Using metagenomic methods to detect organismal contaminants in microbial materials

6 High sensitivity methods such as next generation sequencing and polymerase chain reaction (PCR) are adversely impacted by organismal and DNA contaminants. Current methods for detecting contaminants in microbial materials (genomic DNA and cultures) are not sensitive enough and require either a known or culturable contaminant. Therefore, high sensitivity methods not requiring a priori assumptions about the contaminant are needed. We demonstrate the use of whole genome sequencing (WGS) and a metagenomic taxonomic classification algorithm for assessing the organismal purity of a microbial material. Using this proposed method we characterized the types of false positive contaminants reported and the dependence of detectable contaminant concentration on material and contaminant genome using simulated WGS data. Using the proposed method to characterize microbial material purity will help to ensure that the materials used to validate pathogen detection assays, generate genome assemblies for database submission, and benchmark sequencing methods are free of contaminants adversely impacting measurement results. 7