comparison of dna extraction methods for microbial community profiling with an application to pediatric bronchoalveolar lavage samples微生物群落dna提取方法的比较分析与应用小儿支气管肺泡灌洗样品.pdfVIP

Comparison of DNA Extraction Methods for Microbial Community Profiling with an Application to Pediatric Bronchoalveolar Lavage Samples 1,2 1 3,4 3,4 4,5 Dana Willner *, Joshua Daly , David Whiley , Keith Grimwood , Claire E. Wainwright , Philip Hugenholtz1 1 Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences and Institute of Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia, 2 Diamatina Institute, The University of Queensland, St. Lucia, Queensland, Australia, 3 Queensland Paediatric Infectious Diseases Laboratory, Infection Management and Prevention Service, Royal Children’s Hospital, Brisbane, Queensland, Australia, 4 Queensland Children’s Medical Research Institute, Royal Children’s Hospital, The University of Queensland, St. Lucia, Queensland, Australia, 5 Queensland Children’s Respiratory Centre, Royal Children’s Hospital, Herston, Queensland, Australia 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