MALT: Fast alignment and analysis of metagenomic DNA sequence data applied to the Tyrolean Iceman

Modern next generation sequencing technologies produce vast amounts of data in the context of large-scale metagenomic studies, in which complex microbial communities can be reconstructed to an unprecedented level of detail. Most prominent examples are human microbiome studies that correlate the bacterial taxonomic profile with specific physiological conditions or diseases.\n\nIn order to perform these analyses high-throughput computational tools are needed that are able to process these data within a short time while preserving a high level of sensitivity and specificity.\n\nHere we present MALT (MEGAN ALignment Tool) a program for the ultrafast alignment and analysis of metagenomic DNA sequencing data. MALT processes hundreds of millions of sequencing reads within only a few hours. In addition to the alignment procedure MALT implements a taxonomic binning algorithm that is able to specifically assign reads to bacterial species. Its tight integration with the interactive metagenomic analysis software MEGAN allows for visualization and further analyses of results.\n\nWe demonstrate MALT by its application to the metagenomic analysis of two ancient microbiomes from oral cavity and lung samples of the 5,300-year-old Tyrolean Iceman. Despite the strong environmental background, MALT is able to pick up the weak signal of the original microbiomes and identifies multiple species that are typical representatives of the respective host environment.