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WO 2016/168354 Al 20 October 2016 (20.10.2016) P O P C T (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2016/168354 Al 20 October 2016 (20.10.2016) P O P C T (51) International Patent Classification: (74) Agent: SCHOX, Jeffrey; 500 3rd Street, Suite 515, San A61K 35/74 (2015.01) A61P 1/00 (2006.01) Francisco, CA 94107 (US). A61K35/741 (2015.01) G06F 19/12 (201 1.01) (81) Designated States (unless otherwise indicated, for every (21) International Application Number: kind of national protection available): AE, AG, AL, AM, PCT/US2016/027359 AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, (22) Date: International Filing DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, 13 April 2016 (13.04.2016) HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, (25) Filing Language: English KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, (26) Publication Language: English PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, (30) Priority Data: SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, 62/146,833 13 April 2015 (13.04.2015) US TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. 62/147,202 14 April 2015 (14.04.2015) US (84) Designated States (unless otherwise indicated, for every 62/147,077 14 April 2015 (14.04.2015) us kind of regional protection available): ARIPO (BW, GH, 62/147,058 14 April 2015 (14.04.2015) us GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, 62/147,334 14 April 2015 (14.04.2015) us TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, (71) Applicant: UBIOME, INC. [US/US]; 360 Langton Street, TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, #301, San Francisco, CA 94103 (US). DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, (72) Inventors: APTE, Zachary; 360 Langton Street, #301, SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, San Francisco, CA 94103 (US). ALMONACID, Daniel; GW, KM, ML, MR, NE, SN, TD, TG). 360 Langton Street, #301, San Francisco, CA 94103 (US). RICHMAN, Jessica; 360 Langton Street, #301, San Fran Published: cisco, CA 94103 (US). BEHBAHANI, Siavosh, Rezvan; — with international search report (Art. 21(3)) 360 Langton Street, #301, San Francisco, CA 94103 (US). (54) Title: METHOD AND SYSTEM FOR MICROBIOME-DERIVED DIAGNOSTICS AND THERAPEUTICS FOR CONDI TIONS ASSOCIATED WITH MICROBIOME FUNCTIONAL FEATURES (57) Abstract: A method for at least one of characteriz 100 ing, diagnosing, and treating a condition associated with microbiome functional features in at least a subject, the S110 method comprising: receiving an aggregate set of biolo receiving an aggregate set of samples from a population of subjects gical samples from a population of subjects; generating at T least one of a microbiome composition dataset and a mi characterizing a microbiome composition and/or functional features crobiome functional diversity dataset for the population for each of the aggregate set of samples associated with the of subjects; generating a characterization of the condition population of subjects thereby generating at least one of a microbiome composition dataset and a microbiome functional S120 based upon features extracted from at least one of the mi diversity dataset for the population of subjects crobiome composition dataset and the microbiome func tional diversity dataset; based upon the characterization, receiving a supplementary dataset, associated with at least a subset generating a therapy model configured to correct the con of the population of subjects, wherein the supplementary dataset is S130 dition; and at an output device associated with the sub informative of characteristics associated with the condition associated ject, promoting a therapy to the subject based upon the with micro biome functional features characterization and the therapy model. transforming the supplementary dataset and features extracted from at least one of the microbiome composition dataset and the S140 microbiome functional diversity dataset into a characterization model of the condition associated with micro biome functional features based upon the characterization, generating a therapy configured to improve a state of the condition microbiome functional features FIGURE 1A METHOD AND SYSTEM FOR MICROBIOME-DERIVED DIAGNOSTICS AND THERAPEUTICS FOR CONDITIONS ASSOCIATED WITH MICROBIOME FUNCTIONAL FEATURES CROSS-REFERENCE TO RELATED APPLICATIONS [0001] This application also claims the benefit of U.S. Provisional Application serial number 62/146,833 filed 13-APR-2015, U.S. Provisional Application serial number 62/147,058 filed 14-APR-2015, U.S. Provisional Application serial number 62/147,077 filed 14-APR-2015, U.S. Provisional Application serial number 62/147,202 filed 14-APR-2015, and U.S. Provisional Application serial number 62/147,334 filed 14-APR-2015, which are each incorporated in its entirety herein by this reference. TECHNICAL FIELD [0002] This invention relates generally to the field of medical diagnostics and more