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1. (US20180137930) Method and system for microbiome-derived characterization, diagnostics, and therapeutics for cardiovascular disease conditions
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Claims

1. A method for characterizing an inflammatory heart disease condition, the method comprising:
receiving an aggregate set of samples from a population of subjects;
for each sample of the aggregate set of samples: determining a microorganism nucleic acid sequence based on amplifying nucleic acid material of the aggregate set of samples with a primer set;
generating a microbiome feature dataset for the population of subjects based upon the microorganism nucleic acid sequences;
generating a characterization model of the inflammatory heart disease condition from the microbiome feature dataset;
based upon the characterization model, generating a therapy model that determines a therapy for improving the inflammatory heart disease condition; and
providing the therapy to a subject associated with the inflammatory heart disease condition based upon the characterization model and the therapy model.
2. The method of claim 1, wherein determining the microorganism nucleic acid sequence comprises identifying the primer set for the microorganism nucleic acid sequence associated with the inflammatory heart disease condition based upon a primer selection model.
3. The method of claim 1, wherein determining the microorganism nucleic acid sequence, comprises analyzing any one or more of: fungi, bacteria, archaea, virus, phages, plasmids, synthetic microorganism, and artificial genetic containing structures.
4. The method of claim 1, wherein determining the microorganism nucleic acid sequence comprises generating at least one of metagenomic and metatranscriptomic libraries with experimental methods by at least one of: a) direct processing of microorganism nucleic acid material and b) processing of fragmented nucleic acids, and performing metagenomics and metatranscriptomics analyses to identify genetic targets associated with the inflammatory heart disease condition.
5. The method of claim 2, wherein determining the microorganism nucleic acid sequence comprises performing amplification methods, comprising singleplex and multiplex amplifications, using material directly from microorganism nucleic acids and using primer types compatible with genetic targets associated with the inflammatory heart disease condition.
6. The method of claim 1, wherein generating the characterization model further comprises performing at least one of: assessment of monosodium urate crystals in sample material and a blood test for at least one of the population of subjects.
7. The method of claim 1, wherein determining the microorganism nucleic acid sequence comprises performing, at a library preparation subsystem, multiplex amplification of sample nucleic acid material using the primer set.
8. The method of claim 1, wherein generating the characterization model comprises analyzing a set of features from the microbiome feature dataset with a statistical analysis, wherein the set of features includes features associated with one or more of: presence of microbiome features, absence of microbiome features, a relative abundance of different taxonomic groups represented in the microbiome feature dataset, a ratio between at least two features comprising taxonomic groups and functional features, interactions between different taxonomic groups represented in the microbiome feature dataset, and phylogenetic distance between taxonomic groups represented in the microbiome feature dataset.
9. The method of claim 8, wherein generating the characterization model comprises analyzing the set of features extracted from the microbiome feature dataset with a prediction analysis associated with at least one of: multi hypothesis testing, random forest testing, and principal component analysis.
10. The method of claim 1, wherein generating the characterization model of the inflammatory heart disease condition comprises evaluating features of the microbiome feature dataset associated with a set of taxonomic features associated with Streptococcaceae (family).
11. The method of claim 10, wherein generating the characterization model of the inflammatory heart disease condition comprises evaluating features of the microbiome feature dataset associated with the set of taxonomic features associated with Streptococcus (genus).
12. The method of claim 11, wherein the set of taxonomic features further comprises features associated with at least one of: Streptococcus thermophilus (species), and Streptococcus pseudopneumoniae (species).
13. The method of claim 1, wherein generating the characterization model of the inflammatory heart disease condition comprises evaluating features of the microbiome feature dataset associated with a set of taxonomic features associated with Sutterella (genus).
14. The method of claim 1, wherein generating the characterization model of the inflammatory heart disease condition comprises evaluating features of the microbiome feature dataset associated with a set of functional features comprising at least one of: clusters of orthologous groups of proteins features, genomic functional features from Kyoto Encyclopedia of Genes and Genomes (KEGG), chemical functional features, and systemic functional features.
15. The method of claim 1, wherein amplifying the nucleic acid material comprises amplifying with at least one of: a) bridge amplification substrates of a next generation sequencing platform and b) moiety-bound particles.
16. The method of claim 1, wherein providing the therapy comprises providing a consumable to the subject, the consumable affecting a microorganism component that selectively supports modulation of microbiome function in the subject, associated with improvement of the inflammatory heart disease condition, based on the therapy model.
17. A method for at least one of diagnosing and treating an inflammatory heart disease condition of a subject, the method comprising:
receiving a sample from the subject;
determining nucleic acid sequences of a microorganism component of the sample based on amplifying nucleic acid material of the sample with a primer set;
generating a microbiome feature dataset for the subject based upon the nucleic acid sequences of the microorganism component;
generating a characterization of the inflammatory heart disease condition in the subject upon processing the microbiome feature dataset with a characterization model derived from a population of subjects; and
providing a therapy to the subject with the inflammatory heart disease condition based upon processing the characterization and a therapy model.
18. The method of claim 17, wherein generating the characterization comprises evaluating features of the microbiome feature dataset associated with Streptococcus (genus).
19. The method of claim 17, wherein generating the characterization comprises evaluating features of the microbiome feature dataset associated with Sutterella (genus).
20. The method of claim 17, wherein generating the characterization comprises evaluating features of the microbiome feature dataset associated with a set of microbiome functions.
21. The method of claim 17, wherein providing the therapy comprises providing a consumable to the subject, the consumable affecting a microorganism composition that selectively supports modulation of microbiome function in the subject, associated with improvement of the inflammatory heart disease condition, based on the therapy model.
22. The method of claim 17, wherein providing the therapy comprises providing an anti-inflammatory therapy to the subject.
23. The method of claim 17, wherein providing the therapy further comprises providing a dietary and exercise regimen to the subject.