Modern sequencing technologies produce vast amounts of DNA sequence data in the context of large-scale metagenomic studies revealing the complexity of microbial communities in unprecedented detail. These analyses require high-throughput computational methods that allow for a fast processing of sequencing data while retaining a high level of sensitivity and precision.
Here we present MALT (Megan ALignment Tool) a program for the fast alignment of DNA sequencing reads to large reference genome databases such as GenBank. MALT is able to process hundreds of millions of reads within only a few hours. In addition to the alignment procedure MALT implements a taxonomic binning algorithm that specifically assigns reads to bacterial species or strains. Its tight integration with the interactive metagenomic analysis software MEGAN allows for visualization and further analyses of results. These analyses can be performed in a comparative manner for studying the dynamics of microbial communities over time, or from different habitats or hosts. In particular the human microbiome is of major interest as it is comprised not only of a large number of commensals, but potentially also pathogens that have evolved with their human host. To gain insights into these evolutionary relationships, the field of paleogenetics aims to study ancient DNA extracted from archaeological remains.
In this context we 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.