Document Detail

Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library sizes.
MedLine Citation:
PMID:  21923700     Owner:  NLM     Status:  Publisher    
Technologies for massively parallel sequencing are revolutionizing microbial ecology and are vastly increasing the scale of ribosomal RNA (rRNA) gene studies. Although pyrosequencing has increased the breadth and depth of possible rRNA gene sampling, one drawback is that the number of reads obtained per sample is difficult to control. Pyrosequencing libraries typically vary widely in the number of sequences per sample, even within individual studies, and there is a need to revisit the behaviour of richness estimators and diversity indices with variable gene sequence library sizes. Multiple reports and review papers have demonstrated the bias in non-parametric richness estimators (e.g. Chao1 and ACE) and diversity indices when using clone libraries. However, we found that biased community comparisons are accumulating in the literature. Here we demonstrate the effects of sample size on Chao1, ACE, CatchAll, Shannon, Chao-Shen and Simpson's estimations specifically using pyrosequencing libraries. The need to equalize the number of reads being compared across libraries is reiterated, and investigators are directed towards available tools for making unbiased diversity comparisons.
Thomas M Gihring; Stefan J Green; Christopher W Schadt
Publication Detail:
Type:  LETTER     Date:  2011-9-19
Journal Detail:
Title:  Environmental microbiology     Volume:  -     ISSN:  1462-2920     ISO Abbreviation:  -     Publication Date:  2011 Sep 
Date Detail:
Created Date:  2011-9-19     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  100883692     Medline TA:  Environ Microbiol     Country:  -    
Other Details:
Languages:  ENG     Pagination:  -     Citation Subset:  -    
Copyright Information:
© 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.
Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6038, USA Research Resources Center, University of Illinois at Chicago, Chicago, IL, 60612, USA.
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