MEGAN analysis of metagenomic data

Abstract

Metagenomics is the study of the genomic content of a sample of organisms obtained from a common habitat using targeted or random sequencing. Goals include understanding the extent and role of microbial diversity. The taxonomical content of such a sample is usually estimated by comparison against sequence databases of known sequences. Most published studies use the analysis of paired-end reads, complete sequences of environmental fosmid and BAC clones, or environmental assemblies. Emerging sequencing-by-synthesis technologies with very high throughput are paving the way to low-cost random "shotgun" approaches. This paper introduces MEGAN, a new computer program that allows laptop analysis of large metagenomic data sets. In a preprocessing step, the set of DNA sequences is compared against databases of known sequences using BLAST or another comparison tool. MEGAN is then used to compute and explore the taxonomical content of the data set, employing the NCBI taxonomy to summarize and order the results. A simple lowest common ancestor algorithm assigns reads to taxa such that the taxonomical level of the assigned taxon reflects the level of conservation of the sequence. The software allows large data sets to be dissected without the need for assembly or the targeting of specific phylogenetic markers. It provides graphical and statistical output for comparing different data sets. The approach is applied to several data sets, including the Sargasso Sea data set, a recently published metagenomic data set sampled from a mammoth bone, and several complete microbial genomes. Also, simulations that evaluate the performance of the approach for different read lengths are presented.[MEGAN is freely available at http://www-ab.informatik.uni-tuebingen.de/software/megan.]The genomic revolution of the early 1990s targeted the study of individual genomes of microorganisms, plants, and animals. While this type of analysis has almost become routine, the genomic analysis of complex mixtures of organisms remains challenging. Metagenomics has been defined as "the genomic analysis of microorganisms by direct extraction and cloning of DNA from an assemblage of microorganisms" (Handelsman 2004), and its importance stems from the fact that 99% or more of all microbes are deemed to be unculturable. Goals of metagenomic studies include assessing the coding potential of environmental organisms, quantifying the relative abundances of (known) species, and estimating the amount of unknown sequence information (environmental sequences) for which no species, or only distant relatives, have yet been described. It is useful to extend Handelsman's definition to also include sequences from higher organisms as well as just microorganisms, thus opening the door to "environmental forensics." By vastly extending the currently available sequences in databases, metagenomics promises to lead to the discovery of new genes that have useful applications in biotechnology and medicine (Steele and Streit 2005).Early metagenomics projects (Béja et al. 2000(Béja et...

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