Method and system for microbiome-derived diagnostics and therapeutics for autoimmune system conditions

A method for characterizing a gluten intolerance spectrum disorder, the method comprising:

• at a sample handling network, receiving an aggregate set of samples from a population of subjects;
• generating a microbiome composition dataset for the population of subjects upon processing nucleic acid content of each of the aggregate set of samples;
• 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 gluten intolerance spectrum disorder;
• transforming the supplementary dataset and features extracted from the microbiome composition dataset into a characterization model of the gluten intolerance spectrum disorder;
• based upon the characterization model, generating a therapy model configured to improve a state of the gluten intolerance spectrum disorder;
• and
• providing a therapy for the gluten intolerance spectrum disorder based on the therapy model.

A method for at least one of characterizing, diagnosing, and treating a gluten intolerance spectrum disorder, the method comprising:

• at a sample handling network, processing nucleic acid content of a sample from a subject, thereby generating a microbiome composition dataset and a microbiome functional diversity dataset associated with the sample;
• identifying an association between the sample and 1) a taxonomic feature from the microbiome composition dataset and 2) a functional feature from the microbiome functional diversity dataset, upon processing the sample from the subject, wherein the taxonomic feature is associated with at least one of Bifidobacterium (genus), Bifidobacteriaceae (family), and Bifidobacteriales (order), and wherein the functional feature is related to ribosome biogenesis;
• based upon the association, diagnosing the subject with the gluten intolerance spectrum disorder;
• and
• providing a therapy to the subject, wherein providing the therapy comprises promoting a microbiome modifying therapy to the subject in order to improve a state of a gluten intolerance spectrum disorder in the subject.