Robust species taxonomy assignment algorithm for 16S rRNA NGS reads: application to oral carcinoma samples.

ABSTRACT:

Background

Usefulness of next-generation sequencing (NGS) in assessing bacteria associated with oral squamous cell carcinoma (OSCC) has been undermined by inability to classify reads to the species level.

Objective

The purpose of this study was to develop a robust algorithm for species-level classification of NGS reads from oral samples and to pilot test it for profiling bacteria within OSCC tissues.

Methods

Bacterial 16S V1-V3 libraries were prepared from three OSCC DNA samples and sequenced using 454's FLX chemistry. High-quality, well-aligned, and non-chimeric reads ≥350 bp were classified using a novel, multi-stage algorithm that involves matching reads to reference sequences in revised versions of the Human Oral Microbiome Database (HOMD), HOMD extended (HOMDEXT)

SUBMITTER: Al-Hebshi NN 

PROVIDER: S-EPMC4590409 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature