Method for establishing a standardized detection system for identifying a microorganism

Abstract

The present invention provides the tools and methodologies for establishing a standardized detection system for identifying a microorganism or a specific function in a microorganism by comparing the gene expression patterns in a test cell line.

Description

BACKGROUND OF THE INVENTION

[0001] 1. Field of the Invention

[0002] The invention mainly relates to a method for establishing a standardized detection system for identifying a microorganism.

[0003] 2. Description of the Related Art

[0004] With the development of molecular biology, many methods based on DNA or rDNA sequence analysis are developed for identification of a microorganism (Torriani et al., Differentiation of Lactobacillus plantarum, L. pentosus, and L. paraplantarum by recA Gene Sequence Analysis and Multiplex PCR Assay with recA Gene-Derived Primers. Appl Environ Microbiol. August 2001; 67(8): 3450-3454.). Examples of these methods are (1) randomly amplified polymorphic DNA (RAPD analysis) where a 10-15 bp primer participates for generating a fingerprint of the microorganism to be analyzed (Hayford et al., Use of Conserved Randomly Amplified Polymorphic DNA (RAPD) Fragments and RAPD Pattern for Characterization of Lactobacillus fermentum in Ghanaian Fermented Maize Dough. Appl Environ Microbiol. July 1999; 65(7): 3213-3221); (2) ribotyping through a Southern blot pattern formed on restriction enzymes digested fragments of chromosomal DNA of the microorganism to be identified; (3) pulsed-field electrophoresis (PFGE) providing a specific pattern of genomic DNA of the microorganism to be identified after electrophoresis; and (4) PCR analysis of 16S rRNA or 16S-23S rRNA intergenic spacer region sequence with species-specific primers (Tannock et al., Identification of Lactobacillus Isolates from the Gastrointestinal Tract, Silage, and Yoghurt by 16S-23S rRNA Gene Intergenic Spacer Region Sequence Comparisons. Appl Environ Microbiol. September 1999; 65(9): 4264-4267; Matsuki et al., Distribution of Bifidobacterial Species in Human Intestinal Microflora Examined with 16S rRNA-Gene-Targeted Species-Specific Primers. Appl Environ Microbiol. October 1999; 65(10): 4506-4512; Rossi et al., Genus- and Species-Specific PCR-Based Detection of Dairy Propionibacteria in Environmental Samples by Using Primers Targeted to the Genes Encoding 16S rRNA. Appl Environ Microbiol. September 1999; 65(9): 4241-4244; and Harmsen et al., Extensive Set of 16S rRNA-Based Probes for Detection of Bacteria in Human Feces. Appl Environ Microbiol. June 2002; 68(6): 2982-2990).

SUMMARY OF THE INVENTION

[0005] The invention provides a method for establishing a standardized detection system for identifying a microorganism by comparing the gene expression patterns in a test cell line cultured with and without the microorganism.

[0006] One object of the invention is to provide a method for establishing a standardized detection system for identifying a microorganism, which comprises:

[0007] (i) providing a test cell line;

[0008] (ii) culturing the test cell line with and without the microorganism;

[0009] (iii) profiling the gene expression patterns of the test cell line cultured with and without the microorganism;

[0010] (iv) selecting a group of genes, whose expression in the test cell line cultured without the microorganism is significantly different from that cultured with the microorganism as markers; and

[0011] (v) storing the marker data obtained as the standardized detection system.

[0012] Another object of the invention is to provide a method for identifying an unknown microorganism as a standardized and recognized microorganism, which comprises:

[0013] (a) providing a standardized detection system for a standardized and recognized microorganism, wherein the detection system is prepared by the steps of:

[0014] (i) providing a test cell line;

[0015] (ii) culturing the test cell line with and without the standardized and recognized microorganism;

[0016] (iii) profiling the gene expression patterns of the test cell line cultured with and without the standardized and recognized microorganism;

[0017] (iv) selecting a group of genes, whose expression in the test cell line cultured without the standardized and recognized microorganism is significantly different from that cultured with the standardized and recognized microorganism as markers; and

[0018] (v) storing the marker data obtained as the standardized detection system;

[0019] (b) culturing the test cell line with and without the unknown microorganism;

[0020] (c) profiling the gene expression patterns of the test cell line cultured with and without the unknown microorganism;

[0021] (d) selecting a group of genes, whose expression in the test cell line cultured without the unknown microorganism is significantly different from that cultured with the unknown microorganism as markers;

[0022] (e) comparing the marker data obtained in step (d) with the marker data obtained in step (a), whereby the unknown microorganism is identified as the standardized and recognized microorganism if the marker data obtained in step (d) is similar to the marker data obtained in step (a) within an acceptable level.

[0023] The invention also provides a method for establishing a standardized detection system for detecting a specific function in a microorganism, which comprises:

[0024] (i) providing a test cell line;

[0025] (ii) culturing the test cell line with and without a reference microorganism having a specific function;

[0026] (iii) profiling the gene expression patterns related to the specific function of the test cell line cultured with and without the reference microorganism;

[0027] (iv) selecting a group of genes, whose expression in the test cell line cultured without the reference microorganism is significantly different from that cultured with the reference microorganism as markers; and

[0028] (v) storing the marker data obtained as the standardized detection system.

[0029] In another aspect, the invention provides a method for detecting a test microorganism having a specific function, which comprises:

[0030] (a) providing a standardized detection system for identifying the specific function in a reference microorganism, wherein the detection system is prepared by the steps of:

[0031] (i) providing a test cell line;

[0032] (ii) culturing the test cell line with and without the reference microorganism;

[0033] (iii) profiling the gene expression patterns related to the specific function of the test cell line cultured with and without the reference microorganism;

[0034] (iv) selecting a group of genes, whose expression in the test cell line cultured without the reference microorganism is significantly different from that cultured with the reference microorganism as markers; and

[0035] (v) storing the marker data obtained as the standardized detection system;

[0036] (b) culturing the test cell line with and without the test microorganism;

[0037] (c) profiling the gene expression pattern related to the specific function of the test cell line cultured with and without the test microorganism;

[0038] (d) selecting a group of genes, whose expression in the test cell line cultured without the test microorganism is significantly different from that with the test microorganism as markers;

[0039] (e) comparing the marker data obtained in step (d) with the marker data obtained in step (a), whereby the test microorganism is identified to have the specific function if the marker data obtained in step (d) is similar to the maker data obtained in step (a) within an acceptable level.

DETAILED DESCRIPTION OF THE INVENTION

[0040] The present invention provides a method for establishing a standardized detection system for identifying a microorganism, which comprises:

[0041] (i) providing a test cell line;

[0042] (ii) culturing the test cell line with and without the microorganism;

[0043] (iii) profiling the gene expression patterns of the test cell line cultured with and without the microorganism;

[0044] (iv) selecting a group of genes, whose expression in the test to cell line cultured without the microorganism is significantly different from that cultured with the microorganism as markers; and

[0045] (v) storing the marker data obtained as the standardized detection system.

[0046] As used herein, the term “microorganism” refers to any genus and species of microorganism. In a preferred embodiment of the invention, the microorganism is a bacterium, and in a more preferred embodiment, the microorganism is a lactic acid bacterium.

[0047] The term “test cell line” as used herein refers to a cell line in which the gene expression patterns are profiled in different conditions. The cell line should be co-cultured with the microorganism to be identified. A test cell line group comprising more than one cell line can be used in the invention; wherein the cell lines should be derived from the same species. The use of the test cell line group minimizes cell variability for establishing the standardized detection system according to the invention. Preferably, the test cell line is selected from mammalian cells, and wherein more preferably, from human cells. The combination of the test cell line group depends on the microorganism to be identified. In some embodiments of the invention, the cell line includes liver cells such as Hep G2 cells, blood cells such as HL-60 and Turkat cells, and intestinal epithelium cells such as Caco-2 cells.

[0048] In the step (ii) of the method for establishing a standardized detection system for identifying a microorganism, the test cell line is cultured with and without the microorganism. The condition of each culture manipulation should be substantially equivalent or the same for minimizing experimental errors.

[0049] In the step (iii) of the method for establishing a standardized detection system for identifying a microorganism, the gene expression patterns of the test cell line cultured with and without the microorganism are profiled. The term “gene expression pattern” as used herein refers to a characteristic pattern of gene expression when culturing the test cell line in a given condition. The term “profiling the gene expression patterns” as used herein refers to a way of making unique patterns from the gene expression. The gene expression pattern can be used to distinguish a biological source from the other biological source. In one embodiment of the invention, the gene expression pattern is profiled by determining each gene expression in the test cell line. Normally, multiple assays for profiling are performed to obtain an average value of each gene expression.

[0050] Preferably, the gene expression patterns are conducted in a microarray. As used herein, the term “microarray” refers to a system for detecting multiple oligonucleotide interactions in multiple positions. The microarray is also known as terms “biochip”, “DNA chip” or “gene chip”. In one embodiment of the invention, the microarray comprises a chip including a solid support. The support comprises a plurality of spatially defined addresses and each said address has at least one copy of a single species of oligonucleotide probe attached thereto. When a sample comprising a target oligonucleotide having specific affinity for one of the probe, a specific signal can be detected and quantified by a scanner to give a recognition pattern.

[0051] In the step (iv) of the method for establishing a standardized detection system for identifying a microorganism, a group of genes are selected. The expression of the group of genes in the test cell line cultured without the microorganism is significantly different from that cultured with the microorganism, and therefore, the group of genes are used as markers. The gene expression pattern of the test cell line cultured without the microorganism acts as a baseline set of data by which various other sets of data are compared. The gene expression pattern of the test cell line cultured with the microorganism is compared with the baseline set of data. In one embodiment of the invention, the marker genes are selected to have an expression ratio of the test cell line cultured with the microorganism to that cultured without the microorganism larger than 0.2. Preferably, the ratio is larger than 1.5. Preferably, the expression difference between the marker genes of test, cell line cultured with the microorganism and that cultured without the microorganism is also incorporated into the markers. The difference indicates that the marker genes in the test cell line are up- or down-regulated in response to culturing with and without the microorganism.

[0052] According to the invention, the gene expression patterns when cultured with and without the microorganism in the test cell line are significantly different.

[0053] In the step (v) of the method for establishing a standardized detection system for identifying a microorganism, the marker data obtained in step (iv) is stored as the standardized detection system.

[0054] In one embodiment of the invention, the standardized detection system further comprises: (1) means for data acquisition and analysis; (2) means for database development; (3) means for integration and links; and (4) means for analysis of the resulting database. Preferably, the means are incorporated as a computer for storing the marker data according to the invention and for data analysis.

[0055] Another object of the invention is to provide a method for identifying an unknown microorganism as a standardized and recognized microorganism, which comprises:

[0056] (a) providing a standardized detection system for a standardized and recognized microorganism, wherein the detection system is prepared by the steps of:

[0057] (i) providing a test cell line;

[0058] (ii) culturing the test cell line with and without the standardized and recognized microorganism;

[0059] (iii) profiling the gene expression patterns of the test cell line cultured with and without the standardized and recognized microorganism;

[0060] (iv) selecting a group of genes, whose expression in the test cell line cultured without the standardized and recognized microorganism is significantly different from that cultured with the standardized and recognized microorganism as markers; and

[0061] (v) storing the marker data obtained as the standardized detection system;

[0062] (b) culturing the test cell line with and without the unknown microorganism;

[0063] (c) profiling the gene expression patterns of the test cell line cultured with and without the unknown microorganism;

[0064] (d) selecting a group of genes, whose expression in the test cell line cultured without the unknown microorganism is significantly different from that cultured with the unknown microorganism as markers;

[0065] (e) comparing the marker data obtained in step (d) with the marker data obtained in step (a), whereby the unknown microorganism is identified as the standardized and recognized microorganism if the marker data obtained in step (d) is similar to the marker data obtained in step (a) within an acceptable level.

[0066] As used herein, the term “unknown microorganism” refers to a microorganism to be identified. As used herein, the term “a standardized and recognized microorganism” refers to a microorganism which is well characterized and demonstrates a stable biological response in a particular biosystem. The standardized and recognized microorganism is usually standardized by genetical, chemical or biological tests well known by those skilled in this field and the identification criteria thereof have been set.

[0067] According to the invention, in the step (a), a standardized detection system for a standardized and recognized microorganism is provided and the detection system is prepared as mentioned above.

[0068] In the step (b), the unknown microorganism is co-cultured with and without the test cell line in the detection system. For the accuracy of identification, the culture conditions are substantially the same with the culture conditions in preparing the detection system.

[0069] In the step (c), the gene expression patterns of the test cell line cultured with and without the unknown microorganism are profiled. Preferably, a microarray can be used in preparing the detection system. Generally, multiple assays for the profiling are performed to obtain an average value of each gene expression. In one embodiment of the invention, the gene expression pattern of the test cell line cultured without the unknown microorganism is the gene expression pattern of the test cell line cultured without the standardized and recognized microorganism for preparing the detection system.

[0070] In the step (d) of the method for identifying an unknown microorganism as a standardized and recognized microorganism, a group of genes are selected as markers. The gene expression of the marker genes in the test cell line cultured without the unknown microorganism is significantly different from that cultured with the microorganism. The gene expression pattern of the test cell line cultured without the unknown microorganism acts as a baseline set of data. The gene expression pattern of the test cell line cultured with the unknown microorganism is compared with the baseline set of data.

[0071] In the step (e), a group of genes obtained in step (d) are selected as markers and compared with the marker data obtained in step (a), whereby the unknown microorganism is identified as the standardized and recognized microorganism if the marker data obtained in step (d) is similar to the marker data obtained in step (a) within an acceptable level. The difference of the gene expression can also be incorporated for comparison.

