Microbe Decoder uncovers functional traits of microbes in microbiome datasets

Microbe Decoder is a web server that predicts functional traits of microbes in microbiome sequencing datasets. Sequencing has revealed thousands of organisms in most ecosystems, but the functional traits of many organisms remain unclear. Existing tools can predict names of organisms or their genes, but they rarely predict concrete biological functions (e.g. fermentation or anaerobic growth). Microbe Decoder fills this gap using three complementary tools relying on taxonomy, metabolic networks, or machine learning. These tools accept either names or gene functions as inputs and are integrated into an easy-to-use web app. When tested against data for microbial isolates, Microbe Decoder showed good predictive performance (e.g. balanced accuracy of 0.85). When applied to datasets from the gut, sediment, and sea, it predicted shifts in functional traits over space and time. Microbe Decoder is designed for use with prokaryotes, with the goal of including eukaryotes in the future. By revealing functional traits of microbes in biological systems, Microbe Decoder will advance biology, medicine, and environmental science. Microbe Decoder is available at https://www.microbe-decoder.org/.