White, J. R., Navlakha, S., Nagarajan, N., Ghodsi, M. R., Kingsford, C., Pop, M. (March 2010) Alignment and clustering of phylogenetic markers--implications for microbial diversity studies. BMC Bioinformatics, 11 (3). p. 152. ISSN 1471-2105
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Abstract
BACKGROUND: Molecular studies of microbial diversity have provided many insights into the bacterial communities inhabiting the human body and the environment. A common first step in such studies is a survey of conserved marker genes (primarily 16S rRNA) to characterize the taxonomic composition and diversity of these communities. To date, however, there exists significant variability in analysis methods employed in these studies. RESULTS: Here we provide a critical assessment of current analysis methodologies that cluster sequences into operational taxonomic units (OTUs) and demonstrate that small changes in algorithm parameters can lead to significantly varying results. Our analysis provides strong evidence that the species-level diversity estimates produced using common OTU methodologies are inflated due to overly stringent parameter choices. We further describe an example of how semi-supervised clustering can produce OTUs that are more robust to changes in algorithm parameters. CONCLUSIONS: Our results highlight the need for systematic and open evaluation of data analysis methodologies, especially as targeted 16S rRNA diversity studies are increasingly relying on high-throughput sequencing technologies. All data and results from our study are available through the JGI FAMeS website http://fames.jgi-psf.org/.
| Item Type: | Paper |
|---|---|
| Additional Information: | BMC bioinformatics |
| Uncontrolled Keywords: | Cluster Analysis DNA, Bacterial/genetics Genetic Markers/*genetics *Genetic Variation *Phylogeny RNA, Bacterial/genetics RNA, Ribosomal, 16S/genetics Sequence Alignment |
| Subjects: | bioinformatics > genomics and proteomics > analysis and processing > alignment processing bioinformatics > genomics and proteomics > annotation > phylogenetic tree annotation bioinformatics > genomics and proteomics > alignment > sequence alignment bioinformatics > computational biology |
| CSHL Authors: | |
| Communities: | CSHL labs > Navlakha lab |
| Depositing User: | Matthew Dunn |
| Date: | 24 March 2010 |
| Date Deposited: | 08 Nov 2019 14:44 |
| Last Modified: | 08 Nov 2019 14:44 |
| PMCID: | PMC2859756 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/38681 |
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