Deep sequencing analyses of low density microbial communities: working at the boundary of accurate microbiota detection.

ABSTRACT:

Introduction

Accurate analyses of microbiota composition of low-density communities (10(3)-10(4) bacteria/sample) can be challenging. Background DNA from chemicals and consumables, extraction biases as well as differences in PCR efficiency can significantly interfere with microbiota assessment. This study was aiming to establish protocols for accurate microbiota analysis at low microbial density.

Methods

To examine possible effects of bacterial density on microbiota analyses we compared microbiota profiles of serial diluted saliva and low (nares, nasopharynx) and high-density (oropharynx) upper airway communities in four healthy individuals. DNA was extracted with four different extraction methods (Epicentre Masterpure, Qiagen DNeasy, Mobio Powersoil and a phenol bead-beatin

SUBMITTER: Biesbroek G 

PROVIDER: S-EPMC3295791 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature