1. A method for diagnosing and treating an immune microbial dysfunction in a subject, the method comprising: receiving an aggregate set of biological samples from a population of subjects; for each biological sample of the aggregate set of biological samples: determining a microorganism nucleic acid sequence, comprising: identifying primers for nucleic acid sequences associated with the immune microbial dysfunction; fragmenting nucleic acid material from the biological sample; and amplifying the fragmented nucleic acid material using the identified primers; and determining an alignment of the microorganism nucleic acid sequence to a reference nucleic acid sequence associated with the immune microbial dysfunction; generating a microbiome composition dataset and a microbiome functional diversity dataset for the population of subjects based upon the alignment; receiving a supplementary dataset, associated with at least a subset of the population of subjects, wherein the supplementary dataset is informative of characteristics associated with the immune microbial dysfunction; generating a characterization of the immune microbial dysfunction based upon the supplementary dataset and 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 that determines a therapy for correcting the immune microbial dysfunction; and at an output device associated with the subject, providing a therapy to the subject with the immune microbial dysfunction based upon the characterization and the therapy model, wherein the therapy modulates microbiome composition of the subject towards an equilibrium state.