BactQuant: an enhanced broad-coverage bacterial quantitative real-time PCR assay.

ABSTRACT:

Background

Bacterial load quantification is a critical component of bacterial community analysis, but a culture-independent method capable of detecting and quantifying diverse bacteria is needed. Based on our analysis of a diverse collection of 16 S rRNA gene sequences, we designed a broad-coverage quantitative real-time PCR (qPCR) assay--BactQuant--for quantifying 16 S rRNA gene copy number and estimating bacterial load. We further utilized in silico evaluation to complement laboratory-based qPCR characterization to validate BactQuant.

Methods

The aligned core set of 4,938 16 S rRNA gene sequences in the Greengenes database were analyzed for assay design. Cloned plasmid standards were generated and quantified using a qPCR-based approach. Coverage analysis was performed comp

SUBMITTER: Liu CM 

PROVIDER: S-EPMC3464140 | biostudies-literature | 2012 Apr

REPOSITORIES: biostudies-literature