High-resolution microbial community reconstruction by integrating short reads from multiple 16S rRNA regions.

Nucleic Acids Res
Authors
Keywords
Abstract

The emergence of massively parallel sequencing technology has revolutionized microbial profiling, allowing the unprecedented comparison of microbial diversity across time and space in a wide range of host-associated and environmental ecosystems. Although the high-throughput nature of such methods enables the detection of low-frequency bacteria, these advances come at the cost of sequencing read length, limiting the phylogenetic resolution possible by current methods. Here, we present a generic approach for integrating short reads from large genomic regions, thus enabling phylogenetic resolution far exceeding current methods. The approach is based on a mapping to a statistical model that is later solved as a constrained optimization problem. We demonstrate the utility of this method by analyzing human saliva and Drosophila samples, using Illumina single-end sequencing of a 750 bp amplicon of the 16S rRNA gene. Phylogenetic resolution is significantly extended while reducing the number of falsely detected bacteria, as compared with standard single-region Roche 454 Pyrosequencing. Our approach can be seamlessly applied to simultaneous sequencing of multiple genes providing a higher resolution view of the composition and activity of complex microbial communities.

Year of Publication
2013
Journal
Nucleic Acids Res
Volume
41
Issue
22
Pages
e205
Date Published
2013 Dec
ISSN
1362-4962
URL
DOI
10.1093/nar/gkt1070
PubMed ID
24214960
PubMed Central ID
PMC3905898
Links
Grant list
P50 GM068763 / GM / NIGMS NIH HHS / United States