Classification of 16S rRNA reads is improved using a niche-specific database constructed by near-full length sequencing.

ABSTRACT: Surveys of microbial populations in environmental niches of interest often utilize sequence variation in the gene encoding the ribosomal small subunit (the 16S rRNA gene). Generally, these surveys target the 16S genes using semi-degenerate primers to amplify portions of a subset of bacterial species, sequence the amplicons in bulk, and assign to putative taxonomic categories by comparison to databases purporting to connect specific sequences in the main variable regions of the gene to specific organisms. Due to sequence length constraints of the most popular bulk sequencing platforms, the primers selected amplify one to three of the nine variable regions, and taxonomic assignment is based on relatively short stretches of sequence (150-500 bases). We demonstrate that taxonomic assignment is

SUBMITTER: Myer PR 

PROVIDER: S-EPMC7357769 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature