Design of 16S rRNA gene primers for 454 pyrosequencing of the human foregut microbiome.

ABSTRACT:

Aim

To design and validate broad-range 16S rRNA primers for use in high throughput sequencing to classify bacteria isolated from the human foregut microbiome.

Methods

A foregut microbiome dataset was constructed using 16S rRNA gene sequences obtained from oral, esophageal, and gastric microbiomes produced by Sanger sequencing in previous studies represented by 219 bacterial species. Candidate primers evaluated were from the European rRNA database. To assess the effect of sequence length on accuracy of classification, 16S rRNA genes of various lengths were created by trimming the full length sequences. Sequences spanning various hypervariable regions were selected to simulate the amplicons that would be obtained using possible primer pairs. The sequences were compared with fu

SUBMITTER: Nossa CW 

PROVIDER: S-EPMC2932916 | biostudies-literature | 2010 Sep

REPOSITORIES: biostudies-literature