Shotgun metagenomics and marker gene amplicon sequencing can be used to directly measure or predict the functional repertoire of the microbiota en masse, but current methods do not readily estimate the functional capability of individual microorganisms. Here we present BugBase, an algorithm that predicts organism-level coverage of functional pathways as well as biologically interpretable phenotypes such as oxygen tolerance, Gram staining, and pathogenic potential, within complex microbiomes using either whole-genome shotgun or marker gene sequencing data. We find the organism-level pathway coverage of BugBase predictions to be statistically higher powered than current bag-of-genes approaches for discerning functional changes in both host-associated and environmental microbiomes.

BugBase Predicts Organism Level Microbiome Phenotypes