Patent US10169541

Method and systems for characterizing skin related conditions
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US10169541

1. A system for evaluating a skin-related condition in relation to a user, the system comprising: (4) (3)

a handling network operable to collect containers comprising material from a set of users, the handling network comprising: a library preparation system operable to fragment and perform multiplex amplification on the material using a primer compatible with a genetic target associated with the skin-related condition;

a sequencing system operable to determine microorganism sequences from sequencing the material;

a microbiome characterization system operable to: determine microbiome composition data and microbiome functional diversity data based on an alignment between the microorganism sequences and reference sequences associated with the skin-related condition,

collect supplementary data associated with the skin-related condition for the set of users, and

transform the supplementary data and features extracted from the microbiome composition data and the microbiome functional diversity data into a characterization model for the skin-related condition; and

a treatment system operable to provide a treatment to the user for the skin-related condition based on characterizing the user with the characterization model in relation to the skin-related condition.

2. The system of claim 1, wherein the microbiome characterization system is further operable to: (1) (2)

obtain a set of skin-related feature-selection rules correlating the skin-related condition to a subset of microbiome composition features and a subset of microbiome functional diversity features; and

generate the features based on evaluating the microbiome composition data and the microbiome functional diversity data against the set of skin-related feature-selection rules, wherein the set of skin-related feature-selection rules are operable to improve the microbiome characterization system by facilitating decreased processing time to transform the supplementary data and the features into the characterization model.

3. The system of claim 2, wherein the microbiome functional diversity features comprises at least one of: a cluster of orthologous group of proteins feature, a genomic functional feature, a taxonomic feature, a chemical functional feature, and a systemic functional feature. (0)

4. The system of claim 1, wherein the handling network further comprises a library preparation system operable to fragment and perform multiplex amplification on the material using a primer compatible with a genetic target associated with the skin-related condition. (0)

5. The system of claim 1, further comprising an interface operable to improve display of skin-related condition information derived from the characterization model, wherein the skin-related condition information comprises a microbiome composition for the user relative to a user group sharing a demographic characteristic, and wherein the microbiome composition comprises a set of taxa comprising at least one of: Marvinbryantia (genus), Erysipelotrichales (order), Erysipelotrichia (class), Bacteroidetes (phylum), Staphylococcus (genus), Staphylococcaceae (family), Bacillales (order), Actinobacteria (class), Firmicutes (phylum), Actinobacteria (phylum), and Propionibacterium (genus). (1) (0)

7. The system of claim 1, wherein the features comprise at least one of a Kyoto Encyclopedia of Genes and Genomes (KEGG) functional feature and a Clusters of Orthologous Groups (COG) functional feature, and wherein the features comprise transformation microbiome features derived from at least one of: a relative abundance monotonic transformation and a non-monotonic transformation. (2) (0)

10. A method for characterizing a skin-related condition in relation to a first user, the method comprising: (9) (1)

generating a microbiome composition dataset and a microbiome functional diversity dataset based on microorganism sequences derived from biological samples from a set of users, wherein generating the microbiome composition dataset and the microbiome functional diversity dataset comprises: identifying primers for nucleic acid sequences associated with the skin-related condition,

fragmenting nucleic acid material,

amplifying the fragmented nucleic acid material using the identified primers, and

determining an alignment of the microorganism sequences to reference sequences associated with the skin-related condition;

receiving a supplementary dataset informative of the skin-related condition for the set of users;

obtaining a set of skin-related feature-selection rules correlating the skin-related condition to a subset of microbiome composition features and a subset of microbiome functional diversity features;

generating a feature set based on evaluating the microbiome composition dataset and the microbiome functional diversity dataset against the set of skin-related feature-selection rules;

applying the feature set with the supplementary dataset to generate a characterization model for the skin-related condition;

generating a first characterization of the first user in relation to the skin-related condition using the characterization model; and

providing a therapy to the first user for the skin-related condition based on the first characterization.

11. The method of claim 10, wherein the characterization model is an eczema-related characterization model, the method further comprising: (2) (3)

generating a second feature set based on the microbiome composition dataset and the microbiome functional diversity dataset;

applying the second feature set to generate a scalp-related characterization model; and

generating a second characterization of the first user in relation to a scalp-related condition using the scalp-related characterization model.

12. The method of claim 11, further comprising: (0) (2)

14. The method of claim 11, further comprising: (2) (3)

generating a user microbiome composition feature for the first user based on a first skin-related feature-selection rule of the set of skin-related feature-selection rules; and

generating a user microbiome functional feature for the first user based on a second skin-related feature-selection rule of the set of skin-related feature-selection rules, wherein the first and the second skin-related feature-selection rules improve the characterization model, and

wherein generating the first characterization comprises generating the first characterization based on the user microbiome composition feature, the user microbiome functional feature, and characterization model.

15. The method of claim 14, (0) (3)

16. The method of claim 14, further comprising: (0) (2)

13. The method of claim 10, wherein promoting the therapy comprises automatically initiating a signal that controls a treatment system to promote the therapy based on the first characterization of the first user in relation to the skin-related condition. (0)

17. The method of claim 10, further comprising: (1) (3)

after promoting the therapy, receiving a post-therapy biological sample from the first user;

generating a post-therapy characterization of the first user in relation to the skin-related condition based on the characterization model and the post-therapy biological sample; and

characterizing modulation of the skin-related condition in relation to the first user based on the post-therapy characterization and the characterization.

18. The method of claim 17, (1) (3)

wherein the therapy is operable to facilitate modification of a microbiome composition and a microbiome functional diversity of the first user, and the method further comprising:

determining post-therapy user microbiome composition features and post-therapy microbiome functional diversity features based on the post-therapy biological sample and the set of skin-related feature-selection rules, wherein the post-therapy user microbiome composition features are associated with the subset of microbiome composition features, wherein the post-therapy microbiome functional diversity features are associated with the subset of microbiome functional diversity features, and

wherein generating the post-therapy characterization comprises generating the post-therapy characterization based on the post-therapy user microbiome composition features, the post-therapy microbiome functional diversity features, and the characterization model.

19. The method of claim 18, wherein the therapy is selected based on a therapy model, the method further comprising: (0) (3)

20. The method of claim 10, further comprising: (0) (4)

identifying a primer compatible with a genetic target associated with the skin-related condition, wherein identifying a primer compatible with a genetic target associated with the skin-related condition comprises identifying the primer based on the set of skin-related feature-selection rules;

amplifying nucleic acid material using the identified primer and a user biological sample from the first user; and

sequencing the nucleic acid material to determine user microorganism sequences,

wherein generating the first characterization for the first user comprises generating the first characterization based on the characterization model and the user microorganism sequences.

21. The method of claim 10, wherein the skin-related condition comprises Eczema, and wherein the subset of microbiome composition features comprises a composition feature associated with a set of taxa comprising at least one of: Streptococcaceae, Streptococcus, Lactobacillales, and Veillonella. (2) (0)

22. The method of claim 21, further comprising: (0) (3)

23. The method of claim 21, wherein the composition feature for a single microorganism is associated with at least one of the following metrics: relative abundance, differential relative abundance, presence, and absence. (0)

24. The method of claim 10, wherein the skin-related condition comprises a scalp-related condition including dandruff, and wherein the subset of microbiome composition features comprises a variety of features associated with a set of taxa comprising and including at least one of: Propionibacterium sp. MSP09A (species), Bacteroides vulgatus (species, Streptococcus sp. BS35a (species), Staphylococcus sp. C9I2 (species), Phascolarctobacterium sp. 377 (species), Faecalibacterium prausnitzii (species), Alistipes putredinis (species), Alistipes sp. EBA6-25cl2 (species), Alistipes sp. RMA 9912 (species) Anaerostipes sp. 5_1_63FA (species), Bacteroides acidifaciens (species), Bacteroides caccae (species), Bacteroides fragilis (species), Bacteroides plebeius (species), Bacteroides sp. AR20 (species), Bacteroides sp. AR29 (species), Bacteroides sp. D22 (species), Bacteroides sp. DJF (species), Bacteroides sp. SLC1-38 (species), Bacteroides sp. XB12B (species), Bacteroides vulgatus (species), Blautia faecis (species), Blautia luti (species), Blautia sp. YHC-4 (species), Blautia stercoris (species), Blautia wexlerae (species), Collinsella aerofaciens (species), Corynebacterium sp. (species), Corynebacterium spheniscorum (species), Corynebacterium ulcerans (species), Dorea formicigenerans (species), Dorea longicatena (species), Lachnospira pectinoschiza (species), Odoribacter splanchnicus (species), Parabacteroides distasonis (species), Parabacteroides merdae (species), Phascolarctobacterium faecium (species), Propionibacterium acnes (species), Propionibacterium granulosum (species), Propionibacterium sp. MSP09A (species), Roseburia intestinalis (species), Roseburia inulinivorans (species), Roseburia sp. 11SE39 (species), Staphylococcus sp. C9I2 (species), Staphylococcus sp. WB18-16 (species), Streptococcus sp. BS35a (species), Streptococcus sp. oral taxon G59 (species), Streptococcus thermophilus (species), Subdoligranulum variabile (species), Sutterella stercoricanis (species), Sutterella wadsworthensis Propionibacterium (genus), Staphylococcus (genus), Roseburia (genus), Blautia (genus), Bacteroides (genus), Pseudobutyrivibrio (genus), Alistipes (genus), Faecalibacterium (genus), Collinsella (genus), Clostridium (genus), Anaerostipes (genus), Dorea (genus), Subdoligranulum (genus), Sarcina (genus), Lachnospira (genus), Anaerotruncus (genus), Parabacteroides (genus), Flavonifractor (genus), Intestinibacter (genus), Erysipelatoclostridium (genus), Phascolarctobacterium (genus), Streptococcus (genus), Odoribacter (genus), Sutterella (genus), Bifidobacterium (genus), Corynebacterium (genus), Bilophila (genus), Terrisporobacter (genus), Dialister (genus), Prevotella (genus), Marvinbryantia (genus), Propionibacteriaceae (family), Staphylococcaceae (family), Porphyromonadaceae (family), Lachnospiraceae (family), Peptostreptococcaceae (family), Coriobacteriaceae (family), Clostridiaceae (family), Ruminococcaceae (family), Bacteroidaceae (family), Erysipelotrichaceae (family), Rikenellaceae (family), Prevotellaceae (family), Sutterellaceae (family), Flavobacteriaceae (family), Streptococcaceae (family), Veillonellaceae (family), Acidaminococcaceae (family), Desulfovibrionaceae (family), Oscillospiraceae (family), Bifidobacteriaceae (family), Corynebacteriaceae (family), Pasteurellaceae (family), Bacteroidales (order), Actinomycetales (order), Selenomonadales (order), Bacillales (order), Coriobacteriales (order), Clostridiales (order), Erysipelotrichales (order), Lactobacillales (order), Burkholderiales (order), Flavobacteriales (order), Desulfovibrionales (order), Bifidobacteriales (order), Pasteurellales (order), Actinobacteria (class), Bacteroidia (class), Negativicutes (class), Betaproteobacteria (class), Clostridia (class), Erysipelotrichia (class), Flavobacteriia (class), Bacilli (class), Deltaproteobacteria (class), Gammaproteobacteria (class), Bacteroidetes (phylum), Actinobacteria (phylum), Proteobacteria (phylum), Firmicutes (phylum), and Verrucomicrobia (phylum). (1) (0)

25. The method of claim 24, wherein the subset of microbiome functional diversity features comprises a Kyoto Encyclopedia of Genes and Genomes (KEGG) functional features associated with at least one of: a glycan biosynthesis and metabolism KEGG L2 derived feature, an environmental adaptation KEGG L2 derived feature, a cancers KEGG L2 derived feature, an immune system diseases KEGG L2 derived feature, a transcription KEGG L2 derived feature, a signaling molecules and interaction KEGG L2 derived feature, a membrane transport KEGG L2 derived feature, a cell motility KEGG L2 derived feature, a cellular processes and signaling KEGG L2 derived feature, a metabolism of cofactors and vitamins KEGG L2 derived feature, a metabolism KEGG L2 derived feature, a neurodegenerative diseases KEGG L2 derived feature, a metabolic diseases KEGG L2 derived feature, an enzyme families KEGG L2 derived feature, a cell growth and death KEGG L2 derived feature, a carbohydrate metabolism KEGG L2 derived feature, a transport and catabolism KEGG L2 derived feature, a genetic information processing KEGG L2 derived feature, a replication and repair KEGG L2 derived feature, an energy metabolism KEGG L2 derived feature, a digestive system KEGG L2 derived feature, an amino acid metabolism KEGG L2 derived feature, a metabolism of other amino acids KEGG L2 derived feature, a biosynthesis of other secondary metabolites KEGG L2 derived feature, a folding, sorting and degradation KEGG L2 derived feature, a lipid metabolism KEGG L2 derived feature, an infectious diseases KEGG L2 derived feature, a nucleotide metabolism KEGG L2 derived feature, a metabolism of terpenoids and polyketides KEGG L2 derived feature, a renal cell carcinoma KEGG L3 derived feature, an ubiquinone and other terpenoid-quinone biosynthesis KEGG L3 derived feature, an amyotrophic lateral sclerosis KEGG L3 derived feature, a lipoic acid metabolism KEGG L3 derived feature, a cyanoamino acid metabolism KEGG L3 derived feature, a glutathione metabolism KEGG L3 derived feature, a toluene degradation KEGG L3 derived feature, a riboflavin metabolism KEGG L3 derived feature, a plant-pathogen interaction KEGG L3 derived feature, a prenyltransferases KEGG L3 derived feature, a biosynthesis of ansamycins KEGG L3 derived feature, an ABC transporters KEGG L3 derived feature, an inositol phosphate metabolism KEGG L3 derived feature, a citrate cycle (TCA cycle) KEGG L3 derived feature, a chromosome KEGG L3 derived feature, a glycolysis/gluconeogenesis KEGG L3 derived feature, a valine, leucine and isoleucine degradation KEGG L3 derived feature, a primary immunodeficiency KEGG L3 derived feature, a DNA replication proteins KEGG L3 derived feature, a cytoskeleton proteins KEGG L3 derived feature, a peroxisome KEGG L3 derived feature, a transcription machinery KEGG L3 derived feature, a protein folding and associated processing KEGG L3 derived feature, a d-alanine metabolism KEGG L3 derived feature, a translation proteins KEGG L3 derived feature, a glycine, serine and threonine metabolism KEGG L3 derived feature, a lipopolysaccharide biosynthesis proteins KEGG L3 derived feature, an energy metabolism KEGG L3 derived feature, a lipid metabolism KEGG L3 derived feature, a peptidases KEGG L3 derived feature, a carbohydrate digestion and absorption KEGG L3 derived feature, a caprolactam degradation KEGG L3 derived feature, a glycerolipid metabolism KEGG L3 derived feature, a carbon fixation in photosynthetic organisms KEGG L3 derived feature, a membrane and intracellular structural molecules KEGG L3 derived feature, a fatty acid biosynthesis KEGG L3 derived feature, a type I diabetes mellitus KEGG L3 derived feature, a phosphotransferase system (pts) KEGG L3 derived feature, a base excision repair KEGG L3 derived feature, a sporulation KEGG L3 derived feature, a transporters KEGG L3 derived feature, a protein kinases KEGG L3 derived feature, a pantothenate and CoA biosynthesis KEGG L3 derived feature, a cell cycle—Caulobacter KEGG L3 derived feature, a butirosin and neomycin biosynthesis KEGG L3 derived feature, a mismatch repair KEGG L3 derived feature, a pores ion channels KEGG L3 derived feature, an oxidative phosphorylation KEGG L3 derived feature, a cell division KEGG L3 derived feature, a replication, recombination and repair proteins KEGG L3 derived feature, a bacterial motility proteins KEGG L3 derived feature, a carbon fixation pathways in prokaryotes KEGG L3 derived feature, a transcription factors KEGG L3 derived feature, a vitamin b6 metabolism KEGG L3 derived feature, a chloroalkane and chloroalkene degradation KEGG L3 derived feature, a peptidoglycan biosynthesis KEGG L3 derived feature, a drug metabolism—other enzymes KEGG L3 derived feature, a proteasome KEGG L3 derived feature, a RNA transport KEGG L3 derived feature, an ascorbate and aldarate metabolism KEGG L3 derived feature, a cysteine and methionine metabolism KEGG L3 derived feature, a galactose metabolism KEGG L3 derived feature, a tetracycline biosynthesis KEGG L3 derived feature, a translation factors KEGG L3 derived feature, a glycerophospholipid metabolism KEGG L3 derived feature, a pentose phosphate pathway KEGG L3 derived feature, a tyrosine metabolism KEGG L3 derived feature, a photosynthesis proteins KEGG L3 derived feature, a Vibrio cholerae pathogenic cycle KEGG L3 derived feature, an amino sugar and nucleotide sugar metabolism KEGG L3 derived feature, a bacterial chemotaxis KEGG L3 derived feature, a tryptophan metabolism KEGG L3 derived feature, a nicotinate and nicotinamide metabolism KEGG L3 derived feature, a histidine metabolism KEGG L3 derived feature, a biotin metabolism KEGG L3 derived feature, a secretion system KEGG L3 derived feature, a cellular antigens KEGG L3 derived feature, a sulfur relay system KEGG L3 derived feature, a taurine and hypotaurine metabolism KEGG L3 derived feature, a photosynthesis KEGG L3 derived feature, a zeatin biosynthesis KEGG L3 derived feature, a methane metabolism KEGG L3 derived feature, a RNA degradation KEGG L3 derived feature, a phosphatidylinositol signaling system KEGG L3 derived feature, a glyoxylate and dicarboxylate metabolism KEGG L3 derived feature, an adipocytokine signaling pathway KEGG L3 derived feature, a starch and sucrose metabolism KEGG L3 derived feature, a chaperones and folding catalysts KEGG L3 derived feature, a vitamin metabolism KEGG L3 derived feature, a pyruvate metabolism KEGG L3 derived feature, a porphyrin and chlorophyll metabolism KEGG L3 derived feature, a geraniol degradation KEGG L3 derived feature, a tuberculosis KEGG L3 derived feature, a tropane, piperidine and pyridine alkaloid biosynthesis KEGG L3 derived feature, a beta-alanine metabolism KEGG L3 derived feature, a PPAR signaling pathway KEGG L3 derived feature, a lysine biosynthesis KEGG L3 derived feature, a protein export KEGG L3 derived feature, an arachidonic acid metabolism KEGG L3 derived feature, a thiamine metabolism KEGG L3 derived feature, a phenylpropanoid biosynthesis KEGG L3 derived feature, a ribosome biogenesis KEGG L3 derived feature, a nucleotide excision repair KEGG L3 derived feature, a synthesis and degradation of ketone bodies KEGG L3 derived feature, a benzoate degradation KEGG L3 derived feature, a sulfur metabolism KEGG L3 derived feature, a metabolism of xenobiotics by cytochrome p450 KEGG L3 derived feature, a penicillin and cephalosporin biosynthesis KEGG L3 derived feature, a drug metabolism—cytochrome p450 KEGG L3 derived feature, a purine metabolism KEGG L3 derived feature, a novobiocin biosynthesis KEGG L3 derived feature, a propanoate metabolism KEGG L3 derived feature, a limonene and pinene degradation KEGG L3 derived feature, an aminobenzoate degradation KEGG L3 derived feature, a Huntington's disease KEGG L3 derived feature, a C5-branched dibasic acid metabolism KEGG L3 derived feature, a folate biosynthesis KEGG L3 derived feature, and a phenylalanine metabolism KEGG L3 derived feature. (0)

26. The method of claim 10, wherein the skin-related condition comprises dry skin, and wherein the subset of microbiome composition features comprises a composition feature associated with a set of taxa including at least one of: Staphylococcus (genus), Staphylococcaceae (family), Bacillales (order), Actinobacteria (class), Firmicutes (phylum), Actinobacteria (phylum), and Propionibacterium (genus). (1) (0)

28. The method of claim 10, wherein the skin-related condition comprises photosensitivity, and wherein the subset of microbiome composition features comprises a composition feature associated with a set of taxa comprising at least one of: Marvinbryantia (genus), Erysipelotrichales (order), Erysipelotrichia (class), and Bacteroidetes (phylum). (1) (0)

30. The method of claim 10, wherein the skin-related condition comprises a pimple-related condition, and wherein the subset of microbiome composition features comprises a composition feature associated with a set of taxa comprising Lactobacillales. (0)

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Patent US10169541

Method and systems for characterizing skin related conditions

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