[0072] According to the invention, the detection system and the method for identifying an unknown microorganism can be applied in quality control when manufacturing a microorganism composition. The detection system provides a qualified and quantified index for checking or identifying the microorganism in the stocks or products.

[0073] The invention also provides a method for establishing a standardized detection system for detecting a specific function in a microorganism, which comprises:

[0074] (i) providing a test cell line;

[0075] (ii) culturing the test cell line with and without a reference microorganism having a specific function;

[0076] (iii) profiling the gene expression patterns related to the specific function of the test cell line cultured with and without the reference microorganism;

[0077] (iv) selecting a group of genes, whose expression in the test cell line cultured without the reference microorganism is significantly different from that cultured with the reference microorganism as markers; and

[0078] (v) storing the marker data obtained as the standardized detection system.

[0079] According to the invention, the method for establishing a standardized detection system for detecting a specific function in a microorganism, which is generally used for screening the microorganism having a specific function, is similar to the method for establishing a standardized detection system for identifying a microorganism as mentioned above.

[0080] As used herein, the term “a specific function” refers to a distinct biological effect peculiar to a microorganism on a given biosystem. The specific function includes, but is not limited to, an ability to changing physiological condition of a subject administrated with the microorganism or pharmaceutical effects of a disease or a syndrome.

[0081] As used herein, the term “reference microorganism” refers to a microorganism which is well characterized to have a specific function. The reference microorganism which is similar to the standardized and recognized microorganism as mentioned above is usually standardized by genetical, chemical or biological tests well known by those skilled in this field and the identifying criteria thereof have been set.

[0082] Particularly, in the step (iii) of the method for establishing a standardized detection system for detecting a specific function, in a microorganism, the gene expression patterns related to the specific function of the test cell line cultured with and without the reference microorganism are profiled. In one embodiment of the invention, the gene expression pattern is profiled by determining each gene expression found to be directly or indirectly related to the specific function in the test cell line. The genes found to be directly or indirectly related to the specific function include, but are not limited to, genes encoding proteins participating the machanism of the specific function, genes encoding regulatory factors of the production of these proteins, genes encoding proteins for transportion, or genes encoding cytokines for controlling the specific function.

[0083] In another aspect, the invention provides a method for detecting a test microorganism having a specific function, which comprises:

[0084] (a) providing a standardized detection system for identifying the specific function in a reference microorganism, wherein the detection system is prepared by the steps of:

[0085] (i) providing a test cell line;

[0086] (ii) culturing the test cell line with and without the reference microorganism;

[0087] (iii) profiling the gene expression patterns related to the specific function of the test cell line cultured with and without the reference microorganism;

[0088] (iv) selecting a group of genes, whose expression in the test cell line cultured without the reference microorganism is significantly different from that cultured with the reference microorganism as markers; and

[0089] (v) storing the marker data obtained as the standardized detection system;

[0090] (b) culturing the test cell line with and without the test microorganism;

[0091] (c) profiling the gene expression pattern related to the specific function of the test cell line cultured with and without the test microorganism;

[0092] (d) selecting a group of genes, whose expression in the test cell line cultured without the test microorganism is significantly different from that with the test microorganism as markers;

[0093] (e) comparing the marker data obtained in step (d) with the marker data obtained in step (a), whereby the test microorganism is identified to have the specific function if the marker data obtained in step (d) is similar to the maker data obtained in step (a) within an acceptable level.

[0094] According to the invention, the method for detecting a test microorganism having a specific function is similar to the method for identifying an unknown microorganism as a standardized and recognized microorganism as mentioned above. Particularly, as used herein, the term “test microorganism” refers to a microorganism to be screened to have the specific function.

[0095] The following Examples are given for the purpose of illustration only and are not intended to limit the scope of the present invention.

EXAMPLE 1

A Standardized Detection System for Identifying a Lactic Acid Bacterium

[0096] Test cell line and co-culturing with and without lactic acid bacteria: Hep G2 cell line was taken as the test cell line. The cells were refreshed by adding a fresh medium and cultured for 16 hours. The cells were divided into two groups, and wherein one was for the culture with the microorganism and the other was for the culture without the microorganism. When the cell concentration reached 1×107/10 mL, 1×107 lactic acid bacteria #7 (Lactobacillus plantarum), #73 (Lactobacillus gasseri) or #74 (Lactobacillus gasseri) were then added into the cells and co-cultured for 24 hours. The cells in the culture without the microorganism cells were cultured as well.

[0097] Profiling the gene expression patterns: The total RNAs were extracted from the test cell line cultured with and without the microorganism.

[0098] Eight μL of the RNA and 2 μL oligo poly-dT (12-18 mer, 0.1 μg/L) were well mixed and, kept at 70° C. for 10 minutes and then were cooled with ice for 2 minutes. The RNAs obtained were mixed with reverse transcription labeling mixture in dark and 3 μL Cy5-dUTP (1 mM), 2 μL SuperScript II (200 U/μL), and Rnasin (1 μL). The mixture was incubated at 42° C. for 2 hours for reverse transcription, and the reaction was terminated by adding 1.5 μL 20 mM EDTA. The RNAs were degraded by adding 1.5 μL 500 mM NaOH and heated for 10 minutes. The NaOH retained in the sample was then neutralized by adding 1.5 μL 500 mM HCl, and excess Cy5 was removed by spinning in ProbeQuant G-50 Micro Column. All the DNAs labeled with Cy5 were stored at −20° C.

[0099] Hundreds of genes chosen were amplified through polymerase chain reaction and then dissolved in spotting buffer for spotting on a chip. After denaturing at 95° C. for 3 minutes, the DNAs were attached to a glass carrier by ultra-violet rays using a spotting machine to form the chip for detection of gene expression.

[0100] The chip with the DNAs of chosen gene was pretreated with n-methyl-pyrilidinone/succinic anhydride/sodium borate and 5×SSC/0.1% SDS/1% BSA to eliminate nonspecific hybridization by blocking active groups on the glass carrier. The DNAs obtained from the test cell line labeled with Cy5 in hybridization buffer (50% formamide/0.2% SDS/10×SSC) were denatured at 95° C. for 5 minutes and cooled, and then loaded to the chip. Hybridizations were performed at 42° C. for 18 hours. Three solutions of 1×SSC/0.1% SDS, 0.1×SSC/0.1% SDS and 0.1×SSC were used to wash the samples and to remove the nucleotides which were not hybridized.

[0101] Gene expressions were detected and analyzed by scanning the chips using a fluorescence scanner and further quantified to obtain expression values. The fluorescent signals were quantified with GenePix™ Pro 3.0 (Axon Instruments, Inc.) and the backgrounds were then deduced, and then divided by the GAPDH (glyceraldehydes phosphate dehydrogenase, a house keeping gene). Mouse cDNA (ATBS) and plants DNA (RbCL) were both chosen as negative control.

[0102] Each of the expression values was represented in a mean of duplicate.

