Method and system for microbiome-derived diagnostics and therapeutics for oral health

A method for determining a classification of the presence or absence of a microbiome indicative of an oral health issue and/or determine a course of treatment for an individual human having a microbiome indicative of an oral health issue, the method comprising performing, by a computer system:

• receiving sequence reads of bacterial DNA obtained from analyzing a test sample from the individual human;
• mapping the sequence reads to a bacterial sequence database to obtain a plurality of mapped sequence reads, the bacterial sequence database including a plurality of reference sequences of a plurality of bacteria;
• assigning the mapped sequence reads to sequence groups based on the mapping to obtain assigned sequence reads assigned to at least one sequence group, wherein a sequence group includes one or more of the plurality of reference sequences;
• determining a total number of assigned sequence reads;
• for each sequence group of a disease signature set of one or more sequence groups selected from TABLEs A or B:
• determining a relative abundance value of assigned sequence reads assigned to the sequence group relative to the total number of assigned sequence reads, the relative abundance values forming a test feature vector;
• comparing the test feature vector to calibration feature vectors generated from relative abundance values of calibration samples having a known status of oral health;
• and
• determining the classification of the presence or absence of the microbiome indicative of an oral health issue and/or determining the course of treatment for the individual human having the microbiome indicative of an oral health issue based on the comparing.

A method for at least one of characterizing, diagnosing, and treating an oral health issue in at least a subject, the method comprising:

• at a sample handling network, receiving an aggregate set of samples from a population of subjects;
• at a computing system in communication with the sample handling network, generating a microbiome composition dataset and a microbiome functional diversity dataset for the population of subjects upon processing nucleic acid content of each of the aggregate set of samples with a fragmentation operation, a multiplexed amplification operation using a set of primers, a sequencing analysis operation, and an alignment operation;
• at the computing system, receiving a supplementary dataset, associated with at least a subset of the population of subjects, wherein the supplementary dataset is informative of characteristics associated with the oral health issue;
• at the computing system, transforming the supplementary dataset and features extracted from at least one of the microbiome composition dataset and the microbiome functional diversity dataset into a characterization model of the oral health issue;
• based upon the characterization model, generating a therapy model configured to correct the oral health issue;
• and
• at an output device associated with the subject and in communication with the computing system, promoting a therapy to the subject with the oral health issue, upon processing a sample from the subject with the characterization model, in accordance with the therapy model.

A method for characterizing an oral health issue, 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 at least one of the microbiome composition dataset and the microbiome functional diversity dataset into a characterization model of the oral health issue, wherein the characterization model is diagnostic of the oral health issue producing observed changes in dental and/or gingival health;
• and
• based upon the characterization model, generating a therapy model configured to improve a state of the oral health issue.