Methods for comparative metagenomics

Abstract

Background: Metagenomics is a rapidly growing field of research that aims at studying uncultured organisms to understand the true diversity of microbes, their functions, cooperation and evolution, in environments such as soil, water, ancient remains of animals, or the digestive system of animals and humans. The recent development of ultra-high throughput sequencing technologies, which do not require cloning or PCR amplification, and can produce huge numbers of DNA reads at an affordable cost, has boosted the number and scope of metagenomic sequencing projects. Increasingly, there is a need for new ways of comparing multiple metagenomics datasets, and for fast and user-friendly implementations of such approaches.

Results: This paper introduces a number of new methods for interactively exploring, analyzing and comparing multiple metagenomic datasets, which will be made freely available in a new, comparative version 2.0 of the stand-alone metagenome analysis tool MEGAN.

Conclusion: There is a great need for powerful and user-friendly tools for comparative analysis of metagenomic data and MEGAN 2.0 will help to fill this gap.

Figure 1

A discovery rate plot computed by MEGAN 2.0 for the mouse gut dataset. The x-axis represents the percentage of reads subsampled from the total dataset and the y-axis represents the number of strong nodes (with t = 5) computed by the LCA algorithm, approximating the number of identified species. The datapoint at 10 × t % is based on t independent runs.

Figure 2

A classification of all COGs determined in the mouse gut sample.

Figure 3

Summary of the microbial attributes of the soil dataset based on the NCBI's "Prokaryotic Attributes Table". In each pie chart, the number of classified species having the indicated property is displayed.

Figure 4

Two multiple-comparative tree views of a human gut metagenome [16] shown in red and a mouse gut metagenome [17] shown in green, as computed by MEGAN 2.0, using normalized counts. In (a), we show an overview of the taxonomy down to the phylum level, whereas in (b) we display a part of a class-level analysis. In bold we show the support values as listed in Table 1.

Figure 5

A multiple-comparative tree view of a soil metagenome [18] shown in green and a marine metagenome [19] shown in red, as computed by MEGAN 2.0. In (a), we show an overview of the taxonomy down to the phylum level, whereas in (b) we display a part of a class-level analysis. In bold we show the support values as listed in Table 2.

Figure 6

A summary of the comparison of the marine (red) and soil (green) datasets, generated at different taxonomical ranks.