[0103] The gene expression profiles of the Hep G2 cell cultured with and without the lactic acid bacteria #7 (Lactobacillus plantarum), #73 (Lactobacillus gasseri), or #74 (Lactobacillus gasseri) were then obtained and listed in Table 1.

TABLE 1
			Cultured	Cultured	Cultured
Gene No.	Gene name	Cell only	with #7	with #73	with #74
TL00356	Serine/threonine kinase 4	0.195	0.251	0.103	0.110
TL00348	Carnitine palmitoyltransferase I,	0.195	0.257	0.090	0.102
	liver
TL00340	Branched chain alpha-ketoacid	0.188	0.248	0.100	0.110
	dehydrogenase kinase
TL00334	Serine/threonine kinase 10	0.195	0.270	0.103	0.108
TL00578	FGF2	0.693	0.420	0.824	0.856
TL00556	Small inducible cytokine A4	0.195	0.238	0.105	0.121
	(homologous to mouse Mip-1b)
TL00555	C—C CHEMOKINE	0.188	0.235	0.097	0.101
	RECEPTOR TYPE 2
TL00554	Early growth response protein 1	0.201	0.266	0.115	0.114
TL00553	Small inducible cytokine A2	0.201	0.260	0.103	0.106
	(monocyte chemotactic protein
	1,
TL00552	Interleukin 10 receptor	0.396	0.323	0.258	0.104
TL00551	Transforming growth factor,	0.218	0.273	0.139	0.120
	beta receptor II (70-80 kD)
TL00549	hepatocyte growth factor	0.215	0.254	0.106	0.108
	activator inh
TL00545	Guanylate binding protein 1,	0.201	0.229	0.092	0.106
	interferon-inducible, 67 kD
TL00544	interleukin-13 receptor mRNA,	0.224	0.260	0.097	0.121
	complete cds
TL00593	IL-16	0.231	0.254	0.095	0.104
TL00592	TGFb receptor associate protein	0.254	0.273	0.102	0.127
	1
TL00591	Transforming growth factor,	0.231	0.241	0.097	0.108
	beta 3
TL00587	EGF	0.224	0.257	0.097	0.097
TL00584	Interleukin 4 receptor	0.281	0.288	0.161	0.129
TL00583	Interleukin 7	0.208	0.273	0.098	0.118
TL00582	Lymphotoxin alpha (formerly	0.356	0.301	0.203	0.150
	tumor necrosis factor beta)
TL00581	Annexin V (lipocortin V;	0.508	0.539	0.476	0.243
	endonexin II)
TL00579	TGF-beta superfamily protein,	0.373	0.408	0.361	0.254
	complete
TL00578	FGF2	1.086	1.022	1.039	0.958
TL00438	serine/threonine protein kinase	0.221	0.357	0.160	0.127
	KKIALRE
TL00437	thymidine kinase 1, soluble	0.323	0.345	0.211	0.260
TL00428	Homo sapiens protein kinase A	0.218	0.301	0.132	0.178
	binding protein AKAP110
	mRNA, complete cds
TL00417	MAP/ERK kinase kinase 3	0.756	1.179	0.776	0.956
TL00594	IL-1 receptor type 1	0.429	0.495	0.339	0.444
TL00918	IL-1β□	0.201	0.292	0.106	0.101
TL00915	INF-β	0.201	0.304	0.115	0.102
TL00610	CD30	0.188	0.238	0.097	0.102
TL00608	HGF	0.188	0.235	0.100	0.097
TL00603	IL-15	0.188	0.229	0.095	0.097
TL00601	IFN-γ	0.201	0.245	0.102	0.104
TL00598	IL-5 receptor α	0.198	0.260	0.113	0.114
TL00575	GAMMA-INTERFERON-	0.505	0.470	0.373	0.332
	INDUCIBLE PROTEIN IP-30
	PRECURSOR
TL00574	metallothionein I-B gene	0.287	0.357	0.339	0.435
TL00573	INTERFERON-INDUCIBLE	0.234	0.273	0.148	0.135
	PROTEIN 9-27
TL00571	Interferon regulatory factor 5	0.238	0.273	0.103	0.099
TL00564	Fibroblast growth factor 7	0.231	0.226	0.100	0.095
	(keratinocyte growth factor)
TL00563	Interferon (alpha, beta and	0.264	0.279	0.126	0.125
	omega) receptor 2
TL00561	Interleukin 2 receptor gamma	0.224	0.245	0.103	0.104
	chain
TL00560	INTERFERON-ALPHA/BETA	0.205	0.226	0.094	0.099
	RECEPTOR ALPHA CHAIN
	PRECURSOR
TL00559	Interleukin 6 (B cell stimulatory	0.205	0.251	0.100	0.101
	factor 2)
TL00558	Connective tissue growth factor	0.221	0.273	0.161	0.190
TL00557	INTERFERON-GAMMA	0.195	0.273	0.160	0.165
	RECEPTOR ALPHA CHAIN
	PRECURSOR
TL00596	metallothionein-III	1.327	1.232	1.152	1.281
TL00788	Signal transducer and activator	0.198	0.276	0.108	0.121
	of transcription 3 (acute-ph
TL00775	Angiopoietin-1	0.182	0.241	0.095	0.101
TL00765	Interleukin 6 signal transducer	0.198	0.260	0.110	0.118
	(gp130, oncostatin M receptor)
TL00762	nitric oxide synthase 3	0.201	0.276	0.108	0.118
	(endothelial cell)
TL00798	Superoxide dismutase 2,	0.185	0.248	0.100	0.104
	mitochondrial
TL00668	growth associated protein43	0.201	0.257	0.105	0.102
TL00666	stat2(Signal transducer and	0.191	0.266	0.106	0.106
	activator of transcription 2)
TL00655	telomeric DNA sequence	0.218	0.288	0.176	0.178
TL00650	p53-associated gene	0.591	0.536	0.360	0.482
TL00635	Colony-stimulating factor 1 (M-	0.188	0.229	0.100	0.099
	CSF)
TL00632	N-myc	0.205	0.248	0.108	0.110
TL00631	c-src tyrosine kinase	0.195	0.257	0.108	0.106
TL00630	myc proto-oncogene (c-myc)	0.231	0.313	0.121	0.123
TL00626	Transforming growth factor,	0.218	0.260	0.102	0.108
	beta receptor III (betaglycan, 3
TL00625	stat-like protein (Fe65) mRNA,	0.274	0.295	0.129	0.125
	complete cds
TL00535	Proteasome 26S subunit,	0.254	0.285	0.116	0.110
	ATPase, 3
TL00534	calpamodulin mRNA	0.238	0.238	0.097	0.099
TL00508	Homo sapiens apoptotic	0.208	0.219	0.095	0.099
	protease activating factor 1
	(Apaf-1)
TL00495	UBIQUITIN CARBOXYL-	0.244	0.238	0.103	0.102
	TERMINAL HYDROLASE
	ISOZYME L1
TL00484	mitochondrial processing	0.297	0.323	0.263	0.233
	peptidase beta-subunit
TL00459	protease inhibitor 12 (PI12;	0.205	0.238	0.118	0.112
	neuroserpin)
TL00458	Ubiquitin-conjugating enzyme	0.221	0.241	0.132	0.152
	E2A (RAD6 homolog)
TL00457	ubiquitin conjugating enzyme	0.188	0.226	0.098	0.101
	(UbcH8) mRNA, comp
TL00456	Ubiquitin-conjugating enzyme	0.221	0.295	0.495	0.457
	E2B (RAD6 homolog)
TL01081	Protein kinase clk1	0.191	0.266	0.103	0.101
TL01071	Interferon-gamma receptor alpha	0.191	0.248	0.100	0.104
	chain precursor
TL01068	Beta-2 adrenergic receptor	0.195	0.241	0.097	0.099
TL01066	apoptotic cysteine protease	0.198	0.254	0.106	0.112
	mch4
TL00064	RAC-ALPHA	0.191	0.245	0.100	0.106
	SERINE/THREONINE
	KINASE
TL00060	Deoxyguanosine kinase	0.356	0.345	0.266	0.249
TL00059	Choline kinase	0.201	0.251	0.121	0.133
TL00054	NUCLEOSIDE	0.426	0.502	0.216	0.214
	DIPHOSPHATE KINASE A
TL00047	Glycerol kinase	0.393	0.339	0.202	0.235
TL00046	flavin containing	0.188	0.238	0.100	0.104
	monooxygenase 5 (FMO5)
	mRNA.
TL00036	Hexokinase 1	0.449	0.458	0.410	0.178
TL00031	Adenosine kinase	0.244	0.292	0.147	0.214
TL00028	Human 53K isoform of Type II	1.106	0.950	0.253	0.231
	phosphatidylinositol-4-
	phosphate 5-kinase (PIPK)
	mRNA, complete cds
TL00027	Cyclin-dependent kinase 2	0.201	0.226	0.102	0.102
TL00022	TYROSINE-PROTEIN	0.475	0.442	0.340	0.315
	KINASE CSK
TL00018	Pyruvate kinase, liver	0.218	0.235	0.115	0.112
TL00015	CDC28 protein kinase 2 (CKS2)	0.419	0.483	0.406	0.455
	mRNA.
TL00900	mitochondrial transcription	0.264	0.298	0.103	0.101
	termination factor
TL00894	signal transducer and activator	0.429	1.492	1.187	0.243
	of transcription 6, interleukin-4
	induced
TL00888	Transcription factor AP-4	0.815	0.840	0.956	0.913
	(activating enhancer-binding
	prote
TL00885	STAT-1alpha/beta	0.231	0.332	0.118	0.097
TL00737	c-rel	0.195	0.248	0.111	0.104
TL00873	transcription elongation factor	0.191	0.232	0.123	0.120
	S-II, hS-II-T
TL00801	DNA repair helicase ERCC3	0.627	0.580	0.539	0.609
TL00570	Bone morphogenetic protein	0.191	0.260	0.102	0.104
	receptor, type II (serine/threoni
TL00569	ESTs, Highly similar to	0.188	0.257	0.098	0.104
	INTERFERON-INDUCED
	GUANYLATE-BINDIN
TL00568	ESTs, Weakly similar to type 1	0.185	0.257	0.100	0.106
	procollagen C-proteinase enha
TL00567	Complement component 4-	0.198	0.257	0.113	0.129
	binding protein, alpha
TL00194	Protein-tyrosine kinase 7	0.215	0.257	0.131	0.125
TL00182	TYROSINE-PROTEIN	0.195	0.248	0.102	0.106
	KINASE SYK
TL00177	Human activated p21cdc42Hs	0.191	0.254	0.111	0.114
	kinase (ack) mRNA, complete
	cds
TL00165	protein serine/threonine kinase	0.198	0.235	0.108	0.112
	stk2
TL00161	pyruvate dehydrogenase kinase	0.191	0.238	0.102	0.112
	isoenzyme 3 (PDK3) mRNA,
	complete cds
TL00159	Deoxycytidine kinase	0.195	0.270	0.103	0.106
TL00150	Lymphocyte-specific protein	0.185	0.245	0.100	0.099
	tyrosine kinase
TL00146	Human putative serine/threonine	0.185	0.241	0.097	0.101
	protein kinase PRK (prk)
	mRNA, complete cds
TL00140	Human integrin-linked kinase	0.191	0.210	0.092	0.099
	(ILK) mRNA, complete cds
TL00136	stress-activated protein kinase 3	0.201	0.235	0.095	0.099
	(SAPK3) mRNA.
TL00132	Human diacylglycerol kinase	0.218	0.251	0.121	0.110
	zeta mRNA, complete cds
TL00119	Urokinase-type plasminogen	0.238	0.270	0.106	0.106
	activator
TL00109	RIBOSOMAL PROTEIN, S6	0.215	0.229	0.097	0.104
	KINASE
TL00098	Human adenylate kinase 2	0.274	0.357	0.145	0.118
	(adk2) mRNA, complete cds
TL00096	Protein kinase C, alpha	0.248	0.245	0.105	0.099
TL00084	PROTO-ONCOGENE	0.264	0.276	0.124	0.116
	TYROSINE-PROTEIN
	KINASE FES/FPS
TL00082	Human mitochondrial creatine	0.231	0.310	0.126	0.095
	kinase (CKMT) gene, complete
	cds
TL00079	src-like kinase (slk) mRNA,	0.201	0.219	0.111	0.114
	complete cds.
TL00071	Hemopoietic cell kinase	0.182	0.213	0.092	0.093
TL00070	BMK1 alpha kinase mRNA,	0.178	0.210	0.103	0.101
	complete cds
TL00602	PDGF associate protein	0.191	0.248	0.106	0.114
TL00599	HGF activator	0.191	0.238	0.108	0.104
TL00597	LIF	0.422	0.398	0.316	0.330
TL00595	ICSBP1	0.195	0.254	0.100	0.099
TL00672	stat5a(Signal transducer and	0.182	0.232	0.100	0.106
	activator of transcription 5A)
TL00323	MAP kinase-interacting	0.191	0.282	0.116	0.104
	serine/threonine kinase 1
TL00656	Tumor protein p53	0.195	0.238	0.126	0.123
TL00319	Protein kinase mitogen-activated	0.198	0.248	0.134	0.127
	7 (MAP kinase)
TL00309	Serine/threonine kinase 2	0.234	0.270	0.147	0.135
TL00307	Protein kinase mitogen-activated	0.182	0.226	0.097	0.099
	8 (MAP kinase)
TL00302	Fms-related tyrosine kinase 3	0.175	0.223	0.098	0.101
TL00299	Leukocyte tyrosine kinase	0.185	0.223	0.095	0.101
TL00290	Mevalonate kinase	0.185	0.204	0.094	0.104
TL00287	Human protein tyrosine kinase	0.353	0.282	0.182	0.190
	mRNA, complete cds
TL00280	protein kinase, mitogen-	0.188	0.216	0.092	0.101
	activated 4 (MAP kinase 4;
	p63)(PRKM4) mRNA.
TL00278	focal adhesion kinase (FAK)	0.205	0.219	0.100	0.106
	mRNA, complete cds
TL00276	Creatine kinase B	0.234	0.257	0.134	0.148
TL00263	Neurotrophic tyrosine kinase,	0.221	0.229	0.103	0.101
	receptor, type 3 (TrkC)
TL00244	Glucokinase (hexokinase 4,	0.218	0.229	0.100	0.102
	maturity onset diabetes of the
	young 2)
TL00240	H. sapiens mRNA for protein	0.277	0.276	0.142	0.127
