Comparative phenotype analysis

• US 6,727,076 B2
• Filed: 08/23/2002
• Issued: 04/27/2004
• Est. Priority Date: 04/12/1995
• Status: Expired due to Term

• Current Assignee: Biolog, Inc.
• Original Assignee: Biolog, Inc.
• Inventors: Bochner, Barry
• Primary Examiner(s): TATE, CHRISTOPHER ROBIN
• Application Number:
  US10/226,436
• Publication Number:
  US 20030148413A1
• Time in Patent Office: 613 Days
• Field of Search: 437/34, 437/29, 437/32, 437/4, 437/7.31, 437/7.32
• US Class Current: 435/34
• CPC Class Codes: C12Q 1/04 Determining presence or kind of microorganism; Use of selective media for testing antibiotics or bacteriocides; Compositions containing a chemical indicator therefor C12Q1/6897 takes precedence
• CPC Class Codes: C12Q 2304/20 Redox indicators
• CPC Class Codes: C12Q 2304/22 Resazurin; Resorufin
• CPC Class Codes: C12Q 2304/24 Tetrazolium; Formazan
• CPC Class Codes: G01N 2035/00148 Test cards, e.g. Biomerieux or McDonnel multiwell test cards
• CPC Class Codes: G01N 2333/36 from Actinomyces; from Streptomyces (G)
• CPC Class Codes: Y10S 435/81 Packaged device or kit
• CPC Class Codes: Y10S 435/822 using bacteria or actinomycetales
• CPC Class Codes: Y10S 435/911 using fungi
• CPC Class Codes: Y10S 435/975 Kit

Abstract

The present invention relates to growing and testing microorganisms in a multitest format which utilizes a gel forming matrix for the rapid screening of clinical and environmental cultures. The present invention is suited for the characterization of commonly encountered microorganisms (e.g., E. coli, S. aureus, etc.), as well as commercially and industrially important organisms from various and diverse environments (e.g., the present invention is particularly suited for the growth and characterization of the actinomycetes and fungi). The present invention is also particularly suited for comparative analysis of phenotypic differences between cell types, including strains of microorganisms that have been designated as the same genus and species, as well as other cell types (e.g., mammalian, insect, and plant cells).

Claims

1. A method for comparing at least two cell preparations, comprising the steps of:

a) providing a testing device comprising a plurality of testing wells and at least two test substrates selected from the group consisting of phosphorus sources selected from the group consisting of phosphorus-containing compounds, sulfur sources selected from the group consisting of sulfur-containing compounds, and auxotrophic supplements selected from the group consisting of amino acids, vitamins, polyamines, lactones, fatty acids, nucleic acid bases, nucleosides, and nucleotides, wherein each well comprises at least one of said test substrates;

b) preparing a first cell preparation and a second cell preparation, wherein said first and said second cell preparations are each in an aqueous solution;

c) introducing said first and second cell preparations into said testing wells of said testing device;

d) detecting the response of said first and second cell preparations to said at least two test substrates using a single colorimetric indicator; and

e) comparing the response of said first and second cell preparations.

2. The method of claim 1, wherein said phosphorus sources are selected from the group consisting of phosphate, pyrophosphate, trimetaphosphate, tripolyphosphate, hypophosphite, thiophosphate, adenosine 2′

-monophosphate, adenosine 3′

-monophosphate, adenosine 5′

-monophosphate, adenosine 2′

;

3′

-cyclic monophosphate, adenosine 3′

;

5′

-cyclic monophosphate, dithiophosphate, DL-α

-glycero-phosphate, β

-glycero-phosphate, phosphatidyl glycerol, phosphoenol pyruvate, phosphocreatine, 2′

deoxy glucose 6-phosphate, guanosine 2′

-monophosphate, guanosine 3′

-monophosphate, guanosine 5′

-monophosphate, guanosine 2′

;

3′

-cyclic monophosphate, guanosine 3′

;

5′

-cyclic monophosphate, glucose 1-phosphate, glucose 6-phosphate, fructose 1-phosphate, fructose 6-phosphate, mannose 1-phosphate, mannose 6-phosphate, arabinose 5-phosphate, cytidine 2′

-monophosphate, cytidine 3′

-monophosphate, cytidine 5′

-monophosphate, cytidine 2′

;

3′

-cyclic monophosphate, cytidine 3′

;

5′

-cyclic monophosphate, glucosamine 1-phosphate, glucosamine 6-phosphate, phospho-L-arginine, O-phospho-D-serine, O-phospho-L-serine, O-phospho-D-tyrosin, O-phospho-L-tyrosine, uridine 2′

-monophosphate, uridine 3′

-monophosphate, uridine 5′

-monophosphate, uridine 2′

;

3′

-cyclic monophosphate, uridine 3′

;

5′

-cyclic monophosphate, O-phospho-L-threonine, inositol hexaphosphate, nitrophenyl phosphate, 2-aminoethyl phosphonate, 6-phosphogluconic acid, 2-phosphoglyeric acid, phosphoglycolic acid, phosphonoacetic acid, thymidine 3′

-monophosphate, thymidine 5′

-monophosphate, methylene diphosphonic acid, and thymidine 3′

;

5′

-cyclic monophosphate.

3. The method of claim 1, wherein said sulfur sources are selected from the group consisting of sulfate, thiosulfate, tetrathionate, thiophosphate, dithiophosphate, L-cysteine, cysteinyl-glycine, L-cysteic acid, cysteamine, L-cysteine-sulphinic acid, cystathionine, lanthionine, DL-ethionine, glutathione (reduced form), L-methionine, glycyl-DL-methionine, S-methyl-L-cysteine, L-methionine sulfoxide, L-methionine sulfone, taurine, N-acetyl-DL-methionine, N-acetyl cysteine, isethionate, thiourea, thiodiglycol, thioglycolic acid, thiodiglycolic acid, 1-dodecane-sulfonic acid, taurocholic acid, tetramethylene sulfone, hypotaurine, O-acetyl-serine, 3′

;

3′

thiodipropionic acid, L-djenkolic acid, and 2-mercaptoethylamine, metabisulfite, dithionite, polysufide, cystine, glycyl-cysteine, L-2-thiohistidine, and S-ethyl-cysteine.

4. The method of claim 1, wherein said auxotrophic supplements are selected from the group consisting of L-alanine, L-arginine, L-asparagine, L-aspartic acid, adenine, adenosine, 2′

-deoxyadenosine, adenosine 3′

;

5′

-cyclic monophosphate, adenosine 3′

-monophosphate, adenosine 5′

-monophosphate, L-cysteine, L-glutamic acid, L-glutamine, L-glycine, L-histidine, L-isoleucine, guanine, guanosine, 2′

-deoxyguanosine, guanosine 3′

;

5′

-cyclic monophosphate, guanosine 3′

-monophosphate, guanosine 5′

-monophosphate, L-leucine, L-lysine, L-methionine, L-phenylalanine, L-proline, L-serine, cytosine, cytidine, 2′

-deoxycytidine, cytidine 3′

;

5 ′

-cyclic monophosphate, cytidine 3′

-monophosphate, cytidine 5′

-monophosphate, L-tryptophan, L-tyrosine, L-threonine, L-valine, D-alanine, D-aspartic acid, thymine, thymidine, thymidine 3′

;

5′

-cyclic monophosphate, thymidine 3′

-monophosphate, thymidine 5′

-monophosphate, D-glutamic acid, (5)4-amino-imidazole-4(5)-carboxamide, DL-α

,ε

-diaminopimelic acid, D-biotin, DL-α

-lipoic acid, caprylic acid, uracil, uridine, 2′

-deoxyuridine, uridine3′

;

5′

-cyclic monophosphate, uridine 3′

-monophosphate, uridine 5′

-monophosphate, p-amino-benzoic acid, shikimic acid, molybdic acid, folic acid, α

-ketoisovaleric acid, D-pantothenic acid, hypoxanthine, inosine, 2′

-deoxyinosine, inosine 3′

;

5′

-cyclic monophosphate, inosine 3′

-monophosphate, inosine 5′

-monophosphate, thiamine, riboflavin, pyridoxal, pyridoxine, pyridoxamine, quinolinic acid, reduced glutathione, L-homoserine lactone, α

-ketobutyric acid, β

-nicotinamide adenine dinucleotide, nicotinic acid, nicotinamide, N-α

-acetyl-L-ornithine, L-ornithine, L-citrulline, putrescine, spermidine, spermine, tween 20, tween 40, tween 60, tween 80, and δ

-amino-levulinic acid.

