A tool for rapidly and accurately determining the phylogenetic makeup of large microbial communities is reported online this week in Nature Methods. The work combines data from the Human Microbiome Project and MetaHIT (metagenomics of the human intestinal tract) for the largest metagenomic profile of the human gut to date.
Microorganisms play an important role in all natural environments and their influence on human health is coming under more and more scrutiny. To really understand their impact one needs to know the composition of microbial communities, an endeavor made possible by high throughput sequencing. But current computational methods to determine community profiles from sequence data are either too slow to deal with large datasets or cannot achieve accurate assignment at the species or genus level.
Curtis Huttenhower and colleagues solved these problems with a program that is both fast and highly accurate. MetaPhlAn (metagenomic phylogenetic analysis) can assign millions of short sequence reads to the correct taxon in minutes and also estimates their abundance. It achieves this speed and accuracy by mapping reads to a database of markers, each unequivocally assigning a read to its species, genus or higher taxonomic level.