	kinase CK1
TL00239	H. sapiens mRNA for FAST	0.208	0.248	0.110	0.097
	kinase
TL00236	Human kinase (TTK) mRNA,	0.211	0.263	0.126	0.108
	complete cds
TL00233	PHOSPHATIDYLINOSITOL	0.208	0.219	0.135	0.125
	4-KINASE ALPHA
TL00231	MAP kinase activated protein	0.482	0.458	0.400	0.380
	kinase
TL00414	Cyclin-dependent kinase	0.205	0.254	0.150	0.129
	inhibitor 3 (CDK2-associated
	dual specificity phosphatase)
TL00405	Cytokine suppressive anti-	0.201	0.245	0.103	0.108
	inflammatory drug binding
	protein 1 (p38 MAP kinase)
TL00402	Phosphprylase kinase, beta	0.198	0.248	0.106	0.110
TL00392	Tyrosine kinase 2	0.224	0.260	0.111	0.116
TL00379	pyruvate dehydrogenase kinase,	0.251	0.248	0.118	0.118
	isoenzyme 4
TL00376	phosphorylase kinase, alpha 2	0.221	0.226	0.105	0.104
	(liver), glycogen storage disease
	IX
TL00373	pyruvate dehydrogenase kinase,	0.228	0.248	0.108	0.110
	isoenzyme 3
TL00371	protein tyrosine kinase 6	0.234	0.235	0.111	0.102
TL00370	serine/threonine kinase 9	0.221	0.254	0.113	0.099
TL00367	Mitogen-activated protein	0.205	0.257	0.118	0.101
	kinase kinase kinase kinase 5
TL00365	serine/threonine protein-kinase	0.201	0.245	0.119	0.118
TL00360	Pyridoxal (pyridoxine, vitamin	0.175	0.226	0.108	0.101
	B6) kinase
TL00761	Tumor necrosis factor receptor 2	0.208	0.273	0.126	0.106
TL00750	IkB kinase beta subunit mRNA	0.370	0.307	0.206	0.156
TL00725	Caspase-4 (Ich-2 protease	0.238	0.273	0.140	0.125
	precursor)
TL00723	Caspase-9 (Human cysteine	0.221	0.248	0.110	0.102
	protease ice-lap6)
TL00717	Phospholipase C	0.492	0.498	0.318	0.351
TL00715	Caspase-8 (Apoptotic cysteine	0.261	0.257	0.106	0.106
	protease mch5 (mach-alpha-1))
TL00707	Bcl2, p53 binding protein	0.248	0.248	0.123	0.112
	Bbp/53BP2 (BBP/53BP2)
	mRNA,
TL00687	Growth associated protein 43	0.241	0.235	0.115	0.101
TL01032	Glutathione S-transferase M1	0.304	0.292	0.255	0.214
TL01020	Protein kinase clk3	0.696	0.577	0.224	0.184
TL00449	serine/threonine kinase 11	0.198	0.241	0.123	0.116
	(Peutz-Jeghers syndrome
TL00445	syntaxin 8	0.409	0.329	0.261	0.218
TL00633	Breast cancer 1, early onset	0.221	0.257	0.132	0.129
	(BRCA1) mRNA
TL00274	tyrosine kinase receptor (axl)	0.205	0.248	0.108	0.114
	mRNA, complete cds
TL00272	JNK ACTIVATING KINASE 1	0.215	0.248	0.108	0.116
TL01038	Glutathione S-transferase 12	0.228	0.273	0.121	0.108
	(microsomal)
TL01027	Tumor necrosis factor-inducible	0.238	0.254	0.111	0.101
	protein TSG-6 precursor
TL01015	Insulin-like growth factor I	0.234	0.238	0.108	0.106
	receptor precursor
TL00999	Estrogen sulfotransferase (ste)	0.228	0.226	0.106	0.106
TL00998	Monocyte chemotactic protein 1	0.248	0.245	0.118	0.099
TL00991	Leukocyte adhesion protein beta	0.271	0.270	0.137	0.110
	subunit
TL00977	T-cell surface glycoprotein CD	0.218	0.241	0.121	0.116
	4, p55
TL00965	voltage-gated calcium channel	0.191	0.245	0.111	0.097
	beta subunit
TL00793	Topoisomerase (DNA) II beta	0.182	0.219	0.110	0.108
	(180 kD)
TL00705	Cyclin-dependent kinase	0.198	0.245	0.106	0.108
	inhibitor 1C (p57, Kip2)
TL00662	K-RAS	0.208	0.245	0.118	0.114
TL00653	Rb	0.201	0.251	0.111	0.102
TL00641	GTPase-activating protein ras	0.231	0.251	0.134	0.129
	p21 (RASA)
TL00606	IGF binding protein 1	0.360	0.404	0.361	0.292
TL00550	IL-13Ra	0.224	0.251	0.105	0.108
TL00548	vascular endothelial growth	0.218	0.235	0.100	0.102
	factor related protein vrp
	(VEGF-C)
TL00547	transcriptional corepressor	0.231	0.248	0.126	0.120
	hKAP1/TIF1B mRNA,
	complete
TL00546	fibroblast growth factor	0.215	0.226	0.102	0.101
	homologous factor 1 (FHF-1) m
TL00543	FGF1	0.205	0.238	0.111	0.099
TL00542	vascular endothelial growth	0.185	0.229	0.106	0.101
	factor related protein VRP
TL00541	Nerve growth factor receptor	0.182	0.229	0.105	0.099
TL00742	bcl-xL mRNA.	0.211	0.254	0.165	0.156
TL00736	Ros	0.188	0.238	0.105	0.097
TL00711	Bcl-2 binding component 6	0.198	0.254	0.129	0.108
	(bbc6) mRNA, complete cds.
TL00707	Bcl2, p53 binding protein	0.224	0.251	0.119	0.102
	Bbp/53BP2 (BBP/53BP2)
	mRNA,
TL00589	sis, PDGF B chain	0.231	0.260	0.124	0.104
TL00588	Placental growth factor (P1GF)	0.254	0.273	0.126	0.127
TL00586	Humig mRNA	0.238	0.260	0.106	0.101
TL00585	CD27L RECEPTOR	0.248	0.266	0.126	0.110
	PRECURSOR
TL00580	B-cell translocation gene 1, anti-	0.238	0.238	0.124	0.108
	proliferative
TL00577	retinoic acid- and interferon-	0.221	0.235	0.111	0.099
	inducible 58K protein RI
TL00576	EBI1-ligand chemokine,	0.195	0.235	0.108	0.095
	complete cds
TL00572	eIF-1A, Y isoform (EIF1AY)	0.215	0.254	0.152	0.192
	mRNA, complete cds
	GAPDH	1.000	1.000	1.000	1.000
	b-actin	0.333	0.455	0.340	0.389
TL00751	Caspase-1	0.195	0.241	0.106	0.101
TL00566	Homo sapiens F1F0-type ATP	0.459	0.527	0.632	0.630
	synthase subunit g mRNA,
	complete
TL00613	NEU differentiation factor	0.221	0.232	0.116	0.104
TL00612	IRF-1	0.218	0.235	0.108	0.099
TL00611	SDF-1b	0.231	0.226	0.116	0.110
TL00609	ALK-1	0.215	0.235	0.118	0.104
TL00607	IL-12 bchain	0.231	0.260	0.124	0.110
TL00605	EGR-1	0.188	0.238	0.124	0.104
TL00604	MGDF	0.208	0.263	0.148	0.120