specifically to a new and useful method and system for microbiome-derived diagnostics and therapeutics in the field of medical diagnostics. BACKGROUND [0003] A microbiome is an ecological community of commensal, symbiotic, and pathogenic microorganisms that are associated with an organism. The human microbiome comprises as many microbial cells as human cells present in the entire human body, but characterization of the human microbiome is still in nascent stages due to limitations in sample processing techniques, genetic analysis techniques, and resources for processing large amounts of data. Nonetheless, the microbiome is suspected to play at least a partial role in a number of health/disease-related states (e.g., preparation for childbirth, diabetes, gastrointestinal disorders, etc.). [0004] Given the profound implications of the microbiome in affecting a subject's health, efforts related to the characterization of the microbiome, the generation of insights from the characterization, and the generation of therapeutics configured to rectify states of dysbiosis should be pursued. Current methods and systems for analyzing the microbiomes of humans and providing therapeutic measures based on gained insights have, however, left many questions unanswered. In particular, methods for characterizing certain health conditions and therapies (e.g., probiotic therapies) tailored to specific subjects have not been viable due to limitations in current technologies. [0005] As such, there is a need in the field of microbiology for a new and useful method and system for characterizing conditions associated with microbiome functional features in an individualized and population-wide manner. This invention creates such a new and useful method and system. BRIEF DESCRIPTION OF THE FIGURES [0006] FIGURE lA is a flowchart of an embodiment of a method for characterizing a microbiome-derived condition and identifying therapeutic measures; [0007] FIGURE lB is a flowchart of an embodiment of a method for generating microbiome-derived diagnostics; [0008] FIGURE lC is a flowchart of a portion of a variation of a method for generating microbiome-derived diagnostics and therapeutics; [0009] FIGURE 2 depicts an embodiment of a method and system for generating microbiome-derived diagnostics and therapeutics; [0010] FIGURE 3 depicts variations of a portion of an embodiment of a method for generating microbiome-derived diagnostics and therapeutics; [001 1] FIGURE 4 depicts a variation of a process for generation of a model in an embodiment of a method and system for generating microbiome-derived diagnostics and therapeutics; [0012] FIGURE 5 depicts variations of mechanisms by which probiotic-based therapies operate in an embodiment of a method for characterizing a health condition; [0013] FIGURE 6 depicts examples of therapy-related notification provision in an example of a method for generating microbiome-derived diagnostics and therapeutics; and [0014] FIGURE 7 depicts example data associated with a method for generating microbiome-derived diagnostics and therapeutics. DESCRIPTION OF THE EMBODIMENTS [001 5] The following description of the embodiments of the invention is not intended to limit the invention to these embodiments, but rather to enable any person skilled in the art to make and use this invention. Method for Characterizing a Microbiome-derived Condition and Identifying Therapeutic Measures [0016] As shown in FIGURE lA, a first method 100 for diagnosing and treating a condition associated with microbiome functional features comprises: receiving an aggregate set of samples from a population of subjects S o; characterizing a microbiome composition and/or functional features for each of the aggregate set of samples associated with the population of subjects, thereby generating at least one of a microbiome composition dataset and a microbiome functional diversity dataset for the population of subjects S120; 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 condition S130; and transforming the supplementary dataset and features extracted from at least one of the microbiome composition dataset and the microbiome functional diversity dataset into a characterization model of the condition S140. In some variations, the first method 100 can further include: based upon the characterization, generating a therapy model configured to improve a state of the condition S150. [0017] Variations of the first method 100 can additionally or alternatively comprise clustering otherwise unrelated conditions based upon features extracted from at least one of a microbiome functional diversity dataset and/or a microbiome composition dataset by way of a characterization model S140'; and diagnosing a subject with a condition based upon identification of microbiome functional features and/or microbiome composition features, determined upon processing a sample from the subject, in a non-obvious manner S141', as shown in FIGURE lC.
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