5. The method of claim 1, wherein said testing device comprises more than 95 testing wells.

6. The method of claim 1, wherein said testing wells further contain a gel-initiating agent and said first and second cell preparations further comprise a gelling agent that remains ungelled until said first and second cell preparations are introduced into said testing wells.

7. The method of claim 6, wherein said gelling agent is selected from the group consisting of gellan gum, carageenan, and alginate.

8. The method of claim 1, further comprising at least one antimicrobial in said testing wells or in said aqueous solution.

9. The method of claim 8, wherein said at least one antimicrobial is present in said testing wells.

10. The method of claim 8, wherein said at least one antimicrobial is present in said aqueous solution.

11. The method of claim 1, further comprising at least one colorimetric indicator in said testing wells or in said aqueous solution.

12. The method of claim 11, wherein said at least one colorimetric indicator is present in said testing wells.

13. The method of claim 11, wherein said at least one colorimetric indicator is present in said aqueous solution.

14. The method of claim 11, wherein said colorimetric indicator is selected from the group consisting of chromogenic compounds, fluorochromic compounds, fluorogenic compounds, pH indicators, oxidation-reduction indicators, and luminogenic compounds.

15. The method of claim 14, wherein said oxidation-reduction indicator comprises a tetrazolium dye.

16. The method of claim 15, wherein said oxidation-reduction indicator comprises redox purple.

17. The method of claim 1, wherein said first and second cell suspensions further comprise at least one additional substrate selected form the group consisting of carbon sources, nitrogen sources, phosphorus sources, sulfur sources, and auxotrophic supplements.

18. The method of claim 17, wherein said carbon sources are selected from the group consisting of dextrin, tween 40, tween 60, tween 80, N-acetyl-D-galactosamine, N-acetyl-D-glucosamine, L-arabinose, D-fructose, L-fucose, D-galactose, α

-D-glucose, α

-D-lactose, maltose, D-mannitol, D-mannose, D-melibiose, β

-methyl-D-glucoside, L-rhamnose, D-sorbitol, D-trehalose, methyl pyruvate, mono-methyl succinate, acetic acid, D-galactonic acid lactone, D-galacturonic acid, D-gluconic acid, D-glucuronic acid, α

-ketobutyric acid, D,L-lactic acid, propionic acid, succinic acid, bromosuccinic acid, alaninamide, D-alanine, L-alanine, L-alanyl-glycine, L-asparagine, L-aspartic acid, glycyl-L-aspartic acid, glycyl-L-glutamic acid, D-serine, L-serine, inosine, uridine, thymidine, glycerol, D,L-α

-glycerol phosphate, glucose-1-phosphate, and glucose-6-phosphate, α

-cyclodextrin, adonitol, D-arabitol, cellobiose, i-erythritol, xylitol, citric acid, D-glucosaminic acid, β

-hydroxybutyric acid, γ

-hydroxybutyric acid, p-hydroxyphenylacetic acid, itaconic acid, α

-ketovaleric acid, malonic acid, quinic acid, sebacic acid, L-histidine, hydroxy L-proline, L-leucine, and D,L-carnitine, glycogen, D-psicose, succinamic acid, glucuronamide, gentiobiose, m-inositol, cis-aconitic acid, L-phenylalanine, L-pyroglutamic acid, phenylethylamine, putrescine, 2-amino ethanol, 2,3-butanediol, lactulose, D-raffinose, formic acid, α

-hydroxybutyric acid, L-glutamic acid, L-proline, sucrose, L-ornithine, turanose, α

-ketoglutaric acid, D-saccharic acid, L-threonine, γ

-aminobutyric acid and urocanic acid.