[0104] Selecting marker genes: A group of genes having the expression ratio in Hep G2 cultured with lactic acid bacteria #7, #73 or #74 to that cultured without the bacteria larger than 1.5 were selected. The results were shown in Table 2:

TABLE 2
Gene No.	#7/cell	cell/#7	Selected	#73/cell	cell/#73	Selected	#74/cell	cell/#74	Selected
TL00356	1.288	0.776		0.530	1.886	YES	0.565	1.769	YES
TL00348	1.32	0.758		0.464	2.156	YES	0.526	1.900	YES
TL00340	1.316	0.76		0.532	1.881	YES	0.585	1.709	YES
TL00334	1.385	0.722		0.530	1.886	YES	0.555	1.800	YES
TL00578	0.606	1.65	YES	1.189	0.841		1.235	0.810
TL00556	1.224	0.817		0.538	1.857	YES	0.624	1.603	YES
TL00555	1.25	0.8		0.514	1.944	YES	0.535	1.871	YES
TL00554	1.324	0.756		0.569	1.758	YES	0.566	1.768	YES
TL00553	1.292	0.774		0.513	1.950	YES	0.528	1.895	YES
TL00552	0.815	1.227		0.652	1.535	YES	0.264	3.795	YES
TL00551	1.252	0.799		0.637	1.570	YES	0.549	1.822	YES
TL00549	1.184	0.845		0.496	2.015	YES	0.504	1.983	YES
TL00545	1.137	0.88		0.457	2.190	YES	0.528	1.895	YES
TL00544	1.159	0.863		0.431	2.319	YES	0.541	1.848	YES
TL00593	1.099	0.91		0.412	2.428	YES	0.452	2.214	YES
TL00592	1.073	0.932		0.400	2.501	YES	0.500	1.999	YES
TL00591	1.045	0.957		0.419	2.387	YES	0.468	2.136	YES
TL00587	1.145	0.873		0.431	2.319	YES	0.431	2.319	YES
TL00584	1.028	0.973		0.575	1.739	YES	0.460	2.174	YES
TL00583	1.312	0.762		0.473	2.113	YES	0.566	1.767	YES
TL00582	0.844	1.184		0.570	1.754	YES	0.421	2.378	YES
TL00581	1.061	0.943		0.936	1.068		0.478	2.093	YES
TL00579	1.093	0.915		0.969	1.032		0.682	1.467
TL00578	0.941	1.062		0.957	1.045		0.883	1.133
TL00438	1.616	0.619	YES	0.722	1.385		0.575	1.739	YES
TL00437	1.066	0.938		0.653	1.531	YES	0.804	1.244
TL00428	1.382	0.724		0.607	1.647	YES	0.819	1.221
TL00417	1.56	0.641	YES	1.027	0.974		1.265	0.790
TL00594	1.154	0.866		0.789	1.267		1.035	0.966
TL00918	1.448	0.691		0.529	1.891	YES	0.500	2.002	YES
TL00915	1.51	0.662	YES	0.569	1.758	YES	0.509	1.965	YES
TL00610	1.266	0.79		0.514	1.944	YES	0.545	1.836	YES
TL00608	1.25	0.8		0.532	1.881	YES	0.514	1.944	YES
TL00603	1.216	0.822		0.506	1.977	YES	0.514	1.944	YES
TL00601	1.215	0.823		0.505	1.981	YES	0.518	1.929	YES
TL00598	1.314	0.761		0.570	1.754	YES	0.575	1.739	YES
TL00575	0.931	1.074		0.738	1.355		0.658	1.521	YES
TL00574	1.245	0.803		1.180	0.848		1.513	0.661	YES
TL00573	1.164	0.859		0.633	1.579	YES	0.575	1.739	YES
TL00571	1.148	0.871		0.434	2.302	YES	0.415	2.408	YES
TL00564	0.977	1.024		0.433	2.310	YES	0.411	2.435	YES
TL00563	1.057	0.946		0.476	2.099	YES	0.474	2.108	YES
TL00561	1.09	0.918		0.460	2.174	YES	0.465	2.150	YES
TL00560	1.103	0.907		0.457	2.187	YES	0.482	2.074	YES
TL00559	1.226	0.816		0.489	2.046	YES	0.491	2.035	YES
TL00558	1.233	0.811		0.729	1.371		0.858	1.165
TL00557	1.401	0.714		0.820	1.219		0.848	1.180
TL00596	0.929	1.077		0.868	1.152		0.965	1.036
TL00788	1.393	0.718		0.546	1.832	YES	0.613	1.631	YES
TL00775	1.33	0.752		0.524	1.907	YES	0.554	1.805	YES
TL00765	1.314	0.761		0.554	1.805	YES	0.594	1.683	YES
TL00762	1.37	0.73		0.537	1.863	YES	0.584	1.711	YES
TL00798	1.34	0.746		0.541	1.848	YES	0.565	1.771	YES
TL00668	1.277	0.783		0.521	1.920	YES	0.509	1.965	YES
TL00666	1.392	0.718		0.556	1.798	YES	0.555	1.801	YES
TL00655	1.324	0.755		0.807	1.239		0.819	1.221
TL00650	0.907	1.102		0.609	1.642	YES	0.816	1.226
TL00635	1.216	0.822		0.532	1.881	YES	0.525	1.907	YES
TL00632	1.21	0.826		0.528	1.894	YES	0.538	1.859	YES
TL00631	1.32	0.758		0.555	1.802	YES	0.546	1.832	YES
TL00630	1.357	0.737		0.524	1.910	YES	0.534	1.873	YES
TL00626	1.194	0.837		0.466	2.144	YES	0.497	2.014	YES
TL00625	1.076	0.93		0.471	2.123	YES	0.457	2.187	YES
TL00535	1.123	0.891		0.457	2.188	YES	0.433	2.309	YES
TL00534	1.003	0.997		0.407	2.455	YES	0.415	2.408	YES
TL00508	1.055	0.948		0.458	2.185	YES	0.475	2.107	YES
TL00495	0.976	1.025		0.423	2.366	YES	0.420	2.383	YES
TL00484	1.087	0.92		0.885	1.130		0.786	1.273
TL00459	1.164	0.859		0.575	1.738	YES	0.547	1.828	YES
