Alignment and clustering of phylogenetic markers - implications for microbial diversity studies

dc.contributor.authorWhite, James R
dc.contributor.authorNavlakha, Saket
dc.contributor.authorNagarajan, Niranjan
dc.contributor.authorGhodsi, Mohammad-Reza
dc.contributor.authorKingsford, Carl
dc.contributor.authorPop, Mihai
dc.date.accessioned2013-01-10T21:28:29Z
dc.date.available2013-01-10T21:28:29Z
dc.date.issued2010-03-24
dc.description.abstractBackground: 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/.en_US
dc.description.urihttps://doi.org/10.1186/1471-2105-11-152
dc.identifier.citationWhite, J.R., Navlakha, S., Nagarajan, N. et al. Alignment and clustering of phylogenetic markers - implications for microbial diversity studies. BMC Bioinformatics 11, 152 (2010).en_US
dc.identifier.urihttp://hdl.handle.net/1903/13373
dc.language.isoen_USen_US
dc.relation.isAvailableAtCollege of Computer, Mathematical & Natural Sciencesen_us
dc.relation.isAvailableAtComputer Scienceen_us
dc.relation.isAvailableAtDigital Repository at the University of Marylanden_us
dc.relation.isAvailableAtUniversity of Maryland (College Park, MD)en_us
dc.subjectphylogenetic markersen_US
dc.subjectmicrobial diversityen_US
dc.titleAlignment and clustering of phylogenetic markers - implications for microbial diversity studiesen_US
dc.typeArticleen_US

Files

Original bundle
Now showing 1 - 1 of 1
Loading...
Thumbnail Image
Name:
White, et al.pdf
Size:
1.64 MB
Format:
Adobe Portable Document Format
License bundle
Now showing 1 - 1 of 1
No Thumbnail Available
Name:
license.txt
Size:
1.57 KB
Format:
Item-specific license agreed upon to submission
Description: