METHODS OF IDENTIFYING AN ORGANISM FROM A HETEROGENEOUS SAMPLE

1 . A method of identifying at least one organism from a heterogeneous sample, the method comprising:

(a) obtaining nucleic acid from at least one organism in a heterogeneous sample;

(b) imaging said nucleic acid;

(c) obtaining a restriction map of said nucleic acid; and

(d) correlating said restriction map or maps with a restriction map database, thereby identifying at least one organism in the heterogeneous sample.

2 . The method of claim 1 , wherein said nucleic acid is obtained from a plurality of distinct organisms in said heterogeneous sample.

3 . The method of claim 1 , wherein nucleic acid is obtained from fewer than all organisms in said heterogeneous sample.

4 . The method of claim 1 , wherein nucleic acid is obtained from each organism in said heterogeneous sample.

5 . The method of claim 1 , wherein the organism is a microorganism.

6 . The method of claim 1 , wherein the organism is a bacterium.

7 . The method of claim 1 , wherein the organism is a virus.

8 . The method of claim 1 , wherein the organism is a fungus.

9 . The method of claim 1 , wherein said nucleic acid sample comprises all genomic DNA of one or more of said organisms.

10 . The method of claim 1 , wherein said nucleic acid sample comprises a transcriptome of said organism.

11 . The method of claim 1 , wherein said nucleic acid is deoxyribonucleic acid.

12 . The method of claim 1 , wherein said nucleic acid is ribonucleic acid.

13 . The method of claim 1 , wherein the sample is a human tissue or body fluid.

14 . The method of claim 1 , further comprising digesting each nucleic acid with one or more enzymes prior to said imaging step.

15 . The method of claim 14 , wherein the enzymes are selected from the group consisting of: BglII, NcoI, XbaI, and BamHI.

16 . The method of claim 1 , wherein the imaging step comprises differently labeling nucleic acid from organism in the sample.

17 . The method of claim 1 , wherein the database comprises a restriction map similarity cluster.

18 . The method of claim 1 , wherein the database comprises a restriction map from at least one member of a lade of the organism.

19 . The method of claim 1 , wherein the database comprises a restriction map from at least one subspecies of the organism.

20 . The method of claim 1 , wherein the database comprises a restriction map from a genus, a species, a strain, a sub-strain, or an isolate of each organism.

21 . The method of claim 1 , wherein the database comprises a restriction map comprising motifs common to a genus, a species, a strain, a sub-strain, or an isolate of each organism.

22 . A method of diagnosing a disease or disorder in a subject, the method comprising:

(a) obtaining a sample from a subject;

(b) imaging nucleic acid from at least one organism in the sample;

(c) obtaining a restriction map of said nucleic acid;

(d) identifying said at least one organism by correlating the restriction map of each nucleic acid with a restriction map database; and

(e) correlating the identity of said at least one organism with the disease or disorder.

23 . The method of claim 22 , wherein the organism is a microorganism.

24 . The method of claim 22 , wherein the organism is a bacterium.

25 . The method of claim 22 , wherein the organism is a virus.

26 . The method of claim 22 , wherein the organism is a fungus.

27 . The method of claim 22 , wherein each nucleic acid sample comprises all genomic DNA of each organism.

28 . The method of claim 22 , wherein said nucleic acid sample comprises a transcriptome of said organism.

29 . The method of claim 22 , wherein said nucleic acid is deoxyribonucleic acid.

30 . The method of claim 22 , wherein said nucleic acid is ribonucleic acid.

31 . The method of claim 22 , wherein the sample is a human tissue or body fluid.

32 . The method of claim 22 , further comprising digesting each nucleic acid from each organism with one or more enzymes prior to said imaging step.

33 . The method of claim 32 , wherein the enzymes are selected from the group consisting of: BglII, NcoI, XbaI, and BamHI.

34 . The method of claim 22 , wherein the imaging step comprises differently labeling each nucleic acid from each organism.

35 . The method of claim 22 , wherein the database comprises a restriction map similarity cluster.

36 . The method of claim 22 , wherein the database comprises a restriction map from at least one member of a lade of the organism.

37 . The method of claim 22 , wherein the database comprises a restriction map from at least one subspecies of the organism.

38 . The method of claim 22 , wherein the database comprises a restriction map from a genus, a species, a strain, a sub-strain, or an isolate of the organism.

39 . The method of claim 22 , wherein the database comprises a restriction map comprising motifs common to a genus, a species, a strain, a sub-strain, or an isolate of the organism.

40 . A method of treating a disease or disorder in a subject, the method comprising diagnosing the disease or disorder in the subject by the method of claim 22 and providing treatment to the subject to ameliorate the disease or disorder.

41 . The method of claim 40 , wherein the providing treatment step comprises administering a drug to the subject.

42 . A method for identifying at least one organism from a heterogeneous sample, the method comprising the steps of:

Obtaining a heterogeneous sample suspected to contain at least two organisms;

Preparing a restriction map of at least one nucleic acid in said sample Imaging said nucleic acid;

Comparing said restriction map of said nucleic acid to a database containing restriction maps of known organisms.

43 . A method for identifying at least one organism from a heterogeneous sample, the method comprising the steps of:

Obtaining a heterogeneous sample suspected to contain at least two organisms;

Preparing an optical map of one or more restriction digests of at least one nucleic acid obtained from said sample;

Comparing each optical map to a map of restrictions digests of known organisms; and

Identifying at least one organism based upon results of said comparing step.

44 . The method of claim 43 , wherein said sample is selected from food, blood, sputum, saliva, air, water, soil, plant material, and unknown material.

45 . A method of identifying at least one organism from a heterogeneous sample, the method comprising:

(a) obtaining a nucleic acid from at least one organism in a heterogeneous sample;

(b) obtaining a restriction map of said nucleic acid;

(c) imaging said nucleic acid; and

(d) correlating the restriction map of said nucleic acid with a restriction map database, thereby identifying at least one organism in the heterogeneous sample.