Benchmarking Community-Wide Estimates of Growth Potential from Metagenomes Using Codon Usage Statistics.

ABSTRACT: Trait inference from mixed-species assemblages is a central problem in microbial ecology. Frequently, sequencing information from an environment is available, but phenotypic measurements from individual community members are not. With the increasing availability of molecular data for microbial communities, bioinformatic approaches that map metagenome to (meta)phenotype are needed. Recently, we developed a tool, gRodon, that enables the prediction of the maximum growth rate of an organism from genomic data on the basis of codon usage patterns. Our work and that of other groups suggest that such predictors can be applied to mixed-species communities in order to derive estimates of the average community-wide maximum growth rate. Here, we present an improved maximum growth rate predictor desig

SUBMITTER: Weissman JL 

PROVIDER: S-EPMC9600850 | biostudies-literature | 2022 Oct

REPOSITORIES: biostudies-literature