Method and system for microbiome-derived diagnostics and therapeutics

A method for diagnosing and treating a Crohn's disease condition for 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 a primer for a nucleic acid sequence associated with the Crohn's disease condition;
• fragmenting nucleic acid material based on the biological sample;
• and
• amplifying the fragmented nucleic acid material based on the identified primer;
• and
• determining an alignment of the microorganism nucleic acid sequence to a reference nucleic acid sequence set associated with the Crohn's disease condition;
• generating a microbiome composition diversity dataset and a microbiome functional diversity dataset for the population of subjects based upon the alignments;
• collecting a supplementary dataset, associated with at least a subset of the population of subjects, wherein the supplementary dataset is informative of a characteristic associated with the Crohn's disease condition;
• generating a characterization of the Crohn's disease condition based upon the supplementary dataset and at least one of the microbiome composition diversity dataset and the microbiome functional diversity dataset;
• based upon the characterization, generating a therapy model that determines a therapy for correcting the Crohn's disease condition;
• and
• at an output device associated with the subject, providing the therapy to the subject with the Crohn's disease condition based upon the characterization and the therapy model, wherein the therapy modulates microbiome composition of the subject towards an equilibrium state.