Abstract
Microbial diversity is typically characterized by clustering ribosomal RNA (SSU-rRNA) sequences into operational taxonom ic units (OTUs). Targeted sequencing of environmental SSU-rRNA markers via PCR may fail to detect OTUs due to biases in priming and amplification. Analysis of shotgun sequenced environmental DNA, known as metagenomics, avoids amplification bias but generates fragmentary, non-overlapping sequence reads that cannot be clustered by existing OTUfinding methods. To circumvent these limitations, we developed PhylOTU, a computational workflow that identifies OTUs from metagenomic SSU-rRNA sequence data through the use of phylogenetic principles and probabilistic sequence profiles. Using simulated metagenomic data, we quantified the accuracy with which PhylOTU clusters reads into OTUs. Comparisons of PCR and shotgun sequenced SSU-rRNA markers derived from the global open ocean revealed that while PCR libraries identify more OTUs per sequenced residue, metagenomic libraries recover a greater taxonomic diversity of OTUs. In addition, we discover novel species, genera and families in the metagenomic libraries, including OTUs from phyla missed by analysis of PCR sequences. Taken together, these results suggest that PhylOTU enables characterization of part of the biosphere currently hidden from PCR-based surveys of diversity?
| Original language | English (US) |
|---|---|
| Article number | e1001061 |
| Journal | PLoS Computational Biology |
| Volume | 7 |
| Issue number | 1 |
| DOIs | |
| State | Published - Jan 2011 |
Fingerprint
ASJC Scopus subject areas
- Cellular and Molecular Neuroscience
- Ecology
- Molecular Biology
- Genetics
- Ecology, Evolution, Behavior and Systematics
- Modeling and Simulation
- Computational Theory and Mathematics
Cite this
PhyLOTU : A high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data. / Sharpton, Thomas J.; Riesenfeld, Samantha J.; Kembel, Steven W.; Ladau, Joshua; O'Dwyer, James P.; Green, Jessica L.; Eisen, Jonathan A; Pollard, Katherine S.
In: PLoS Computational Biology, Vol. 7, No. 1, e1001061, 01.2011.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - PhyLOTU
T2 - A high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data
AU - Sharpton, Thomas J.
AU - Riesenfeld, Samantha J.
AU - Kembel, Steven W.
AU - Ladau, Joshua
AU - O'Dwyer, James P.
AU - Green, Jessica L.
AU - Eisen, Jonathan A
AU - Pollard, Katherine S.
PY - 2011/1
Y1 - 2011/1
N2 - Microbial diversity is typically characterized by clustering ribosomal RNA (SSU-rRNA) sequences into operational taxonom ic units (OTUs). Targeted sequencing of environmental SSU-rRNA markers via PCR may fail to detect OTUs due to biases in priming and amplification. Analysis of shotgun sequenced environmental DNA, known as metagenomics, avoids amplification bias but generates fragmentary, non-overlapping sequence reads that cannot be clustered by existing OTUfinding methods. To circumvent these limitations, we developed PhylOTU, a computational workflow that identifies OTUs from metagenomic SSU-rRNA sequence data through the use of phylogenetic principles and probabilistic sequence profiles. Using simulated metagenomic data, we quantified the accuracy with which PhylOTU clusters reads into OTUs. Comparisons of PCR and shotgun sequenced SSU-rRNA markers derived from the global open ocean revealed that while PCR libraries identify more OTUs per sequenced residue, metagenomic libraries recover a greater taxonomic diversity of OTUs. In addition, we discover novel species, genera and families in the metagenomic libraries, including OTUs from phyla missed by analysis of PCR sequences. Taken together, these results suggest that PhylOTU enables characterization of part of the biosphere currently hidden from PCR-based surveys of diversity?
AB - Microbial diversity is typically characterized by clustering ribosomal RNA (SSU-rRNA) sequences into operational taxonom ic units (OTUs). Targeted sequencing of environmental SSU-rRNA markers via PCR may fail to detect OTUs due to biases in priming and amplification. Analysis of shotgun sequenced environmental DNA, known as metagenomics, avoids amplification bias but generates fragmentary, non-overlapping sequence reads that cannot be clustered by existing OTUfinding methods. To circumvent these limitations, we developed PhylOTU, a computational workflow that identifies OTUs from metagenomic SSU-rRNA sequence data through the use of phylogenetic principles and probabilistic sequence profiles. Using simulated metagenomic data, we quantified the accuracy with which PhylOTU clusters reads into OTUs. Comparisons of PCR and shotgun sequenced SSU-rRNA markers derived from the global open ocean revealed that while PCR libraries identify more OTUs per sequenced residue, metagenomic libraries recover a greater taxonomic diversity of OTUs. In addition, we discover novel species, genera and families in the metagenomic libraries, including OTUs from phyla missed by analysis of PCR sequences. Taken together, these results suggest that PhylOTU enables characterization of part of the biosphere currently hidden from PCR-based surveys of diversity?
UR - http://www.scopus.com/inward/record.url?scp=79551562225&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=79551562225&partnerID=8YFLogxK
U2 - 10.1371/journal.pcbi.1001061
DO - 10.1371/journal.pcbi.1001061
M3 - Article
C2 - 21283775
AN - SCOPUS:79551562225
VL - 7
JO - PLoS Computational Biology
JF - PLoS Computational Biology
SN - 1553-734X
IS - 1
M1 - e1001061
ER -