Deriving accurate microbiota profiles from human samples with low bacterial content through post-sequencing processing of Illumina MiSeq data.

ABSTRACT:

Background

The rapid expansion of 16S rRNA gene sequencing in challenging clinical contexts has resulted in a growing body of literature of variable quality. To a large extent, this is due to a failure to address spurious signal that is characteristic of samples with low levels of bacteria and high levels of non-bacterial DNA. We have developed a workflow based on the paired-end read Illumina MiSeq-based approach, which enables significant improvement in data quality, post-sequencing. We demonstrate the efficacy of this methodology through its application to paediatric upper-respiratory samples from several anatomical sites.

Results

A workflow for processing sequence data was developed based on commonly available tools. Data generated from different sample types showed a mar

SUBMITTER: Jervis-Bardy J 

PROVIDER: S-EPMC4428251 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature