Accurate Estimation of Genome Relative Abundance for Closely Related Species in a Metagenomic Sample

• Activity Number: 393
• Type: Contributed
• Date/Time: Tuesday, August 5, 2014 : 2:00 PM to 3:50 PM
• Sponsor: Biometrics Section
• Author(s): Lingling An*+ and Michael Sohn and Naruekamol Pookhao and Qike Li
• Companies: University of Arizona and University of Arizona and University of Arizona and University of Arizona
• Keywords: next generation sequencing ; metagenomic ; microbial ; genomic similarity ; close related species

Abstract

Metagenomics has a great potential to discover previously unattainable information about microbial communities. A great challenge is that many microbes in an environmental sample may share relatively high similarity in the genomic sequence, and this intrinsic complexity makes it difficult to accurately estimate the taxonomic composition at very low ranks of taxonomy tree (e.g., species or subspecies level). We propose a new homology-based approach, Taxonomic Analysis by Elimination and Correction (TAEC), which utilizes the similarity in the genomic sequence in addition to sequence alignment result. The proposed method is comprehensively tested on various simulated benchmark datasets of diverse complexity of microbial structure. Compared with other available methods that can estimate taxonomic composition at very low taxonomic rank, TAEC demonstrates a greater accuracy in detection and quantification of multiple genomes in simulated metagenomic samples, especially when closely related strains are contained. TAEC is also applied on real metagenomic datasets.