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1. (AU2016250096) Method and system for microbiome-derived characterization, diagnostics and therapeutics for conditions associated with functional features
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CLAIMS
We Claim:
1.           A method for at least one of characterizing, diagnosing, and treating a condition in at least a subject, the method comprising:
* at a sample handling network, processing nucleic acid content of each of an aggregate set of samples, from a population of subjects;
* at a computing system in communication with the sample handling network, generating a microbiome functional diversity dataset upon processing of the aggregate set of samples;
* at the computing system, receiving a supplementary dataset informative of presence of the condition within the population of subjects;
* at the computing system, extracting a set of features from the microbiome functional diversity dataset;
* at the computing system, transforming the supplementary dataset and the set of features into a characterization model of the condition; and
* identifying a feature of the set of features associated with the condition, upon processing a sample from the subject with the characterization model, thereby diagnosing the subject with the condition based upon the set of features.
2.           The method of Claim 1, wherein processing the aggregate set of samples comprises processing with a multiplexed amplification operation using a set of primers, a sequencing analysis operation, and an alignment operation.
3.           The method of Claim 1, wherein transforming the supplementary dataset and the set of features into the characterization model comprises identifying features associated with a set of functions significantly correlated with presence of the condition across a subset of the population of subjects, using a statistical analysis.
4.           The method of Claim 3, further comprising:
- based upon the characterization model, generating a therapy model configured to improve a state of the condition; and
at an output device associated with the subject, promoting a therapy to the subject with the condition based upon the characterization model and the therapy model, wherein promoting the therapy comprises promoting a microbiome functional composition modifying therapy to the subject in order to improve the state of the condition.
5.           The method of Claim 4, further comprising diagnosing the subject with the condition upon identifying a set of taxonomic features associated with the sample from the subject, wherein identifying the set of taxonomic features includes:
extracting candidate features associated with a set of taxonomic aspects of the aggregate set of samples, including features derived from one or more of: a species, a genus, a family, an order, a class and a phylum of microbiome components associated with the microbiome functional diversity dataset.
6.           The method of Claim 5, wherein the set of functions comprises a first functional feature associated with aminobenzoate degradation, such that the method comprises diagnosing the subject with the condition upon identification of the functional feature in association with the sample from the subject.
7.           The method of Claim 6, wherein the condition comprises AIDS, such that diagnosing the subject with the condition comprises diagnosing the subject with AIDS based upon identification of the first functional feature in association with the sample.
8.           The method of Claim 7, wherein the set of functions further includes a second functional feature associated with streptomycin biosynthesis, such that diagnosing the subject with the condition comprises diagnosing the subject with AIDS based upon identification of the set of functions in association with the sample.
9.           The method of Claim 7, wherein diagnosing the subject further comprises diagnosing the subject with AIDS upon identifying a set of taxa associated with the sample, wherein the set of taxa comprises at least one of: Erysipelotrichia (class), Oscillospiraceae (family), and Parasutterella (genus).
10.         The method of Claim 6, wherein the condition comprises Sprue, such that diagnosing the subject with the condition comprises diagnosing the subject with Sprue based upon identification of the first functional feature in association with the sample.
11.         The method of Claim 10, wherein the set of functions further includes at least one of: a first Kyoto Encyclopedia of Genes and Genomes (KEGG) functional feature related to biosynthesis and biodegradation of secondary metabolites, a second KEGG functional feature related to ribosome biogenesis, and a third KEGG functional feature related to peptidoglycan biosynthesis, such that diagnosing the subject with the condition comprises diagnosing the subject with Sprue based upon identification of the set of functions in association with the sample.
12.         The method of Claim 10, wherein diagnosing the subject further comprises diagnosing the subject with Sprue upon identifying a set of taxa associated with the sample, wherein the set of taxa comprises Bifidobacterium (genus), Bifidobacteriaceae (family), and Bifidobacteriales (order).
13.         The method of Claim 5, wherein the condition comprises gastric cancer, such that diagnosing the subject with the condition comprises diagnosing the subject with gastric cancer based upon identification of the first functional feature in association with the sample.
14.         The method of Claim 13, wherein diagnosing the subject further comprises diagnosing the subject with gastric cancer upon identifying a set of taxonomic features associated with the sample, wherein the set of taxonomic features comprises a first taxonomic feature associated with Streptococcus thermophilus (species).
15.         A method for characterizing a condition, the method comprising:
upon processing an aggregate set of 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, the microbiome functional diversity dataset indicative of systemic functions present in the microbiome components of the aggregate set of samples;
- at the computing system, transforming features extracted from at least one of the microbiome composition dataset and the microbiome functional diversity dataset into a characterization model of the conditions, wherein the characterization identifies an association between a functional feature related to an aminobenzoate degradation KEGG L3 derived feature and/or a streptomycin biosynthesis KEGG L3 derived feature in the sample, upon processing the sample from the subject; and * generating a therapy model, associated with the characterization model, configured to improve a state of the condition, wherein the condition comprises one of: AIDS, Sprue, and gastric cancer.
16.         The method of Claim 15, further including diagnosing a subject with the condition upon processing a sample from the subject according to the characterization model; and at an output device associated with the subject, promoting a therapy to the subject based upon the therapy model.
17.         The method of Claim 16, wherein the condition comprises AIDS, such that diagnosing the subject with the condition comprises diagnosing the subject with AIDS based upon identification of at least one of the first and the second functional features in association with the sample, and wherein diagnosing the subject further comprises diagnosing the subject with AIDS upon identifying a set of taxonomic features associated with the sample, wherein the set of taxonomic features comprises: Erysipelotrichia (class), Oscillospiraceae (family), Parasutterella (genus).
18.   The method of Claim 17, wherein diagnosing the subject further comprises identifying features derived from a set of functional features in association with the sample, wherein the set of functional features further includes: a first Kyoto Encyclopedia of Genes and Genomes (KEGG) functional feature related to Glycolysis / Gluconeogenesis, a second KEGG functional feature related to Neurodegenerative Diseases, a third KEGG functional feature related to Restriction enzyme, and a fourth KEGG functional feature related to transcription.
19.         The method of Claim 16, wherein the condition comprises Sprue, such that diagnosing the subject with the condition comprises diagnosing the subject with Sprue based upon identification of at least one of the first and the second functional features in association with the sample, and wherein diagnosing the subject further comprises diagnosing the subject with Sprue upon identifying a set of taxonomic features associated with the sample, wherein the set of taxonomic features includes at least one of: Bifidobacterium (genus), Bifidobacteriaceae (family), and Bifidobacteriales (order).
20.         The method of Claim 19, wherein diagnosing the subject further comprises identifying features derived from a set of functional features in association with the sample, wherein the set of functional features comprises a first Kyoto Encyclopedia of Genes and Genomes (KEGG) functional feature related to biosynthesis and biodegradation of secondary metabolites, a second KEGG functional feature related to ribosome biogenesis, and a third KEGG functional feature related to peptidoglycan biosynthesis.
21.         The method of Claim 16, further comprising diagnosing the subject with the condition upon identifying a set of taxonomic features associated with the sample from the subject, wherein identifying the set of taxonomic features includes: extracting features associated with a set of taxa of a microbiome associated with the sample, wherein extracting features comprises identifying features from at least one of: a species, a genus, a family, an order, a class and a phylum of the microbiome.
22.         The method of Claim 16, wherein promoting the therapy comprises promoting at least one of a probiotic and a prebiotic therapy to the subject, the therapy including a consumable component affecting a microorganism component that selectively modulates one or more of taxa and functions associated with correction of the condition, based on the therapy model.