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 culture-independent method of identifying an indicator for a sample parameter, said parameter not including bacteria, said method comprising the steps of:
 a. providing a plurality of samples at least some of which samples contain the parameter, wherein each sample is independently obtained from humans, animals, plants, parasites, water, soil, air, foodstuffs, cell or tissue cultures;   b. isolating a plurality of genomic DNAs from each of the samples provided in step a;   c. isolating a plurality of rRNA gene segments from each plurality of genomic DNAs isolated in step b;   d. determining the abundance of each of said rRNA gene segments in each plurality of rRNA gene segments isolated in step c;   e. determining the abundance of the parameter in each of the samples provided in step a;   f. correlating the abundance of each rRNA gene segment determined in step d with the abundance of the parameter determined in step e;   g. designating at least one rRNA gene segment whose abundance correlates to the abundance of said parameter, as determined in step f, as an indicator for the sample parameter.   
     
     
         46 . A culture-independent method of identifying a microbial indicator for a sample parameter, said parameter not including bacteria, said method comprising the steps of:
 a. providing a plurality of samples at least some of which samples contain the parameter, wherein each sample is independently obtained from humans, animals, plants, parasites, water, soil, air, foodstuffs, cell or tissue cultures;   b. isolating a plurality of genomic DNAs from each of the samples provided in step a;   c. isolating a plurality of rRNA gene segments from each plurality of genomic DNAs isolated in step b;   d. determining the abundance of each of said rRNA gene segments in each plurality of rRNA gene segments isolated in step c;   e. determining the abundance of the parameter in each of the samples provided in step a;   f. correlating the abundance of each rRNA gene segment determined in step d with the abundance of the parameter determined in step e;   g. selecting at least one rRNA gene segment whose abundance correlates to the abundance of said parameter, as determined in step f;   h. designating a microbe that comprises said rRNA gene segment selected in step g as a microbial indicator.   
     
     
         47 . A culture-independent method of determining the abundance of a sample parameter in an sample, said parameter not including bacteria, comprising the steps of:
 a. providing at least one sample, said sample being obtained from humans, animals, plants, parasites, water, soil, air, foodstuffs, cell or tissue cultures;   b. isolating a plurality of genomic DNAs from said sample(s);   c. determining the abundance of an indicator identified in the method of  claim 45  in the plurality of genomic DNAs isolated in step b; and   d. inferring the abundance of the parameter in said sample(s) based upon the abundance of said indicator in said sample(s).   
     
     
         48 . A culture-independent method of determining the abundance of a sample parameter in an sample, said parameter not including bacteria, comprising the steps of:
 a. providing a first plurality of samples at least some of which samples contain the parameter, wherein each sample is independently obtained from humans, animals, plants, parasites, water, soil, air, foodstuffs, cell or tissue cultures;   b. isolating a plurality of genomic DNAs from each of the samples provided in step a;   c. isolating a plurality of rRNA gene segments from each plurality of genomic DNAs isolated in step b;   d. determining the abundance of each of said rRNA gene segments in each plurality of rRNA gene segments isolated in step c;   e. determining the abundance of the parameter in each of the samples provided in step a;   f. correlating the abundance of each rRNA gene segment determined in step d with the abundance of the parameter determined in step e;   g. selecting at least one rRNA gene segment whose abundance correlates to the abundance of said parameter, as determined in step f;   h. providing a sample set of at least one sample, said sample being obtained from humans, animals, plants, parasites, water, soil, air, foodstuffs, cell or tissue cultures;   i. isolating a plurality of genomic DNAs from each sample of the sample set provided in step h;   j. determining the abundance of said rRNA gene segment selected in step g in each plurality of genomic DNAs isolated in step i; and   k. inferring the abundance of the parameter in each sample of the sample set provided in step h based upon the abundance of said rRNA gene determined in step j in each sample of the sample set provided in step h.   
     
     
         49 . The method according to  claim 45 , wherein said rRNA gene segment is a 16S rRNA gene segment. 
     
     
         50 . The method according to  claim 45 , wherein the sample(s) is a human or animal body tissue sample, a human or animal body fluid sample, a cell culture sample or a tissue culture sample. 
     
     
         51 . The method according to  claim 50 , wherein the parameter is selected from the group consisting of a medical condition, an acute disease state, a chronic disease state, a physiological state and developmental state. 
     
     
         52 . The method according to  claim 45 , wherein the correlation in step g is expressible by an r-value selected from 1, 0.8 to 0.99, 0.5 to 0.7, or 0.3 to 0.4. 
     
     
         53 . The method according to  claim 46 , wherein said rRNA gene segment is a 16S rRNA gene segment. 
     
     
         54 . The method according to  claim 46 , wherein the sample(s) is a human or animal body tissue sample, a human or animal body fluid sample, a cell culture sample or a tissue culture sample. 
     
     
         55 . The method according to  claim 54 , wherein the parameter is selected from the group consisting of a medical condition, an acute disease state, a chronic disease state, a physiological state and developmental state. 
     
     
         56 . The method according to  claim 46 , wherein the correlation in step g is expressible by an r-value selected from 1, 0.8 to 0.99, 0.5 to 0.7, or 0.3 to 0.4. 
     
     
         57 . The method according to  claim 47 , wherein said indicator is a 16S rRNA gene segment. 
     
     
         58 . The method according to  claim 47 , wherein the sample(s) is a human or animal body tissue sample, a human or animal body fluid sample, a cell culture sample or a tissue culture sample. 
     
     
         59 . The method according to  claim 58 , wherein the parameter is selected from the group consisting of a medical condition, an acute disease state, a chronic disease state, a physiological state and developmental state. 
     
     
         60 . The method according to  claim 47 , wherein the abundance of said indicator in said plurality of genomic DNAs is determined using PCR or a hybridization assay. 
     
     
         61 . The method according to  claim 48 , wherein said rRNA gene segment is a 16S rRNA gene segment. 
     
     
         62 . The method according to  claim 48 , wherein the sample(s) is a human or animal body tissue sample, a human or animal body fluid sample, a cell culture sample or a tissue culture sample. 
     
     
         63 . The method according to  claim 62 , wherein the parameter is selected from the group consisting of a medical condition, an acute disease state, a chronic disease state, a physiological state and developmental state. 
     
     
         64 . The method according to  claim 48 , wherein the correlation in step g is expressible by an r-value selected from 1, 0.8 to 0.99, 0.5 to 0.7, or 0.3 to 0.4. 
     
     
         65 . The method according to  claim 48 , wherein the determination in step j, of the abundance of said rRNA gene segment, is done using PCR or a hybridization assay.