Method and system for characterizing mouth-associated conditions

Patent metadata

Field	Value
Publication number	US-10246753-B2
Application number	US-201715452529-A
Country	US
Kind code	B2
Filing date	Mar 7, 2017
Priority date	Apr 13, 2015
Publication date	Apr 2, 2019
Grant date	Apr 2, 2019

Abstract

Embodiments of a system and method for characterizing a mouth-associated condition in relation to a user can include one or more of: a handling network operable to collect containers including material from a set of users, the handling network including 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 the microorganism sequences, collect supplementary data associated with the mouth-associated 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 mouth-associated condition; and/or a therapy system operable to promote a treatment to the user based on characterizing the user with the characterization model in relation to the mouth-associated condition.

First claim

We claim:

1. A system for evaluating a mouth-associated condition in relation to a user, the system comprising:
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 mouth-associated 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 mouth-associated condition,
collect supplementary data associated with the mouth-associated 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 mouth-associated condition; and

a treatment system operable to provide a treatment to the user based on characterizing the user with the characterization model in relation to the mouth-associated condition.

2. The system of claim 1 , wherein the microbiome characterization system is further operable to:
extract microbiome composition features from the microbiome composition data based on a first mouth-associated feature-selection rule; and
extract microbiome functional diversity features from the microbiome functional diversity data based on a second mouth-associated feature-selection rule, wherein the features comprise the microbiome composition features and the microbiome functional diversity features.

3. The system of claim 2 , wherein the first and the second mouth-associated feature-selection rules improve the microbiome characterization system by facilitating decreased processing time to transform the supplementary data and the features into the characterization model.

4. 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.

5. The system of claim 1 , wherein the features comprise Kyoto Encyclopedia of Genes and Genomes (KEGG) functional features associated with at least one of: sulfur relay system, restriction enzyme, energy metabolism, immune system disease, fatty acid biosynthesis, carbon fixation pathways in prokaryotes, selenocompound metabolism, protein kinases, energy metabolism, glycerophospholipid metabolism, inorganic ion transport and metabolism, amino acid related enzymes, and carbon fixation in photosynthetic organisms.

6. The system of claim 5 , wherein the features associated with microbiome composition, comprise features derived from at least one of: relative abundance monotonic transformations and non-monotonic transformations.

7. The system of claim 6 , wherein transformation of features associated with microbiome composition comprise at least one of: normalizations, features vectors derived from latent variables analyses being linear or not-linear alternatives, linear or non-linear regression, kernel methods, features embedding methods, machine learning and/or statistical inference methods.

8. The system of claim 5 , wherein the features comprise a microbiome composition feature associated with a relative abundance of at least of: Neisseria elongata and Bergeyella sp. AF14.

9. The system of claim 1 , further comprising an interface operable to improve display of mouth-associated condition information derived from the characterization model, wherein the mouth-associated condition information comprises a microbiome composition for the user relative to a user group sharing a demographic characteristic, and wherein the microbiome composition comprises taxonomic groups comprising at least one of: Spirochaetes , Firmicutes, Proteobacteria, Actinobacteria, Fusobacteria, Bacteroidetes, TM7, Chloroflexi, Tenericutes, Elusimicrobia, Synergistetes, Porphyromonas gingivalis, Tannerella forsythia, Treponema detnicola, Streptococcus, Rothia, Actinomyces, Haemophilus, Lautropia, Leptotrichia, Prevotella, Porphyromonas, Selenomonas, Peptococcus, Catonella, Eubacterium, Oribacterium (Genus), Bacteroidia (Class), Flavobacteriia (Class), Erysipelotrichia (Class), Epsilonproteobacteria (Class), Clostridia (Class), Coriobacteriaceae (Family), Flavobacteriaceae (Family), Porphyromonadaceae (Family), Erysipelotrichaceae (Family), Peptostreptococcaceae (Family), Lachnospiraceae (Family), Campylobacteraceae (Family), Fusobacteriaceae (Family), Streptococcaceae (Family), Alloprevotella (Genus), Capnocytophaga (Genus), Porphyromonas (Genus), Stomatobaculum (Genus), Kingella (Genus), Campylobacter (Genus), Aggregatibacter (Genus), Bergeyella (Genus), Lachnoanaerobaculum (Genus), Fusobacterium (Genus), Peptostreptococcus (Genus), Coriobacteriales (Order), Bacteroidales (Order), Flavobacteriales (Order), Erysipelotrichales (Order), Campylobacterales (Order), Clostridiales (Order), Lactobacillales (Order), Bacteroidetes (Phylum), Candidatus Saccharibacteria (Phylum), Neisseria elongata (Species), Bergeyella sp. AF14 (Species), Capnocytophaga sputigena (Species), Peptostreptococcus stomatis (Species), Kingella oralis (Species), Prevotella nigrescens (Species), Porphyromonas catoniae (Species), Negativicutes (Class), Clostridiales Family XI, and Incertae Sedis (Family).

10. The system of claim 9 , wherein the mouth-associated condition information comprises a risk of infection for the user for at least one of: a gingivitis-associated condition and a halitosis-associated condition, and wherein the treatment is operable to reduce the risk of infection.

11. A method for characterizing a mouth-associated condition in relation to a first user, the method comprising:
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 mouth-associated 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 mouth-associated condition;

receiving a supplementary dataset informative of the mouth-associated condition for the set of users;
obtaining a set of mouth-associated feature-selection rules correlating the mouth-associated 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 mouth-associated feature-selection rules;
applying the feature set with the supplementary dataset to generate a characterization model for the mouth-associated condition;
generating a first characterization of the first user in relation to the mouth-associated condition using the characterization model; and
providing a therapy to the first user based on the first characterization.

12. The method of claim 11 , wherein the characterization model is a gingivitis-associated characterization model, the method further comprising:
generating a second fea

Assignees

• Ubiome Inc

Inventors

• Apte Zachary
• Valdivia Catalina
• Almonacid Daniel
• Richman Jessica

Classifications

• C12Q2600/112

  Disease subtyping, staging or classification · CPC title

• G16B50/00

  ICT programming tools or database systems specially adapted for bioinformatics · CPC title

• C12Q2600/16

  Primer sets for multiplex assays · CPC title

• G16H50/20

  for computer-aided diagnosis, e.g. based on medical expert systems · CPC title

• G16C20/60

  In silico combinatorial chemistry · CPC title