Comparison of DNA extraction methods for microbial community profiling with an application to pediatric bronchoalveolar lavage samples.

ABSTRACT: Barcoded amplicon sequencing is rapidly becoming a standard method for profiling microbial communities, including the human respiratory microbiome. While this approach has less bias than standard cultivation, several steps can introduce variation including the type of DNA extraction method used. Here we assessed five different extraction methods on pediatric bronchoalveolar lavage (BAL) samples and a mock community comprised of nine bacterial genera to determine method reproducibility and detection limits for these typically low complexity communities. Additionally, using the mock community, we were able to evaluate contamination and select a relative abundance cut-off threshold based on the geometric distribution that optimizes the trade off between detecting bona fide operational taxonom

SUBMITTER: Willner D 

PROVIDER: S-EPMC3326054 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature