PICRUSt

PICRUSt predicts the functional composition of metagenomes from marker gene surveys such as 16S rRNA by phylogenetic inference to estimate gene family presence and abundance.

Key Features:

• Integration with reference genomes: Integrates 16S rRNA marker gene data with a comprehensive database of reference genomes to predict gene family content.
• Extended ancestral-state reconstruction: Uses an extended ancestral-state reconstruction algorithm to infer likely gene families in unobserved taxa.
• Reconstruction of unobserved states: Reconstructs the unobserved states of microbial communities to enable estimation of composite functional potential.
• Gene family prediction: Predicts the abundance and presence of various gene families from marker gene data.
• Quantifiable uncertainty: Provides predictions with quantifiable uncertainty for inferred functional profiles.
• Cross-ecosystem applicability: Applicable to host-associated (including Human Microbiome Project data) and environmental microbial communities.

Scientific Applications:

• Human microbiome functional profiling: Recapitulates and extends functional findings from the Human Microbiome Project for host-associated communities.
• Environmental metagenomics: Estimates functional potential of environmental microbial communities using marker gene surveys.
• Study of uncultivated taxa: Enables functional exploration of thousands of uncultivated microbial communities accessible only via marker gene data.

Methodology:

PICRUSt leverages an extended ancestral-state reconstruction algorithm together with a comprehensive database of reference genomes to reconstruct unobserved states and infer gene family presence and abundance from marker gene (16S rRNA) data.