Evaluation of different partial 16S rRNA gene sequence regions for phylogenetic analysis of microbiomes

Kim, Minseok, Morrison, Mark and Yu, Zhongtang (2011) Evaluation of different partial 16S rRNA gene sequence regions for phylogenetic analysis of microbiomes. Journal of Microbiological Methods, 84 1: 81-87. doi:10.1016/j.mimet.2010.10.020


Author Kim, Minseok
Morrison, Mark
Yu, Zhongtang
Title Evaluation of different partial 16S rRNA gene sequence regions for phylogenetic analysis of microbiomes
Journal name Journal of Microbiological Methods   Check publisher's open access policy
ISSN 0167-7012
1872-8359
Publication date 2011-01-01
Sub-type Article (original research)
DOI 10.1016/j.mimet.2010.10.020
Open Access Status Not Open Access
Volume 84
Issue 1
Start page 81
End page 87
Total pages 7
Place of publication Amsterdam, Netherlands
Publisher Elsevier
Language eng
Abstract Operational taxonomic units (OTUs) are conventionally defined at a phylogenetic distance (0.03-species, 0.05-genus, 0.10-family) based on full-length 16S rRNA gene sequences. However, partial sequences (700. bp or shorter) have been used in most studies. This discord may affect analysis of diversity and species richness because sequence divergence is not distributed evenly along the 16S rRNA gene. In this study, we compared a set each of bacterial and archaeal 16S rRNA gene sequences of nearly full length with multiple sets of different partial 16S rRNA gene sequences derived therefrom (approximately 440-700. bp), at conventional and alternative distance levels. Our objective was to identify partial sequence region(s) and distance level(s) that allow more accurate phylogenetic analysis of partial 16S rRNA genes. Our results showed that no partial sequence region could estimate OTU richness or define OTUs as reliably as nearly full-length genes. However, the V1-V4 regions can provide more accurate estimates than others. For analysis of archaea, we recommend the V1-V3 and the V4-V7 regions and clustering of species-level OTUs at 0.03 and 0.02 distances, respectively. For analysis of bacteria, the V1-V3 and the V1-V4 regions should be targeted, with species-level OTUs being clustered at 0.04 distance in both cases.
Keyword 16S rRNA gene
Diversity
OTUs
Partial sequences
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: UQ Diamantina Institute Publications
 
Versions
Version Filter Type
Citation counts: TR Web of Science Citation Count  Cited 100 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 108 times in Scopus Article | Citations
Google Scholar Search Google Scholar
Created: Mon, 17 Mar 2014, 19:08:37 EST by System User on behalf of UQ Diamantina Institute