Databases for rRNA gene profiling of microbial communities

• US 8,476,016 B2
• Filed: 02/01/2011
• Issued: 07/02/2013
• Est. Priority Date: 04/10/2000
• Status: Expired due to Fees

• Current Assignee: Taxon Biosciences, Inc. (Evogene Ltd)
• Original Assignee: Taxon Biosciences, Inc. (Evogene Ltd)
• Inventors: Ashby, Matthew
• Primary Examiner(s): Strzelecka, Teresa E
• Application Number:
  US13/019,045
• Publication Number:
  US 20110251983A1
• Time in Patent Office: 882 Days
• Field of Search: None
• US Class Current: 435/6.1
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 1/683 involving restriction enzymes, e.g. restriction fragment length polymorphism [RFLP]
• 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 2521/313 Type II endonucleases, i.e. cutting outside recognition site
• CPC Class Codes: C12Q 2525/131 incorporating a restriction site
• CPC Class Codes: C12Q 2525/151 repeat or repeated sequences, e.g. VNTR, microsatellite, concatemer
• CPC Class Codes: C12Q 2525/191 incorporating an adaptor
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 20/40 Population genetics; Linkage disequilibrium
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 30/20 Sequence assembly
• CPC Class Codes: Y10T 436/21 Hydrocarbon

Abstract

The present invention relates to methods for performing surveys of the genetic diversity of a population. The invention also relates to methods for performing genetic analyses of a population. The invention further relates to methods for the creation of databases comprising the survey information and the databases created by these methods. The invention also relates to methods for analyzing the information to correlate the presence of nucleic acid markers with desired parameters in a sample. These methods have application in the fields of geochemical exploration, agriculture, bioremediation, environmental analysis, clinical microbiology, forensic science and medicine.

Claims

1. A method for constructing a marker diversity profile (MDP) database comprising the steps of:

a) sequencing a plurality of rRNA markers from a sample, wherein said sample comprises a microbial population, and wherein each rRNA marker comprises a microbial rRNA gene polymorphic sequence;

b) determining the abundance in said sample of each of said plurality of rRNA markers;

c) transducing the abundance of each rRNA marker into an electrical output signal;

d) storing the plurality of electrical output signals in a matrix data structure and associating in said matrix data structure each electrical output signal with the corresponding sequence of the rRNA marker from whose abundance the electrical output signal was transduced;

e) designating the plurality of electrical output signals corresponding to the plurality of marker abundances from said sample and being stored in the matrix data structure as an MDP;

f) repeating steps a-e for a plurality of other samples, and designating the plurality of MDPs as an MDP database,

wherein at least one MDP of said MDP database further comprises one or more electrical output signals produced by a method comprising the steps of;

i) providing the abundances of one or more non-microbial sample parameters that are associated with the sample from which said MDP is derived;

ii) transducing the abundances of said one or more non-microbial sample parameters into said one or more electrical output signals;

iii) storing said electrical output signals produced in step ii) in a matrix data structure and associating in said structure each output signal with the non-microbial sample parameter from whose abundance the output signal was transduced.

2. The method according to claim 1, wherein said rRNA marker abundance is an abundance relative to the total abundance of said plurality of rRNA markers in the sample.

3. The method according to claim 1, wherein said microbial rRNA gene is a 16S rRNA gene.

4. The method according to claim 1, wherein the sample is a gas reservoir.

5. The method according to claim 1, wherein the non-microbial sample parameter is hydrocarbons.

6. The method according to claim 1, wherein the abundance of the non-microbial sample parameter is obtained from a knowledge base.