A method for at least one of characterizing, diagnosing, and treating a condition associated with microbiome functional features in at least a subject, the method comprising: receiving an aggregate set of biological samples from a population of subjects； generating at least one of a microbiome composition dataset and a microbiome functional diversity dataset for the population of subjects； generating a characterization of the condition based upon features extracted from at least one of the microbiome composition dataset and the microbiome functional diversity dataset； based upon the characterization, generating a therapy model configured to correct the condition； and at an output device associated with the subject, promoting a therapy to the subject based upon the characterization and the therapy model.
