Improved taxonomic assignment of human intestinal 16S rRNA sequences by a dedicated reference database

BMC Genomics

Research Article

Jarmo Ritari¹  Jarkko Salojärvi¹  Leo Lahti²  Willem M. de Vos³ 

[1] Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland;Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland;Laboratory of Microbiology, Wageningen University, Wageningen, the Netherlands;Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland;Laboratory of Microbiology, Wageningen University, Wageningen, the Netherlands;Department of Bacteriology and Immunology, University of Helsinki, Helsinki, Finland;

关键词: Next-generation sequencing;    16S;    Ribosomal RNA;    Human intestinal microbiota;    Bacteria;    Archaea;    Taxonomy;   

DOI  :  10.1186/s12864-015-2265-y

 received in 2015-03-11, accepted in 2015-12-01,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundCurrent sequencing technology enables taxonomic profiling of microbial ecosystems at high resolution and depth by using the 16S rRNA gene as a phylogenetic marker. Taxonomic assignation of newly acquired data is based on sequence comparisons with comprehensive reference databases to find consensus taxonomy for representative sequences. Nevertheless, even with well-characterised ecosystems like the human intestinal microbiota it is challenging to assign genus and species level taxonomy to 16S rRNA amplicon reads. A part of the explanation may lie in the sheer size of the search space where competition from a multitude of highly similar sequences may not allow reliable assignation at low taxonomic levels. However, when studying a particular environment such as the human intestine, it can be argued that a reference database comprising only sequences that are native to the environment would be sufficient, effectively reducing the search space.ResultsWe constructed a 16S rRNA gene database based on high-quality sequences specific for human intestinal microbiota, resulting in curated data set consisting of 2473 unique prokaryotic species-like groups and their taxonomic lineages, and compared its performance against the Greengenes and Silva databases. The results showed that regardless of used assignment algorithm, our database improved taxonomic assignation of 16S rRNA sequencing data by enabling significantly higher species and genus level assignation rate while preserving taxonomic diversity and demanding less computational resources.ConclusionThe curated human intestinal 16S rRNA gene taxonomic database of about 2500 species-like groups described here provides a practical solution for significantly improved taxonomic assignment for phylogenetic studies of the human intestinal microbiota.

【 授权许可】

CC BY   
© Ritari et al. 2015