METHOD AND SYSTEM FOR MICROBIOME ANALYSIS

• US 20150213193A1
• Filed: 01/09/2015
• Published: 07/30/2015
• Est. Priority Date: 01/25/2014
• Status: Active Grant

• Current Assignee: Psomagen, Inc.
• Original Assignee: uBiome, Inc.
• Inventors: Apte, Zachary, Richman, Jessica
• Granted Patent: US 9,663,831 B2
• Time in Patent Office: Days
• US Class Current: 1/1
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 1/6888 for detection or identification of organisms
• CPC Class Codes: C12Q 1/689 for bacteria
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 30/10 Sequence alignment; Homology search
• CPC Class Codes: G16B 30/20 Sequence assembly
• CPC Class Codes: Y02A 90/10 Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation

Abstract

A method and system for analyzing a microbiome of an individual, comprising: providing a sampling kit to the individual at a location remote from the sample processing network, the sampling kit including a sample container having a lysing component and a sample preservation component and configured to receive a sample from a collection site of the individual; receiving the sample container with the sample from the collection site of the individual; generating a microbiome sequence dataset based upon sequencing nucleic acid content of a microorganism portion of the sample; identifying a set of microorganisms represented in the microorganism portion based upon performance of a mapping operation on portions of the microbiome sequence dataset; generating an analysis based upon a set of features related to the microorganism portion; and transmitting information derived from the analysis to the individual.

Claims

1. A method for analyzing a microbiome of an individual, comprising:

from a sample handling network, providing a sampling kit to the individual at a location remote from the sample processing network, 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 individual;

at the sample handling network, receiving the sample container with the sample from the collection site of the individual;

at a sample processing module within the sample handling network, generating a microbiome sequence dataset based upon sequencing nucleic acid content of a microorganism portion of the sample;

at a processing system within the sample handling network, identifying a set of microorganisms represented in the microorganism portion based upon performance of a mapping operation on portions of the microbiome sequence dataset;

at the processing system, generating an analysis based upon a set of features related to the microorganism portion; and

from the processing system, transmitting information derived from the analysis to the individual.

2. The method of claim 1, wherein providing the sampling kit to the individual comprises providing instructions to the individual regarding provision of the sample, providing instructions to the individual regarding pre-processing of the sample, and providing instructions to the individual regarding setup of a user account within a social networking system configured to provide microbiome-derived insights to the individual.

3. The method of claim 2, wherein providing instructions regarding provision of the sample comprises instructing the individual to use permeable substrate of the sampling kit to swab used toilet paper to collect a feces sample, to stir the feces sample within the sample container with the sample preservation component, and to agitate the sample container with the feces sample in order to pre-process the sample.

4. The method of claim 2, wherein providing instructions to the individual regarding pre-processing of the sample comprises guiding the user in accessing instructional content provided through the user account of the social networking system, the instructional content including video instructions to stir the sample within the sample container with the sample preservation component, and to agitate the sample container with the sample.

5. The method of claim 4, wherein receiving the sample container at the sample handling network comprises receiving the sample in a pre-processed state of lysis by individual prior to reception at the sample processing network

6. The method of claim 5, wherein receiving comprises receiving a set of sample containers each containing a pre-processed sample from one of a population of individuals, and wherein the population of individuals comprises individuals of different demographics, different health conditions, different living situations, different dietary habits, different sexual orientations, and different substance-use behaviors.

7. The method of claim 6, wherein generating the analysis comprises receiving a supplementary dataset, by way of the social networking system, comprising survey data with information regarding demographic and behavioral information of each of the population of individuals.

8. The method of claim 7, wherein generating the analysis comprises training a machine-learning classifier to generate a ranking of features of the set of features having high predictive power for demographic classifications of the population of individuals and behavioral classifications of the populations of individuals in association with microbiome composition, determined based upon the supplementary dataset.

9. The method of claim 1, wherein generating the microbiome sequence dataset comprises amplifying nucleic acid material of the sample, with a forward primer and a reverse primer having a forward index sequence, a forward barcode sequence, a linker sequence configured to reduce homogeneity in amplification, a transposase sequence corresponding to a transposase binding site, a target sequence configured to target a target region of nucleic acid material in the sample, a reverse barcode sequence, and a reverse index sequence, wherein the forward barcode sequence and the reverse barcode sequence facilitate unique association of the sample with the individual amongst a set of samples, from a population of individuals, received at the sample handling network.

10. The method of claim 9, wherein generating the microbiome sequence dataset comprises using microbiome standards prepared with colony forming units of Bacillus subtilis, Legionella pneumophilia, Clostridium perfringens, and Enterococcus faecalis, in a ratio of 100:

1000;

2;

1.

