1. 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: at a sample handling network, processing nucleic acid content of each of an aggregate set of samples, from a population of subjects, with a fragmentation operation, a multiplexed amplification operation using a set of primers, a sequencing analysis operation, and an alignment operation; at a computing system in communication with the sample handling network, generating a microbiome functional diversity dataset upon processing of the aggregate set of samples; at the computing system, receiving a supplementary dataset informative of presence of the condition within the population of subjects; at the computing system, extracting a set of functional features from the microbiome functional diversity dataset; at the computing system, transforming the supplementary dataset and the set of functional features into a characterization model of the condition; and identifying at least a subset of the set of functional features associated with the condition, upon processing a sample from the subject with the characterization model, thereby diagnosing the subject with the condition based upon the set of functional features.