19. The method of claim 17, wherein said nitrogen sources are selected from the group consisting of D-alanine, L-alanine, L-arginine, D-asparagine, L-asparagine, D-aspartic acid, L-aspartic acid, L-cysteine, L-cystine, D-glutamic acid, L-glutamic acid, L-glutamine, glycine, L-histidine, L-homoserine, D,L-β

-hydroxy-glutamic acid, L-isoleucine, L-leucine, L-phenylalanine, L-proline, D-serine, L-serine, L-tryptophan, L-tyrosine, glutathione, cytosine, D-glucosamine, D-galactosamine, D-mannosamine, N-acetyl-D-glucosamine, N-acetyl-D-galactosamine, N-acetyl-D-mannosamine, methylamine, ethylamine, butylamine, isobutylamine, amylamine, ethanolamine, ethylenediamine, pentamethylenediamine, hexamethylenetriamine, phenylethylamine, tyramine, piperidine, pyrrole, β

-alanine, acetyiglycocol, phenylglycine-o-carbonic acid, α

-aminovaleric acid, γ

-aminovaleric acid, α

-aminoisovaleric acid, γ

-aminoisovaleric acid, α

-aminocaproic acid, γ

-aminocaprylic acid, acetamide, lactamide, glucuronamide, formamide, propionamide, methoxylamide, thio-acetamide, cyanate, diethylurea, tetraethylurea, biuret, alloxan, alloxantine, allantoin, theobromine, ammonium chloride, sodium nitrite, potassium nitrate, urea, glutathione (reduced form), alloxan, L-citrulline, putrescine, L-ornithine, agmatine, L-lysine, L-methionine, L-threonine, L-valine, D-lysine, D-valine, N-acetyl-glycine, L-pyroglutamic acid, histamine, adenosine, deoxyadenosine, cytosine, adenine, thymine, thymidine, uracil, uridine, deoxycytidine, cytidine, guanine, guanosine, xanthine, xanthosine, inosine, DL-α

-amino-n-butyic acid, γ

-amino-n-butyric acid, ε

-amino-n-caproic acid, DL-α

-amino-caprylic acid, hippuric acid, parabanic acid, uric acid, urocanic acid, δ

-amino-n-valeric acid, 2-amino-valeric acid, gly-glu, ala-gly, ala-his, ala-thr, gly-met, gly-gln, ala-gln, gly-ala, gly-asn, and met-ala.

20. The method of claim 1, wherein said first and second cell preparatons comprise microorganisms selected from the group consisting of bacteria and fungi.

21. The method of claim 1, wherein said first and second cell preparations contain cells of the same genus and species.

22. The method of claim 1, wherein said first and second cell preparations contain cells that differ in one or more genes.

23. The method of claim 1, wherein said detecting is visual.

24. The method of claim 1, wherein said detecting is performed by an instrument.

25. The method of claim 24, wherein said instrument comprises a video camera.

26. The method of claim 1, wherein said detecting is conducted over time.

27. A method for comparing at least two cell preparations, comprising the steps of:

a) providing a testing device comprising a plurality of testing wells and at least two test substrates selected from the group consisting of nitrogen sources selected from the group consisting of nitrogen-containing compounds, phosphorus sources selected from the group consisting of phosphorus-containing compounds, sulfur sources selected from the group consisting of sulfur-containing compounds, and auxotrophic supplements selected from the group consisting of amino acids, vitamins, polyamines, lactones, fatty acids, nucleic acid bases, nucleosides, and nucleotides, wherein each well comprises at least one test substrate;

b) preparing a first cell preparation and a second cell preparation, wherein said first and said second cell preparations are each in an aqueous solution and said aqueous solution comprises at least one carbon source;

c) introducing said first and second cell preparations into said testing wells of said testing device;

d) detecting the response of said first and second cell preparations to said at least two test substrates using a single colorimetric indicator; and

e) comparing the response of said first and second cell preparations.

28. The method of claim 27, wherein said at least one carbon source is selected from the group consisting of polymers, carbohydrates, acids, esters, amides, amines, alcohols, aldehydes, ketones, amino acids, peptides and nucleosides.

29. The method of claim 28, wherein said at least one carbon source is selected from the group consisting of dextrin, tween 40, tween 60, tween 80, N-acetyl-D-galactosamine, N-acetyl-D-glucosamine, L-arabinose, D-fructose, L-fucose, D-galactose, α

-D-glucose, α

-D-lactose, maltose, D-mannitol, D-mannose, D-melibiose, β

-methyl-D-glucoside, L-rhamnose, D-sorbitol, D-trehalose, methyl pyruvate, mono-methyl succinate, acetic acid, D-galactonic acid lactone, D-galacturonic acid, D-gluconic acid, D-glucuronic acid, α

-ketobutyric acid, D,L-lactic acid, propionic acid, succinic acid, bromosuccinic acid, alaninamide, D-alanine, L-alanine, L-alanyl-glycine, L-asparagine, L-aspartic acid, glycyl-L-aspartic acid, glycyl-L-glutamic acid, D-serine, L-serine, inosine, uridine, thymidine, glycerol, D,L-α

-glycerol phosphate, glucose-1-phosphate, and glucose-6-phosphate, α

-cyclodextrin, adonitol, D-arabitol, cellobiose, i-erythritol, xylitol, citric acid, D-glucosaminic acid, β

-hydroxybutyric acid, γ

-hydroxybutyric acid, p-hydroxyphenylacetic acid, itaconic acid, α

-ketovaleric acid, malonic acid, quinic acid, sebacic acid, L-histidine, hydroxy L-proline, L-leucine, and D,L-carnitine, glycogen, D-psicose, succinamic acid, glucuronamide, gentiobiose, m-inositol, cis-aconitic acid, L-phenylalanine, L-pyroglutamic acid, phenylethylamine, putrescine, 2-amino ethanol, 2,3-butanediol, lactulose, D-raffinose, formic acid, α

-hydroxybutyric acid, L-glutamic acid, L-proline, sucrose, L-ornithine, turanose, α

-ketoglutaric acid, D-saccharic acid, L-threonine, γ

-aminobutyric acid and urocanic acid.

30. The method of claim 27, further comprising at least one additional nutritional component selected from the group consisting of nitrogen sources, phosphorus sources, sulfur sources, and auxotrophic supplements, in said testing wells or in said first and second cell preparations.

31. The method of claim 30, wherein said additional nutritional component is present in said testing wells.

32. The method of claim 30, wherein said first and second cell preparations further comprise said additional nutritional component.

33. The method of claim 27, wherein said aqueous solution furhter comprises at least one additional component selected from the group consisting of buffers, gelling agents, salts, surfactants, and colorimetric indicators.

34. The method of claim 27, wherein said nitrogen sources are selected from the group consisting of D-alanine, L-alanine, L-arginine, D-asparagine, L-asparagine, D-aspartic acid, L-aspartic acid, L-cysteine, L-cystine, D-glutamic acid, L-glutamic acid, L-glutamine, glycine, L-histidine, L-homoserine, D,L-β

-hydroxy-glutamic acid, L-isoleucine, L-leucine, L-phenylalanine, L-proline, D-serine, L-serine, L-tryptophan, L-tyrosine, glutathione, cytosine, D-glucosamine, D-galactosamine, D-mannosamine, N-acetyl-D-glucosamine, N-acetyl-D-galactosamine, N-acetyl-D-mannosamine, methylamine, ethylamine, butylamine, isobutylamine, amylamine, ethanolamine, ethylenediamine, pentamethylenediamine, hexamethylenetriamine, phenylethylamine, tyramine, piperidine, pyrrole, β

-alanine, acetylglycocol, phenylglycine-o-carbonic acid, α

-aminovaleric acid, γ

-aminovaleric acid, α

-aminoisovaleric acid, γ

-aminoisovaleric acid, α

-aminocaproic acid, γ

-aminocaprylic acid, acetamide, lactamide, glucuronamide, formamide, propionamide, methoxylamide, thio-acetamide, cyanate, diethylurea, tetraethylurea, biuret, alloxan, alloxantine, allantoin, theobromine, ammonium chloride, sodium nitrite, potassium nitrate, urea, glutathione (reduced form), alloxan, L-citrulline, putrescine, L-ornithine, agmatine, L-lysine, L-methionine, L-threonine, L-valine, D-lysine, D-valine, N-acetyl-glycine, L-pyroglutamic acid, histamine, adenosine, deoxyadenosine, cytosine, adenine, thymine, thymidine, uracil, uridine, deoxycytidine, cytidine, guanine, guanosine, xanthine, xanthosine, inosine, DL-α

-amino-n-butyic acid, γ

-amino-n-butyric acid, ε

-amino-n-caproic acid, DL-α

-amino-caprylic acid, hippuric acid, parabanic acid, uric acid, urocanic acid, δ

-amino-n-valeric acid, 2-amino-valeric acid, gly-glu, ala-gly, ala-his, ala-thr, gly-met, gly-gln, ala-gln, gly-ala, gly-asn, and met-ala.

35. The method of claim 27, wherein said phosphorus sources are selected from the group consisting of phosphate, pyrophosphate, trimetaphosphate, tripolyphosphate, hypophosphite, thiophosphate, adenosine 2′

-monophosphate, adenosine 3′

-monophosphate, adenosine 5′

-monophosphate, adenosine 2′

;

3′

-cyclic monophosphate, adenosine 3′

;

5′

-cyclic monophosphate, dithiophosphate, DL-α

-glycero-phosphate, β

-glycero-phosphate, phosphatidyl glycerol, phosphoenol pyruvate, phosphocreatine, 2′

deoxy glucose 6-phosphate, guanosine 2′

-monophosphate, guanosine 3′

-monophosphate, guanosine 5′

-monophosphate, guanosine 2′

;

3′

-cyclic monophosphate, guanosine 3′

;

5′

-cyclic monophosphate, glucose 1-phosphate, glucose 6-phosphate, furctose 1-phosphate, fructose 6-phosphate, mannose 1-phosphate, mannose 6-phosphate, arabinose 5-phosphate, cytidine 2′

-monophosphate, cytidine 3′

-monophosphate, cytidine 5′

-monophosphate, cytidine 2′

;

3′

-cyclic monophosphate, cytidine 3′

;

5′

-cyclic monophosphate, glucosamine 1-phosphate, glucosamine 6-phosphate, phospho-L-arginine, O-phospho-D-serine, O-phospho-L-serine, O-phospho-D-tyrosine, O-phospho-L-tyrosine, uridine 2′

-monophosphate, uridine 3′

-monophosphate, uridine 5′

-monophosphate, uridine 2′

;

3′

-cyclic monophosphate, uridine 3′

;

5′

-cyclic monophosphate, O-phospho-L-threonine, inositol hexaphosphate, nitrophenyl phosphate, 2-aminoethyl phosphonate, 6-phosphogluconic acid, 2-phosphoglyceric acid, phosphoglycolic acid, phosphonoacetic acid, thymidine 3′

-monophosphate, thymidine 5′

-monophosphate, methylene diphosphonic acid, and thymidine 3′

;

5′

-cyclic monophosphate.

36. The method of claim 27, wherein said sulfur sources are selected from the group consisting of sulfate, thiosulfate, tetrathionate, thiophosphate, dithiophosphate, L-cysteine, cysteinyl-glycine, L-cysteic acid, cysteamine, L-cysteine-sulphinic acid, cystathionine, lanthionine, DL-ethionine, glutathione (reduced form), L-methionine, glycyl-DL-methionine, S-methyl-L-cysteine, L-methionine sulfoxide, L-methionine sulfone, taurine, N-acetyl-DL-methionine, N-acetyl cysteine, isethionate, thiourea, thiodiglycol, thioglycolic acid, thiodiglycolic acid, 1-dodecane-sulfonic acid, taurocholic acid, tetramethylene sulfone, hypotaurine, O-acetyl-serine, 3′

;

3′

thiodipropionic acid, L-djenkolic acid, and 2-mercaptoethylamine, metabisulfite, dithionite, polysufide, cystine, glycyl-cysteine, L-2-thiohistidine, and S-ethyl-cysteine.

37. The method of claim 27, wherein said auxotrophic supplements are selected from the group consisting of L-alanine, L-arginine, L-asparagine, L-aspartic acid, adenine, adenosine, 2′

-deoxyadenosine, adenosine 3′

;

5′

-cyclic monophosphate, adenosine 3′

-monophosphate, adenosine 5′

-monophosphate, L-cysteine, L-glutamic acid, L-glutamine, L-glycine, L-histidine, L-isoleucine, guanine, guanosine, 2′

-deoxyguanosine, guanosine 3′

;

5′

-cyclic monophosphate, guanosine 3′

-monophosphate, guanosine 5′

-monophosphate, L-leucine, L-lysine, L-methionine, L-phenylalanine, L-proline, L-serine, cytosine, cytidine, 2′

-deoxycytidine, cytidine 3′

;

5′

cyclic monophosphate, cytidine 3′

-monophosphate, cytidine 5′

-monophosphate, L-tryptophan, L-tyrosine, L-threonine, L-valine, D-alanine, D-aspartic acid, thymine, thymidine, thymidine 3′

;

5′

-cyclic monophosphate, thymidine 3′

-monophosphate, thymidine 5′

-monophosphate, D-gultamic acid, (5)4-amino-imidazole-4(5)-carboxamide, DL-α

,ε

-diaminopimelic acid, D-biotin, DL-α

-lipoic acid, caprylic acid, uracil, uridine, 2′

-deoxyuridine, uridine 3′

;

5′

-cyclic monophosphate, uridine 3′

-monophosphate, uridine 5′

-monophosphate, p-amino-benzoic acid, shikimic acid, molybdic acid, folic acid, α

-ketoisovaleric acid, D-pantothenic acid, hypoxanthine, inosine, 2′

-deoxyinosine, inosine 3′

;

5′

-cyclic monophosphate, inosine 3′

-monophosphate, inosine 5′

-monophosphate, thiamine, riboflavin, pyridoxal, pyridoxine, pyridoxamine, quinolinic acid, reduced glutathione, L-homoserine lactone, α

-ketobutyric acid, β

-nicotinamide adenine dinucleotide, nicotinic acid, nicotinamide, N-α

-acetyl-L-ornithine, L-ornithine, L-citrulline, putrescine, spermidine, spermine, tween 20, tween 40, tween 60, tween 80, and δ

-amino-levulinic acid.

38. The method of claim 27, wherein said testing device comprises more than 95 testing wells.

39. The method of claim 27, wherein said testing wells further contain a gel-initiating agent and said first and second cell preparations further comprise a gelling agent that remains ungelled until said first and second cell preparations are introduced into said testing wells.

40. The method of claim 27, further comprising at least one antimicrobial in said testing wells or in said aqueous solution.

41. The method of claim 40, wherein said at least one antimicrobial is present in said testing wells.

42. The method of claim 40, wherein said at least one antimicrobial is present in said aqueous solution.

43. The method of claim 27, further comprising at least one colorimetric indicator in said testing wells or in said aqueous solution.

44. The method of claim 43, wherein said at least one colorimetric indicator is present in said testing wells.

45. The method of claim 43, wherein said at least one colormetric indicator is present in said aqueous solution.

46. The method of claim 43, wherein said colorimetric indicator is selected from the group consisting of chromogenic compounds, fluorochromic compounds, fluorogenic compounds, pH indicators, oxidation-reduction indicators, and luminogenic compounds.

47. The method of claim 46, wherein said oxidation-reduction indicator comprises a tetrazolium dye.

48. The method of claim 46, wherein said oxidation-reduction indicator comprises a redox purple.

49. The method of claim 27, wherein said first and second cell preparations comprise microorganisms selected from the group consisting of bacteria and fungi.

50. The method of claim 27, wherein said first and second cell preparations contain cells of the same genus and species.

51. The method of claim 27, wherein said first and second cell preparations contain cells that differ in one or more genes.

52. The method of claim 27, wherein said detecting is visual.

53. The method of claim 27, wherein said detecting is performed by an instrument.

54. The method of claim 53, wherein said instrument comprises a video camera.

55. The method of claim 27, wherein said detecting is conducted over time.