11. The method of claim 1, wherein performance of the mapping operation on portions of the microbiome sequence dataset comprises performing quality filtering of reads of the microbiome sequence dataset, and identifying and removing human genome-derived sequences from the microbiome sequence dataset.

12. The method of claim 11, wherein sequence reads of the microbiome sequence dataset are encoded into a binary sequence and hashed using a simhash algorithm with clustering in the mapping operation.

13. The method of claim 1, wherein transmitting information derived from the analysis to the individual comprises rendering a graphic derived from the analysis at a display of an electronic device associated with the individual, upon accessing of the user account by the individual at the electronic device, wherein the graphic depicts a distribution of taxonomic groups of microorganisms present in the sample with comparisons to distributions from other groups of individuals.

14. The method of claim 1, wherein generating the microbiome sequence dataset comprises simultaneously amplifying an entire 16S region for each of the set of microorganisms represented in the sample using universal primers;

fragmenting amplicons of the entire 16S region for each of the set of microorganisms to generate a set of amplicon fragments; and

generating an assessment of the set of amplicon fragments, wherein the assessment includes at least one of microorganism population characteristics, microorganism species identifications, and identified target microorganism sequences.

15. The method of claim 14, wherein generating the assessment comprises implementing a Bayesian statistics algorithm for characterization of the microbiome portion of the sample based upon at least one of species identification, strain identification, and gene identification;

assembling a full gene based upon sequenced amplicon fragments; and

detecting specific sequences from the set of amplicon fragments.

16. A system for analyzing a microbiome of an individual comprising:

a sampling kit including a sample container having a pre-process reagent component and configured to receive a sample from a collection site of the individual;

a sample handling network comprising;

a sample processing module configured to receive the sample container, associate the sample container with the individual, and generate a microbiome sequence dataset based upon sequencing nucleic acid content of a microorganism portion of the sample, and

a processing system comprising a first module in communication with the sample processing module and configured to identify a set of microorganisms represented in the microorganism portion based upon performance of a mapping operation on portions of the microbiome sequence dataset, a second module configured to generate an analysis based upon a set of features related to the microorganism portion, and a third module configured to transmit information derived from the analysis to the individual.

17. The system of claim 16, wherein the sampling kit includes a set of permeable substrates, a sample process reagent configured to facilitate sample extraction from the collection site, a return receptacle, and instructions for the individual regarding provision of the sample to the sample handling network using the return receptacle, regarding pre-processing of the sample, and regarding setup of a user account within a social networking system configured to provide microbiome-derived insights derived from the analysis to the individual.

18. The system of claim 17, wherein the sample handling network receives the sample in a pre-processed state of lysing, associates the sample with the individual and the user account of the individual, and transmits microbiome-derived information to the individual upon accessing of the user account within the social networking system by the individual.

19. The system of claim 18, wherein the second module receives a supplementary dataset, by way of the social networking system, comprising survey data with information regarding demographic and behavioral information of each of a population individuals, and trains a machine-learning classifier to generate a ranking of features of the set of features having high predictive power for at least one of demographic classifications and behavioral classifications determined based upon the supplementary dataset.

20. The system of claim 19, wherein the third module renders a graphic derived from the analysis at a display of an electronic device associated with the individual, upon accessing of the user account by the individual at the electronic device, wherein the graphic depicts a distribution of taxonomic groups of microorganisms present in the sample with comparisons to distributions from other groups of individuals.

21. A method for analyzing a microbiome of an individual, comprising:

from a sample handling network, providing a sampling kit to the individual at a location remote from the sample processing network, the sampling kit configured to provide;

a sample container having a lysing component and a sample preservation component and configured to receive a sample from a collection site of the individual, and

instructions for providing the sample, pre-processing the sample, and setting up a user account within a social networking system;

at the sample handling network, receiving the sample container with the sample from the collection site of the individual, the sample pre-processed by the individual;

at a sample processing module within the sample handling network, generating a microbiome sequence dataset based upon sequencing nucleic acid content of a microorganism portion of the sample;

at a processing system within the sample handling network, identifying a set of microorganisms represented in the microorganism portion based upon performance of a mapping operation on portions of the microbiome sequence dataset;

at the processing system, generating an analysis including values of a set of parameters related to the microorganism portion; and

from the processing system, transmitting information derived from the analysis to the individual, as facilitated by the user account within the social networking system.

22. The method of claim 21, wherein providing instructions to the individual regarding pre-processing the sample comprises guiding the user in accessing instructional content provided through the user account of the social networking system, the instructional content including video instructions to stir the sample within the sample container with the sample preservation component, and to agitate the sample container with the sample.