MetaPhlAn (metagenomic phylogenetic analysis) 1 is a method for characterizing the taxonomic profiles of whole-metagenome shotgun (WMS) samples that has been used successfully in large-scale microbial community studies 2, 3. This work complements the original species-level profiling method with a system for eukaryotic and viral quantitation, strain-level identification and strain tracking. These and other extensions make the MetaPhlAn2 computational package (http://segatalab. cibio. unitn. it/tools/metaphlan2/and Supplementary Software) an efficient tool for mining WMS samples.

Our method infers the presence and read coverage of clade-specific markers to unequivocally detect the taxonomic clades present in a microbiome sample and estimate their relative abundance 1. MetaPhlAn2 includes an expanded set of∼ 1 million markers (184±45 for each bacterial species) from> 7,500 species (Supplementary Tables 1–3), based on the approximately tenfold increase in the number of sequenced genomes in the past 2 years. Subspecies markers enable strain-level analyses, and quasi-markers improve accuracy and allow the detection of viruses and eukaryotic microbes (a full list of additions is provided in Supplementary Notes 1–3 and Supplementary Fig. 1).