alignment and clustering of phylogenetic markers - implications for microbial diversity studies对齐和集群系统发育标记u2014u2014对微生物多样性的影响研究.pdfVIP

White et al. BMC Bioinformatics 2010, 11:152 /1471-2105/11/152 RESEARCH ARTICLE Open Access Alignment and clustering of phylogenetic markers - implications for microbial diversity studies 1,3 2,3 4 2,3 2,3 James R White , Saket Navlakha , Niranjan Nagarajan , Mohammad-Reza Ghodsi , Carl Kingsford , Mihai Pop2,3* 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/. Background