Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2015-12

AUTHORS

Yan He, J Gregory Caporaso, Xiao-Tao Jiang, Hua-Fang Sheng, Susan M Huse, Jai Ram Rideout, Robert C Edgar, Evguenia Kopylova, William A Walters, Rob Knight, Hong-Wei Zhou

ABSTRACT

BACKGROUND: The operational taxonomic unit (OTU) is widely used in microbial ecology. Reproducibility in microbial ecology research depends on the reliability of OTU-based 16S ribosomal subunit RNA (rRNA) analyses. RESULTS: Here, we report that many hierarchical and greedy clustering methods produce unstable OTUs, with membership that depends on the number of sequences clustered. If OTUs are regenerated with additional sequences or samples, sequences originally assigned to a given OTU can be split into different OTUs. Alternatively, sequences assigned to different OTUs can be merged into a single OTU. This OTU instability affects alpha-diversity analyses such as rarefaction curves, beta-diversity analyses such as distance-based ordination (for example, Principal Coordinate Analysis (PCoA)), and the identification of differentially represented OTUs. Our results show that the proportion of unstable OTUs varies for different clustering methods. We found that the closed-reference method is the only one that produces completely stable OTUs, with the caveat that sequences that do not match a pre-existing reference sequence collection are discarded. CONCLUSIONS: As a compromise to the factors listed above, we propose using an open-reference method to enhance OTU stability. This type of method clusters sequences against a database and includes unmatched sequences by clustering them via a relatively stable de novo clustering method. OTU stability is an important consideration when analyzing microbial diversity and is a feature that should be taken into account during the development of novel OTU clustering methods. More... »

PAGES

20

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/s40168-015-0081-x

DOI

http://dx.doi.org/10.1186/s40168-015-0081-x

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1029757572

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/25995836


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