Document Type
Article
Publication Date
11-6-2019
Keywords
JGM
JAX Source
Nat Commun 2019 Nov 6; 10(1):5029
Volume
10
Issue
1
First Page
5029
Last Page
5029
ISSN
2041-1723
PMID
31695033
DOI
https://doi.org/10.1038/s41467-019-13036-1
Grant
DE02378901,DK088831
Abstract
The 16S rRNA gene has been a mainstay of sequence-based bacterial analysis for decades. However, high-throughput sequencing of the full gene has only recently become a realistic prospect. Here, we use in silico and sequence-based experiments to critically re-evaluate the potential of the 16S gene to provide taxonomic resolution at species and strain level. We demonstrate that targeting of 16S variable regions with short-read sequencing platforms cannot achieve the taxonomic resolution afforded by sequencing the entire (~1500 bp) gene. We further demonstrate that full-length sequencing platforms are sufficiently accurate to resolve subtle nucleotide substitutions (but not insertions/deletions) that exist between intragenomic copies of the 16S gene. In consequence, we argue that modern analysis approaches must necessarily account for intragenomic variation between 16S gene copies. In particular, we demonstrate that appropriate treatment of full-length 16S intragenomic copy variants has the potential to provide taxonomic resolution of bacterial communities at species and strain level.
Recommended Citation
Johnson J,
Spakowicz D,
Hong B,
Petersen L,
Demkowicz P,
Chen L,
Leopold S,
Hanson B,
Agresta H,
Gerstein M,
Sodergren E,
Weinstock GM.
Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis. Nat Commun 2019 Nov 6; 10(1):5029
Comments
This open access article is licensed under a Creative Commons Attribution 4.0 International License