Application US20180122515

METHOD AND SYSTEM FOR MICROBIOME-DERIVED CHARACTERIZATION, DIAGNOSTICS AND THERAPEUTICS FOR CUTANEOUS CONDITIONS
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US20180122515

1. A method for characterizing a dermatomyositis condition, the method comprising: (8) (6)

receiving an aggregate set of samples from a population of subjects;

for the aggregate set of samples: determining microorganism nucleic acid sequences, comprising: identifying a set of primers for nucleic acid sequences associated with the dermatomyositis condition,

amplifying nucleic acid material from the aggregate set of sample samples based on the set of primers; and

determining alignments of the microorganism nucleic acid sequences to reference sequences associated with the dermatomyositis condition;

generating a microbiome feature dataset for the population of subjects based upon the alignments;

generating a characterization model of the dermatomyositis condition from the microbiome feature dataset;

based upon the characterization model, generating a therapy model that determines a therapy for correcting the dermatomyositis condition; and

at an output device associated with the subject, providing the therapy to a subject diagnosed with the dermatomyositis condition based upon the characterization model and the therapy model.

2. The method of claim 1, wherein determining microorganism nucleic acid sequences comprises identifying the set of primers for the nucleic acid sequence associated with the dermatomyositis condition based upon a primer selection model. (0)

3. The method of claim 1, wherein determining the microorganism nucleic acid sequences, comprises analyzing any one or more of: fungi, bacteria, archaea, virus, phages, plasmids, synthetic microorganism, and artificial genetic containing structures. (0)

4. The method of claim 1, wherein determining the microorganism nucleic acid sequences 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 dermatomyositis condition. (0)

5. The method of claim 1, wherein generating the characterization model further comprises performing at least one of: a biopsy and an electromyography assessment for at least one of the population of subjects. (0)

6. 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 composition dataset, a ratio between at least two features comprising taxonomic groups and functional features, interactions between different taxonomic groups represented in the microbiome composition dataset, and phylogenetic distance between taxonomic groups represented in the microbiome composition dataset. (0)

7. 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. (1) (0)

9. The method of claim 1, wherein generating the characterization model of the dermatomyositis condition comprises evaluating features of the microbiome feature dataset associated with a set of functional features comprising at least one of: an immune system associated feature; an enzyme families associated feature; a transcription associated feature; a metabolism associated feature; a cell motility associated feature; an environmental adaptation associated feature; a cellular processes and signaling associated feature; a signaling molecules and interaction associated feature; a metabolism of cofactors and vitamins associated feature; a cancers associated feature; a metabolism of terpenoids and polyketides associated feature; a metabolic diseases associated feature; a cell growth and death associated feature; a biosynthesis of other secondary metabolites associated feature; a neurodegenerative diseases feature; and a replication and repair associated feature. (1) (0)

10. The method of claim 9, wherein the set of functional features further comprises at least one of: an immune system diseases associated feature; a genetic information processing associated feature; a membrane transport associated feature; a carbohydrate metabolism associated feature; a nervous system associated feature; a nucleotide metabolism associated feature; an energy metabolism associated feature; a D-alanine metabolism associated feature; a chromosome associated feature; a polyketide sugar unit biosynthesis v feature; a sporulation associated feature; a mismatch repair associated feature; a peptidases associated feature; an inositol phosphate metabolism associated feature; a sulfur relay system associated feature; a bacterial toxins associated feature; a replication, recombination, and repair proteins associated feature; and a biosynthesis of ansamycins associated feature. (2) (0)

13. The method of claim 1, wherein generating the characterization model of the dermatomyositis condition comprises evaluating features of the microbiome feature dataset associated with a set of taxonomic features associated with at least one of: Faecalibacterium (genus), Clostridium (genus), Sarcina (genus), Collinsella (genus), Blautia (genus), Subdoligranulum (genus), Dorea (genus), Propionibacterium (genus), Alistipes (genus), Roseburia (genus), Anaerostipes (genus), Pseudobutyrivibrio (genus), Prevotella (genus), Staphylococcus (genus), Anaerotruncus, (genus), Phascolarctobacterium (genus), Lachnospira (genus), Intestinibacter (genus), Bacteroides (genus), Parabacteroides (genus), Ruminococcaceae (family), Lachnospiraceae (family), Clostridiaceae (family), Coriobacteriaceae (family), Erysipelotrichaceae (family), Erysipelotrichaceae (family), Propionibacteriaceae (family), Rikenellaceae (family), Peptostreptococcaceae (family), Veillonellaceae (family), Prevotellaceae (family), Staphylococcaceae, (family) Desulfovibrionaceae (family), Oscillospiraceae (family), Acidaminococcaceae (family), Sutterellaceae (family), Porphyromonadaceae (family), Bacteroidaceae (family), Bacteroidia (class), Clostridia (class), Erysipelotrichia (class), Actinobacteria (class), Negativicutes (class), Deltaproteobacteria (class), Bacilli (class), Bacteroidetes (phylum), Actinobacteria (phylum), Proteobacteria (phylum), and Firmicutes (phylum). (1) (0)

15. A method for diagnosing and treating a dermatomyositis condition of a subject, the method comprising: (6) (5)

receiving a sample from the subject;

determining nucleic acid sequences of a microorganism component of the sample upon amplifying nucleic acid material of the sample with a primer;

generating a microbiome feature dataset for the subject based upon the nucleic acid sequences of the microorganism component;

generating a characterization of the dermatomyositis condition in the subject upon processing the microbiome feature dataset with a characterization model derived from a population of subjects; and

at an output device associated with the subject, providing a therapy to the subject with the dermatomyositis condition upon processing the characterization with a therapy model.

16. The method of claim 15, wherein determining nucleic acid sequences further comprises identifying the primer for the nucleic acid sequence with a primer selection model. (0)

17. The method of claim 15, wherein generating the characterization comprises evaluating features of the microbiome feature dataset associated with at least one of: Faecalibacterium (genus), Clostridium (genus), Sarcina (genus), Collinsella (genus), Blautia (genus), Subdoligranulum (genus), Dorea (genus), Propionibacterium (genus), Alistipes (genus), Roseburia (genus), Anaerostipes (genus), Pseudobutyrivibrio (genus), Prevotella (genus), Staphylococcus (genus), Anaerotruncus, (genus), Phascolarctobacterium (genus), Lachnospira (genus), Intestinibacter (genus), Bacteroides (genus), Parabacteroides (genus), Ruminococcaceae (family), Lachnospiraceae (family), Clostridiaceae (family), Coriobacteriaceae (family), Erysipelotrichaceae (family), Erysipelotrichaceae (family), Propionibacteriaceae (family), Rikenellaceae (family), Peptostreptococcaceae (family), Veillonellaceae (family), Prevotellaceae (family), Staphylococcaceae, (family) Desulfovibrionaceae (family), Oscillospiraceae (family), Acidaminococcaceae (family), Sutterellaceae (family), Porphyromonadaceae (family), Bacteroidaceae (family), Bacteroidia (class), Clostridia (class), Erysipelotrichia (class), Actinobacteria (class), Negativicutes (class), Deltaproteobacteria (class), Bacilli (class), Bacteroidetes (phylum), Actinobacteria (phylum), Proteobacteria (phylum), and Firmicutes (phylum). (0)

18. The method of claim 15, wherein generating the characterization comprises evaluating features of the microbiome feature dataset associated with at least one of: immune system associated functionality; enzyme families associated functionality; transcription associated functionality; metabolism associated functionality; cell motility associated functionality; environmental adaptation associated functionality; cellular processes and signaling associated functionality; signaling molecules and interaction associated functionality; metabolism of cofactors and vitamins associated functionality; cancers associated functionality; metabolism of terpenoids and polyketides associated functionality; metabolic diseases associated functionality; cell growth and death associated functionality; biosynthesis of other secondary metabolites associated functionality; neurodegenerative diseases functionality; and a replication and repair associated functionality. (0)

19. The method of claim 15, 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 correction of the dermatomyositis condition, based on the therapy model. (0)

20. The method of claim 15, wherein providing the therapy further comprises at least one of the following procedures: a light-based therapy, a topical, and a dietary therapy. (0)

21. The method of claim 15, wherein providing the therapy further comprises providing at least one of the following prebiotics: 1,4-dihydroxy-2-naphthoic acid (DHNA), Inulin, trans-Galactooligosaccharides (GOS), Lactulose, Mannan oligosaccharides (MOS), Fructooligosaccharides (FOS), Neoagaro-oligosaccharides (NAOS), Pyrodextrins, Xylo-oligosaccharides (XOS), Isomalto-oligosaccharides (IMOS), Amylose-resistant starch, Soybean oligosaccharide (SBOS), Lactitol, Lactosucrose (LS), Isomaltulose (including Palatinose), Arabinoxylooligosaccharides (AXOS), Raffinose oligosaccharides (RFO), Arabinoxylans (AX), and Polyphenols to the subject. (0)

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Application US20180122515

METHOD AND SYSTEM FOR MICROBIOME-DERIVED CHARACTERIZATION, DIAGNOSTICS AND THERAPEUTICS FOR CUTANEOUS CONDITIONS

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