Improving saliva shotgun metagenomics by chemical host DNA depletion

• DOI: 10.1186/s40168-018-0426-3
• Publication Date: 2018-02-26T23:57:07Z
• Authors: Clarisse A. Marotz; Jon G. Sanders; Cristal Zuniga; Livia S. Zaramela; Rob Knight; Karsten Zengler
• Keywords: Shotgun; Environmental DNA; Medical microbiology

Shotgun sequencing of microbial communities provides in-depth knowledge the microbiome by cataloging bacterial, fungal, and viral gene content within a sample, providing an advantage over amplicon approaches that assess taxonomy but not function are taxonomically limited. However, mammalian DNA can dominate host-derived samples, obscuring changes in populations because few sequence reads from component. We developed optimized novel method for enriching human oral samples compared its efficiency potential taxonomic bias with commercially available kits.