Researchers performing microbial community sampling ask the question: “Who is there?” Single marker–gene sequencing has proven cost-effective for microbe identification, but it cannot reveal what the microbes in a community are capable of doing. To bridge the gap, Langille et al. serve up PICRUSt (phylogenetic investigation of communities by reconstruction of unobserved states), a computational tool that predicts functions from marker-gene profiling data. PICRUSt first extracts gene content from every microbe with a genome sequence in a reference phylogenetic tree; then it predicts the gene content and corresponding traits of related unsequenced microbes using an adaptation of ancestral state reconstruction methods. From 16S ribosomal DNA marker sequences, it can reproduce a large share of the functional information found by shotgun metagenomic sequencing in the Human Microbiome Project and other data sets.
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Extracting microbial function from phylogeny. Nat Methods 10, 934 (2013). https://doi.org/10.1038/nmeth.2670
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DOI: https://doi.org/10.1038/nmeth.2670