BugBase predicts organism-level microbiome phenotypes

Abstract 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 BugBase’s organism-level pathway coverage predictions to be statistically higher powered than current ‘bag-of-genes’ approaches for discerning functional changes in both host-associated and environmental microbiomes.