Improving saliva shotgun metagenomics by chemical host DNA depletion.

ABSTRACT:

Background

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

Results

Three commercially available host depletion kits were directly compared with size filtration and a novel method involving os

SUBMITTER: Marotz CA 

PROVIDER: S-EPMC5827986 | biostudies-literature | 2018 Feb

REPOSITORIES: biostudies-literature