Signal processing for metagenomics: extracting information from the soup

Abstract

Traditionally, studies in microbial genomics have focused on single-genomes from cultured species, thereby limiting their focus to the small percentage of species that can be cultured outside their natural environment. Fortunately, recent advances in high-throughput sequencing and computational analyses have ushered in the new field of metagenomics, which aims to decode the genomes of microbes from natural communities without the need for cultivation. Although metagenomic studies have shed a great deal of insight into bacterial diversity and coding capacity, several computational challenges remain due to the massive size and complexity of metagenomic sequence data. Current tools and techniques are reviewed in this paper which address challenges in 1) genomic fragment annotation, 2) phylogenetic reconstruction, 3) functional classification of samples, and 4) interpreting complementary metaproteomics and metametabolomics data. Also surveyed are important applications of metagenomic studies, including microbial forensics and the roles of microbial communities in shaping human health and soil ecology.

Fig. (1)

Comparison of Speech Classification to the DNA Classification problem.

Fig. (2)

The first metagenomics dataset was shotgun, via the Sanger method, sequenced in 2003. Since then, pyrosequencing is now being used to gain cheaper and highly parallel reads. The timeline illustrates some metagenomics datasets that have been sequenced to date and is a subset of all the projects that are completed [40].