Method and system for microbiome-derived diagnostics
A method for diagnosing and treating an immune microbial dysfunction in a subject, the method comprising: receiving an aggregate set of biological 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; generating a characterization of the immune microbial dysfunction based upon features extracted from at least one of the microbiome composition dataset and the microbiome functional diversity dataset, wherein the characterization is diagnostic of at least one of Crohn's disease, inflammatory bowel disease (IBD), irritable bowel syndrome (IBS), ulcerative colitis, and celiac disease; based upon the characterization, generating a therapy model configured to correct the immune microbial dysfunction; and at an output device associated with the subject, promoting a therapy to the subject based upon the characterization and the therapy model.
1. A method for diagnosing and treating an immune microbial dysfunction, the method comprising:
providing sampling kits to a population of subjects at remote locations, each sampling kit including a sample container having a pre-process reagent component;
receiving an aggregate set of samples from the sampling kits of the population of subjects;
with amplification substrates of a next generation sequencing platform of a sample processing system, generating sequence datasets upon sequencing nucleic acid content of microorganism portions of the aggregate set of samples;
generating a microbiome feature dataset for the population of subjects based upon the sequence datasets for the population of subjects;
generating a characterization model of the immune microbial dysfunction from features extracted from the microbiome feature dataset and a supplementary dataset informative of characteristics associated with the immune microbial dysfunction;
characterizing a subject with the immune microbial dysfunction upon processing a sample from the subject according to the characterization model; and
at an output device associated with the subject, providing a therapy to the subject with the immune microbial dysfunction.
2. The method of claim 1 , wherein generating sequence datasets from the population of subjects further comprises: identifying primers for nucleic acid sequences associated with the immune microbial dysfunction, fragmenting nucleic acid material of the aggregate set of samples, amplifying the fragmented nucleic acid material using the identified primers, and determining alignments to reference sequences associated with the immune microbial dysfunction.
3. The method of claim 1 , wherein the amplification substrates comprise at least one of bridge amplification substrates of the next generation sequencing platform and moiety-bound particles.
4. The method of claim 1 , wherein generating the characterization model comprises performing a statistical analysis to assess features of the microbiome feature dataset having varying degrees of abundance in a first subset of the population of subjects exhibiting the immune microbial dysfunction and a second subset of the population of subjects not exhibiting the immune microbial dysfunction.
5. The method of claim 1 , wherein the microbiome feature dataset comprises at least one of a microbiome composition feature and a microbiome functional feature.
6. The method of claim 1 , wherein generating the characterization model comprises:
extracting candidate features associated with a set of functional aspects of microbiome components of the microbiome feature dataset; and
characterizing the immune microbial dysfunction in association with a subset of the set of functional aspects, the subset derived from at least one of clusters of orthologous groups of proteins features, genomic functional features from the Kyoto Encyclopedia of Genes and Genomes (KEGG), chemical functional features, and systemic functional features.
7. The method of claim 1 , wherein generating the characterization model of the immune microbial dysfunction comprises generating a characterization that is diagnostic of at least one of Crohn's disease, irritable bowel syndrome (IBS), inflammatory bowel disease (IBD), ulcerative colitis, and celiac disease.
8. The method of claim 1 , wherein providing the therapy comprises providing instructions to the subject regarding setup of a user account within a social networking system configured to provide microbiome-derived insights to the subject, and transmitting health information pertaining to the immune microbial dysfunction to the subject.
9. The method of claim 1 , wherein providing the therapy comprises providing a consumable to the subject, the consumable affecting a microorganism component that selectively modulates microbiome function of the subject, in association with correction of the immune microbial dysfunction.
10. A method for diagnosing and treating an immune microbial dysfunction in a subject, the method comprising:
providing a sampling kit to the subject at a remote location, the sampling kit including a sample container having a pre-process reagent component and configured to receive a sample from a collection site of the subject;
receiving the sample from the subject;
with an amplification substrate of a next generation sequencing platform of a sample processing system, generating a microbiome feature dataset upon sequencing nucleic acid content of a microorganism portion of the sample;
generating a characterization of the subject upon processing the microbiome feature dataset with a characterization model derived from a population of subjects having the immune microbial dysfunction;
processing the characterization with a therapy model that determines a therapy for correcting the immune microbial dysfunction; and
at an output device associated with the subject, providing the therapy to the subject with the immune microbial dysfunction.
11. The method of claim 10 , wherein generating the microbiome feature dataset further includes: identifying primers for nucleic acid sequences associated with the immune microbial dysfunction, fragmenting nucleic acid material of the sample, and amplifying the fragmented nucleic acid material using the identified primers.
12. The method of claim 10 , wherein the amplification substrate comprises at least one of a bridge amplification substrate of the next generation sequencing platform and particles coupled to functional moieties.
13. The method of claim 10 , wherein generating the characterization of the subject comprises performing a diagnostic test of at least one of Crohn's disease, irritable bowel syndrome (IBS), inflammatory bowel disease (IBD), ulcerative colitis, and celiac disease.
14. The method of claim 13 , wherein performing the diagnostic test of Crohn's disease comprises performing a characterization operation with the microbiome feature dataset of the subject and features derived from at least one of 1) a set of taxa including: Clostridium (genus), Flavonifractor (genus), Prevotella (genus), Clostridiaceae (family), Prevotellaceae (family), Oscillospiraceae (family), Gammaproteobacteria (class), and Proteobacteria (phylum) and 2) a set of functions associated with: a clusters of orthologous groups (COG) D code, a COG I code, and a COG J code.
15. The method of claim 13 , wherein performing the diagnostic test of IBS comprises performing a characterization operation with the microbiome feature dataset of the subject and features derived from a set of taxa including: Flavonifractor (genus), Odoribacter (genus), Blautia (genus), and Finegoldia (genus).
16. The method of claim 13 , wherein performing the diagnostic test of IBD comprises performing a characterization operation with the microbiome feature dataset of the subject and features derived from at least one of: i) a set of taxa including: Clostridium (genus), Ruminococcus (genus), Clostridiaceae (family), Veillonellaceae (family), Selenomonadales (order), Gammaproteobacteria (class), Negativicutes (class), and Proteobacteria (phylum), and 2) a set of functions associated with at least one of a Kyoto Encyclopedia of Genes and Genomes (KEGG) K13015 code, a KEGG K07094 code, a KEGG K00318 code, and a KEGG K07482 code.
17. The method of claim 13 , wherein performing the diagnostic test of Ulcerative Colitis comprises performing a characterization operation with the microbiome feature dataset of the subject and features derived from a set of taxa including at least one of: Clostridium (genus), Lachnospira (genus), Blautia (genus), Dialister (genus), Ruminococcus (genus), Clostridiaceae (family), Peptostreptococcaceae (family), Veillonellaceae (family), Erysipelotrichaceae (family), Christensenellaceae (family), Erysipelotrichales (order), Gammaproteobacteria (class), and Erysipelotrichia (class).
18. The method of claim 13 , wherein performing the diagnostic test of Celiac Disease comprises performing a characterization operation with the microbiome feature dataset of the subject and features derived from a set of taxa including: Clostridium (genus), Oscillibacter (genus), Sutterella (genus), Clostridiaceae (family), Peptostreptococcaceae (family), Peptococcaceae (family), Oscillospiraceae (family), and Proteobacteria (phylum).
19. The method of claim 10 , wherein providing the therapy comprises providing instructions to the subject regarding setup of a user account within a social networking system configured to provide microbiome-derived insights to the subject, and transmitting diagnostic information and behavioral therapeutic techniques, associated with correcting the immune microbial dysfunction, to the subject.
20. The method of claim 10 , wherein providing the therapy comprises providing a consumable to the subject, the consumable affecting a microorganism component that selectively supports a population size adjustment of a desired taxon associated with correction of the immune microbial dysfunction, based on the therapy model.