Methods for the survey and genetic analysis of populations

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.

1 - 44 . (canceled) 
     
     
         45 . A method for constructing a marker diversity profile (MDP) database comprising the steps of:
 a) sequencing a plurality of at least 148 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 rRNA marker;   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 at least one other sample, and designating the plurality of MDPs as an MDP database.   
     
     
         46 . 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, and assigning to each marker an unique identifier;   b) determining the abundance in said sample of each rRNA marker;   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 at least one other sample, and designating the plurality of MDPs as an MDP database.   
     
     
         47 . 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 an un-cultivated microbial population, and wherein each rRNA marker comprises a microbial rRNA gene polymorphic sequence;   b) determining the abundance in said sample of each rRNA marker;   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 at least one other sample, and designating the plurality of MDPs as an MDP database.   
     
     
         48 . The method according to  claim 45 , wherein at least one MDP of said MDP database further comprises a second plurality of 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 non-microbial sample parameters into a plurality of electrical output signals;   iii) storing said plurality of electrical output signals 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;   iv) designating the plurality of electrical output signals corresponding to the plurality of non-microbial sample parameter abundances and being stored in the matrix data structure as the second plurality of electrical output signals.   
     
     
         49 . The method according to  claim 45 , wherein said rRNA marker abundance is an abundance relative to the total abundance of said plurality of the sequenced rRNA markers in the sample. 
     
     
         50 . The method according to  claim 45 , wherein said microbial rRNA gene is a 16S rRNA gene. 
     
     
         51 . The method according to  claim 45 , wherein said microbial rRNA gene polymorphic sequence is from the intergenic region between a 16S rRNA gene and a 23S rRNA gene. 
     
     
         52 . The method according to  claim 45 , wherein the sample is selected from the group consisting of: a soil sample, a rock sample, a water sample, an air sample, a hydrocarbon sample, a petroleum sample and a biofilm sample. 
     
     
         53 . The method according to  claim 45 , wherein the sample is obtained from the group consisting of: an oil reservoir, a gas reservoir, a building and a roadway. 
     
     
         54 . The method according to  claim 45 , wherein the sample is obtained from the group consisting of: a human, a plant, an animal, a foodstuff, a body tissue sample, a body fluid sample, a cell culture and a tissue culture. 
     
     
         55 . The method according to  claim 46 , wherein at least one MDP of said MDP database further comprises a second plurality of 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 non-microbial sample parameters into a plurality of electrical output signals;   iii) storing said plurality of electrical output signals 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;   iv) designating the plurality of electrical output signals corresponding to the plurality of non-microbial sample parameter abundances and being stored in the matrix data structure as the second plurality of electrical output signals.   
     
     
         56 . The method according to  claim 46 , wherein said rRNA marker abundance is an abundance relative to the total abundance of said plurality of the sequenced rRNA markers in the sample. 
     
     
         57 . The method according to  claim 46 , wherein said microbial rRNA gene is a 16S rRNA gene. 
     
     
         58 . The method according to  claim 46 , wherein said microbial rRNA gene polymorphic sequence is from the intergenic region between a 16S rRNA gene and a 23S rRNA gene. 
     
     
         59 . The method according to  claim 46 , wherein the sample is selected from the group consisting of: a soil sample, a rock sample, a water sample, an air sample, a hydrocarbon sample, a petroleum sample and a biofilm sample. 
     
     
         60 . The method according to  claim 46 , wherein the sample is obtained from the group consisting of: an oil reservoir, a gas reservoir, a building and a roadway. 
     
     
         61 . The method according to  claim 46 , wherein the sample is obtained from the group consisting of: a human, a plant, an animal, a foodstuff, a body tissue sample, a body fluid sample, a cell culture and a tissue culture. 
     
     
         62 . The method according to  claim 47 , wherein at least one MDP of said MDP database further comprises a second plurality of 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 non-microbial sample parameters into a plurality of electrical output signals;   iii) storing said plurality of electrical output signals 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;   iv) designating the plurality of electrical output signals corresponding to the plurality of non-microbial sample parameter abundances and being stored in the matrix data structure as the second plurality of electrical output signals.   
     
     
         63 . The method according to  claim 47 , wherein said rRNA marker abundance is an abundance relative to the total abundance of said plurality of the sequenced rRNA markers in the sample. 
     
     
         64 . The method according to  claim 47 , wherein said microbial rRNA gene is a 16S rRNA gene. 
     
     
         65 . The method according to  claim 47 , wherein said microbial rRNA gene polymorphic sequence is from the intergenic region between a 16S rRNA gene and a 23S rRNA gene. 
     
     
         66 . The method according to  claim 47 , wherein the sample is selected from the group consisting of: a soil sample, a rock sample, a water sample, an air sample, a hydrocarbon sample, a petroleum sample and a biofilm sample. 
     
     
         67 . The method according to  claim 47 , wherein the sample is obtained from the group consisting of: an oil reservoir, a gas reservoir, a building and a roadway. 
     
     
         68 . The method according to  claim 47 , wherein the sample is obtained from the group consisting of: a human, a plant, an animal, a foodstuff, a body tissue sample, a body fluid sample, a cell culture and a tissue culture.