# US 10,311,973 B2 · Method and system for microbiome-derived diagnostics and therapeutics for autoimmune system conditions > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 10,311,973 B2 - Document ID: US10311973B2 - Status: Granted - Kind: B2 - Application number: 15/204,707 - Filed: 2016-07-07 - Published: 2016-11-03 - Granted: 2019-06-04 - Earliest claimed: 2014-10-21 - Assignees: uBiome, Inc. - Applicants: uBiome, Inc. - Inventors: Zachary Apte; Daniel Almonacid; Jessica Richman; Siavosh Rezvan Behbahani - Web page: https://patentgrep.com/patent/US10311973B2 ## CPC - G16H 50/20: for computer-aided diagnosis, e.g. based on medical expert systems - C12Q 1/6883: for diseases caused by alterations of genetic material - G16B 10/00: ICT specially adapted for evolutionary bioinformatics, e.g. phylogenetic tree construction or analysis - G16B 20/00: ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations - G16B 20/20: Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection - G16B 50/00: ICT programming tools or database systems specially adapted for bioinformatics - G16B 50/10: Ontologies; Annotations - G16H 10/40: for data related to laboratory analysis, e.g. patient specimen analysis - G16H 20/10: relating to drugs or medications, e.g. for ensuring correct administration to patients - G16H 20/40: relating to mechanical, radiation or invasive therapies, e.g. surgery, laser therapy, dialysis or acupuncture - G16H 40/63: for local operation - G16H 40/67: for remote operation - Y02A 90/10: Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation - G16H: HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA - C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES - G16B: BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY - Y02A: TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE ## Abstract A method for at least one of characterizing, diagnosing, and treating an autoimmune disorder 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 autoimmune 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 autoimmune condition; and at an output device associated with the subject, promoting a therapy to the subject based upon the characterization and the therapy model. ## Claims ### Claim 1 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 at least one of a microbiome composition dataset and a microbiome functional diversity dataset associated with the sample; identifying an association between the sample and at least one of a taxonomic feature from the microbiome composition dataset and a functional feature from the microbiome functional diversity dataset, upon processing the sample from the subject; 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 the gluten intolerance spectrum disorder in the subject. ### Claim 2 (depends on 1) The method of claim 1, wherein diagnosing the subject with the gluten intolerance spectrum disorder comprises identifying a first taxonomic feature associated with Bifidobacterium (genus) in association with the sample. ### Claim 3 (depends on 2) The method of claim 2, wherein diagnosing the subject with the gluten intolerance spectrum disorder comprises identifying a fourth taxonomic feature associated with Actinobacteria (class) in association with the sample. ### Claim 4 (depends on 3) The method of claim 3, wherein diagnosing the subject with the gluten intolerance spectrum disorder comprises identifying a fifth taxonomic feature associated with Moryella (genus) in association with the sample. ### Claim 5 (depends on 4) The method of claim 4, wherein diagnosing the subject with the gluten intolerance spectrum disorder comprises identifying at least one of: a sixth taxonomic feature associated with Veillonellaceae (family), a seventh taxonomic feature associated with Selenmonadales (order), and an eighth taxonomic feature associated with Negativicutes (class) in association with the sample. ### Claim 6 (depends on 1) The method of claim 1, wherein diagnosing the subject with the gluten intolerance spectrum disorder comprises identifying at least one of a set of functional features in association with the sample, the set of functional features derived from one or more of: clusters of orthologous groups of proteins features, genomic functional features, chemical functional features, and systemic functional features. ### Claim 7 (depends on 6) The method of claim 6, wherein diagnosing the subject with the gluten intolerance spectrum disorder comprises identifying a first functional feature related to ribosome biogenesis in association with the sample. ### Claim 8 (depends on 7) The method of claim 7, wherein diagnosing the subject with the gluten intolerance spectrum disorder comprises identifying a second functional feature related to peptidoglycan biosynthesis in association with the sample. ### Claim 9 (depends on 8) The method of claim 8, wherein diagnosing the subject with the gluten intolerance spectrum disorder comprises identifying a third functional feature related to biosynthesis and biodegradation of secondary metabolites in association with the sample. ### Claim 10 (depends on 9) The method of claim 9, wherein diagnosing the subject with the gluten intolerance spectrum disorder comprises identifying a fourth functional feature related to translation proteins in association with the sample. ### Claim 11 (depends on 9) The method of claim 9, wherein diagnosing the subject with the gluten intolerance spectrum disorder comprises identifying a fifth functional feature related to genetic information processing in association with the sample. ### Claim 12 (depends on 9) The method of claim 9, wherein diagnosing the subject with the gluten intolerance spectrum disorder comprises identifying a sixth functional feature related to Carbohydrate Metabolism in association with the sample. ### Claim 13 (depends on 1) The method of claim 1, wherein providing the therapy comprises promoting a prebiotic therapy to the subject, wherein the prebiotic therapy comprises a consumable that selectively modulates at least one of: a population size of a desired taxon, and a population size of a desired microbiome function, associated with improving the state of the gluten intolerance spectrum disorder in the subject. ### Claim 14 (depends on 1) The method of claim 1, wherein providing the therapy comprises promoting a probiotic therapy to the subject, wherein the probiotic therapy comprises a consumable that affects at least one of: a microorganism component of the subject, and a microbiome function, in promoting improvement of the state of the gluten intolerance spectrum disorder in the subject. ### Claim 15 (depends on 1) The method of claim 1, wherein providing the therapy comprises promoting a microbiota-modifying therapy to the subject, wherein the microbiota-modifying therapy comprises a treatment that affects at least one of: a microorganism component of the subject, and a microbiome function, in promoting improvement of the state of the gluten intolerance spectrum disorder in the subject. ### Claim 16 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. ### Claim 17 (depends on 16) The method of claim 16, wherein processing nucleic acid content of each of the aggregate set of samples comprises processing with a fragmentation operation, a multiplexed amplification operation using a set of primers, a sequencing analysis operation, and an alignment operation. ### Claim 18 (depends on 17) The method of claim 17, further comprising: diagnosing an individual with the gluten intolerance spectrum disorder, according to the characterization model, upon identifying at least one of: a set of taxonomic features, associated with a sample processed from the individual. ### Claim 19 (depends on 18) The method of claim 18, wherein the set of taxonomic features includes a first taxonomic feature associated with Bifidobacterium (genus) in association with the sample. ### Claim 20 (depends on 19) The method of claim 19, wherein providing the therapy comprises: at an output device associated with the individual, promoting a therapy to the individual with the gluten intolerance spectrum disorder, in accordance with the therapy model, wherein promoting the therapy comprises promoting a microbiome modifying therapy to the individual, the microbiome modifying therapy configured to affect at least one of: a taxonomic group associated with the set of taxonomic features, and a functional group associated with a set of functional features, in order to improve a state of the gluten intolerance spectrum disorder in the individual. ### Claim 21 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. ### Claim 22 (depends on 21) The method of claim 21, wherein identifying the association further includes identifying a second taxonomic feature related to Actinobacteria (class) and a second functional feature related to peptidoglycan biosynthesis in association with the sample. ### Claim 23 (depends on 22) The method of claim 22, wherein identifying the association further includes identifying a third taxonomic feature related to Moryella (genus) and a third functional feature related to biosynthesis and biodegradation of secondary metabolites in association with the sample. ### Claim 24 (depends on 21) The method of claim 21, wherein providing the therapy comprises promoting a microbiome modifying therapy to the subject, the microbiome modifying therapy configured to affect a population from Bifidobacterium (genus) in order to improve the state of the gluten intolerance spectrum disorder in the subject.