Bioinformatics for whole-genome shotgun sequencing of microbial communities

Abstract

The application of whole-genome shotgun sequencing to microbial communities represents a major development in metagenomics, the study of uncultured microbes via the tools of modern genomic analysis. In the past year, whole-genome shotgun sequencing projects of prokaryotic communities from an acid mine biofilm, the Sargasso Sea, Minnesota farm soil, three deep-sea whale falls, and deep-sea sediments have been reported, adding to previously published work on viral communities from marine and fecal samples. The interpretation of this new kind of data poses a wide variety of exciting and difficult bioinformatics problems. The aim of this review is to introduce the bioinformatics community to this emerging field by surveying existing techniques and promising new approaches for several of the most interesting of these computational problems.

Figure 1. Blue-Yellow Microarray Figure Applied to KEGG Vectors for Four Metagenomics Projects

The whale-fall and Sargasso sea data are partitioned into three different samples each. The rows correspond to the different datasets and the columns to the 137 KEGG categories. Blue corresponds to underrepresentation and yellow to overrepresentation. Note that some branch lengths have been adjusted for visualization purposes and do not correspond to an actual meaningful distance.

Figure 2. Projection of the KEGG Vectors on the First Two Principle Components