Experimental factors affecting PCR-based estimates of microbial species richness and evenness

Engelbrektson, Anna, Kunin, Victor, Wrighton, Kelly C., Zvenigorodsky, Natasha, Chen, Feng, Ochman, Howard and Hugenholtz, Philip (2010) Experimental factors affecting PCR-based estimates of microbial species richness and evenness. ISME Journal, 4 5: 642-647. doi:10.1038/ismej.2009.153


Author Engelbrektson, Anna
Kunin, Victor
Wrighton, Kelly C.
Zvenigorodsky, Natasha
Chen, Feng
Ochman, Howard
Hugenholtz, Philip
Title Experimental factors affecting PCR-based estimates of microbial species richness and evenness
Journal name ISME Journal   Check publisher's open access policy
ISSN 1751-7362
1751-7370
Publication date 2010-05
Sub-type Article (original research)
DOI 10.1038/ismej.2009.153
Volume 4
Issue 5
Start page 642
End page 647
Total pages 6
Place of publication London, U.K.
Publisher Nature Publishing Group
Language eng
Abstract Pyrosequencing of 16S rRNA gene amplicons for microbial community profiling can, for equivalent costs, yield more than two orders of magnitude more sensitivity than traditional PCR cloning and Sanger sequencing. With this increased sensitivity and the ability to analyze multiple samples in parallel, it has become possible to evaluate several technical aspects of PCR-based community structure profiling methods. We tested the effect of amplicon length and primer pair on estimates of species richness (number of species) and evenness (relative abundance of species) by assessing the potentially tractable microbial community residing in the termite hindgut. Two regions of the 16S rRNA gene were sequenced from one of two common priming sites, spanning the V1–V2 or V8 regions, using amplicons ranging in length from 352 to 1443 bp. Our results show that both amplicon length and primer pair markedly influence estimates of richness and evenness. However, estimates of species evenness are consistent among different primer pairs targeting the same region. These results highlight the importance of experimental methodology when comparing diversity estimates across communities. # # © 2011 International Society for Microbial Ecology
Keyword 16S rRNA
Diversity estimates
Microbial community
Pyrosequencing
Termite
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: Institute for Molecular Bioscience - Publications
 
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Created: Thu, 24 Mar 2011, 09:30:08 EST by Susan Allen on behalf of Institute for Molecular Bioscience