Optimizing protocols for extraction of bacteriophages prior to metagenomic analyses of phage communities in the human gut.

ABSTRACT:

Background

The human gut is densely populated with archaea, eukaryotes, bacteria, and their viruses, such as bacteriophages. Advances in high-throughput sequencing (HTS) as well as bioinformatics have opened new opportunities for characterizing the viral communities harbored in our gut. However, limited attention has been given to the efficiency of protocols dealing with extraction of phages from fecal communities prior to HTS and their impact on the metagenomic dataset.

Results

We describe two optimized methods for extraction of phages from fecal samples based on tangential-flow filtration (TFF) and polyethylene glycol precipitation (PEG) approaches using an adapted method from a published protocol as control (literature-adapted protocol (LIT)). To quantify phage recovery,

SUBMITTER: Castro-Mejia JL 

PROVIDER: S-EPMC4650499 | biostudies-literature | 2015 Nov

REPOSITORIES: biostudies-literature