately. Using a 21 strain mock microbial community mimicking the human gut microbiome, we evaluated multiple DNA extraction protocols through shotgun metagenomic analysis. In addition to the mock microbial community, we extracted microbial DNA from human fecal samples for profile comparison. Here we show that the use of an accurately quantified known community in parallel with real samples is an effective tool for detecting biases introduced during DNA extraction. By benchmarking against a well characterized mock community, metagenomics protocols can be optimized for more effective performance, and reduce biases to improve data reproducibility and cross-study comparisons.