Method for identifying and characterizing organisms

Claim 1

A method of establishing the species of an unknown organism which comprises: (1) providing as chromatographic pattern representing the hybridization of ribosomal RNA information containing nucleic acid from or derived from a known probe organism to restriction endonuclease-digested DNA from an unknown organism, (2) comparing said pattern with a number of additional chromatographic patterns sufficient to enable the establishment of such species; each one of said additional chromatographic patterns representing the hybridization of ribosomal RNA information-containing nucleic acid from or derived from said known probe organism to restriction endonuclease-digested DNA from a known different organism species; and (3) establishing the species of said unknown organism by means of a set of ribosomal RNA sequence-containing restriction fragments present in said chromatographic pattern of said unknown organism; said set being conserved among different strains of said species but not conserved among different species.

Claim 2

A method of establishing the species of an unknown organism which comprises: (1) providing as chromatographic pattern representing the hybridization of ribosomal RNA information containing nucleic acid from or derived from a known probe organism to restriction endonuclease-digested DNA from an unknown organism, (2) comparing said pattern with a number of additional chromatographic patterns sufficient to enable the establishment of such species; each one of said additional chromatographic patterns representing the hybridization of ribosomal RNA information-containing nucleic acid from or derived from said known probe organism to restriction endonuclease-digested DNA from a known different organism species; and (3) establishing the species of said unknown organism by means of a set of ribosomal RNA sequence-containing restriction fragments present in said chromatographic pattern of said unknown organism; said set being conserved among different strains of said species but not conserved among different species.

Claim 5

The method of any of claims 1, 2 or 3 wherein said ribosomal RNA information-containing nucleic acid probe is ribosomal RNA.

Claim 6

The method of any of claims 1, 2 or 3 wherein said ribosomal RNA information-containing nucleic acid probe is DNA complementary to ribosomal RNA.

Claim 7

The method of claims 1, 2 or 3 wherein said ribosomal RNA information-containing nucleic acid probe is DNA obtained by nick-translating or cloning DNA complementary to ribosomal RNA.

Claim 14

The method of any of claims 10 or 12 wherein said unknown prokaryotic organism being characterized is selectively being detected while present in or associated with a eukaryotic organism.

Claim 23

The method of any of claims 9 or 11 which further comprises identifying in said unknown eukaryotic organism being characterized a nucleic acid sequence or sequences creating a taxon below the rank of species or an infrasubspecific subdivision.

Claim 25

A method of establishing the species of an unknown bacterial strain present in a sample, which comprises: (1) providing a chromatographic pattern representing the hybridization of ribosomal RNA information-containing nucleic acid from or derived from a known probe bacterium to restriction endonuclease-digested DNA from an unknown bacterial (2) comparing said pattern with a number of additional chromatographic patterns sufficient to enable the establishment of such species; each one of said additional chromatographic patterns representing the hybridization of ribosomal RNA information-containing nucleic acid from or derived from a known probe bacterium, to restriction endonuclease-digested DNA from a known different bacterial species; and (3) establishing the species of said unknown bacterial strain by means of a set of ribosomal RNA sequence-containing restriction fragments present in said chromatographic pattern of said unknown bacterial strain; said set being conserved among different strains of said species, but not conserved among different species.

Claim 26

A method of establishing the species of an unknown bacterial strain present in a sample, which comprises: (1) providing a chromatographic pattern representing the hybridization of ribosomal RNA information-containing nucleic acid from or derived from a known probe bacterium to restriction endonuclease-digested DNA from an unknown bacterial (2) comparing said pattern with a number of additional chromatographic patterns sufficient to enable the establishment of such species; each one of said additional chromatographic patterns representing the hybridization of ribosomal RNA information-containing nucleic acid from or derived from a known probe bacterium, to restriction endonuclease-digested DNA from a known different bacterial species; and (3) establishing the species of said unknown bacterial strain by means of a set of ribosomal RNA sequence-containing restriction fragments present in said chromatographic pattern of said unknown bacterial strain; said set being conserved among different strains of said species, but not conserved among different species.

Claim 37

The method of any of claims 24, 25, 27, or 29 wherein said unknown bacterium is pathogenic towards plants or animals.

Claim 38

The method of any of claims 24, 25, 27, or 29 wherein said ribosomal RNA information-containing nucleic acid from or derived from said probe bacterium is detectably labeled.

Claim 42

The method of any of claims 1 or 24 wherein said ribosomal RNA sequence containing nucleic acid is part of a plasmid.

Claim 43

The method of any of claims 1 or 24 wherein several chromatographic patterns of restriction endonuclease digested DNA from said unknown organism are prepared, each of said several patterns corresponding to a different restriction endonuclease enzyme.