TL00458	1.092	0.916		0.598	1.672	YES	0.687	1.457
TL00457	1.2	0.833		0.523	1.912	YES	0.535	1.871	YES
TL00456	1.333	0.75		2.239	0.447	YES	2.068	0.484	YES
TL01081	1.392	0.718		0.539	1.854	YES	0.525	1.903	YES
TL01071	1.294	0.773		0.522	1.914	YES	0.545	1.834	YES
TL01068	1.24	0.807		0.497	2.012	YES	0.507	1.973	YES
TL01066	1.282	0.78		0.538	1.860	YES	0.565	1.769	YES
TL00064	1.277	0.783		0.522	1.914	YES	0.555	1.801	YES
TL00060	0.967	1.034		0.747	1.339		0.697	1.434
TL00059	1.246	0.803		0.601	1.664	YES	0.660	1.516	YES
TL00054	1.178	0.849		0.508	1.970	YES	0.504	1.986	YES
TL00047	0.862	1.16		0.513	1.948	YES	0.599	1.669	YES
TL00046	1.266	0.79		0.532	1.881	YES	0.555	1.803	YES
TL00036	1.02	0.981		0.913	1.096		0.397	2.516	YES
TL00031	1.194	0.838		0.601	1.664	YES	0.878	1.139
TL00028	0.859	1.164		0.229	4.366	YES	0.209	4.776	YES
TL00027	1.121	0.892		0.505	1.981	YES	0.509	1.965	YES
TL00022	0.93	1.075		0.716	1.396		0.663	1.509	YES
TL00018	1.079	0.926		0.526	1.902	YES	0.514	1.946	YES
TL00015	1.152	0.868		0.970	1.031		1.087	0.920
TL00900	1.128	0.887		0.391	2.558	YES	0.381	2.625	YES
TL00894	3.478	0.288	YES	2.767	0.361	YES	0.566	1.766	YES
TL00888	1.031	0.97		1.173	0.852		1.120	0.893
TL00885	1.438	0.695		0.510	1.962	YES	0.419	2.387	YES
TL00737	1.272	0.786		0.572	1.750	YES	0.536	1.866	YES
TL00873	1.212	0.825		0.640	1.562	YES	0.625	1.601	YES
TL00801	0.925	1.081		0.859	1.164		0.971	1.029
TL00570	1.359	0.736		0.531	1.884	YES	0.545	1.834	YES
TL00569	1.366	0.732		0.523	1.912	YES	0.555	1.803	YES
TL00568	1.391	0.719		0.541	1.848	YES	0.575	1.739	YES
TL00567	1.298	0.77		0.570	1.754	YES	0.652	1.535	YES
TL00194	1.198	0.835		0.609	1.642	YES	0.584	1.713	YES
TL00182	1.272	0.786		0.522	1.916	YES	0.546	1.832	YES
TL00177	1.327	0.754		0.581	1.720	YES	0.595	1.681	YES
TL00165	1.187	0.842		0.546	1.832	YES	0.565	1.769	YES
TL00161	1.245	0.803		0.531	1.884	YES	0.585	1.710	YES
TL00159	1.385	0.722		0.530	1.886	YES	0.546	1.832	YES
TL00150	1.323	0.756		0.541	1.848	YES	0.534	1.873	YES
TL00146	1.306	0.766		0.524	1.910	YES	0.544	1.838	YES
TL00140	1.097	0.911		0.480	2.082	YES	0.515	1.940	YES
TL00136	1.168	0.856		0.473	2.116	YES	0.490	2.040	YES
TL00132	1.151	0.869		0.555	1.801	YES	0.505	1.979	YES
TL00119	1.135	0.881		0.448	2.232	YES	0.447	2.236	YES
TL00109	1.067	0.937		0.451	2.217	YES	0.486	2.056	YES
TL00098	1.305	0.767		0.530	1.887	YES	0.429	2.328	YES
TL00096	0.988	1.012		0.424	2.361	YES	0.399	2.509	YES
TL00084	1.045	0.957		0.470	2.126	YES	0.438	2.281	YES
TL00082	1.343	0.744		0.545	1.836	YES	0.411	2.435	YES
TL00079	1.09	0.917		0.553	1.809	YES	0.566	1.768	YES
TL00071	1.174	0.852		0.506	1.974	YES	0.512	1.952	YES
TL00070	1.179	0.849		0.579	1.726	YES	0.564	1.772	YES
TL00602	1.294	0.773		0.556	1.798	YES	0.595	1.681	YES
TL00599	1.245	0.803		0.565	1.771	YES	0.545	1.834	YES
TL00597	0.942	1.061		0.748	1.336		0.782	1.279
TL00595	1.304	0.767		0.514	1.947	YES	0.507	1.973	YES
TL00672	1.278	0.782		0.551	1.815	YES	0.585	1.708	YES
TL00323	1.474	0.678		0.607	1.648	YES	0.545	1.834	YES
TL00656	1.224	0.817		0.646	1.548	YES	0.633	1.579	YES
TL00319	1.251	0.8		0.676	1.479		0.642	1.558	YES
TL00309	1.151	0.869		0.626	1.596	YES	0.575	1.739	YES
TL00307	1.243	0.804		0.533	1.876	YES	0.544	1.840	YES
TL00302	1.272	0.786		0.562	1.778	YES	0.575	1.739	YES
TL00299	1.204	0.83		0.515	1.942	YES	0.544	1.838	YES
TL00290	1.102	0.907		0.506	1.976	YES	0.565	1.771	YES
TL00287	0.799	1.252		0.516	1.938	YES	0.537	1.861	YES
TL00280	1.15	0.87		0.489	2.046	YES	0.535	1.871	YES
TL00278	1.072	0.932		0.489	2.046	YES	0.519	1.926	YES
TL00276	1.097	0.912		0.571	1.750	YES	0.632	1.583	YES
TL00263	1.035	0.966		0.467	2.142	YES	0.455	2.199	YES
TL00244	1.051	0.952		0.459	2.178	YES	0.470	2.126	YES
TL00240	0.995	1.005		0.512	1.953	YES	0.459	2.181	YES
TL00239	1.191	0.84		0.527	1.896	YES	0.465	2.149	YES
TL00236	1.247	0.802		0.596	1.679	YES	0.512	1.953	YES
TL00233	1.055	0.948		0.652	1.535	YES	0.602	1.660	YES
TL00231	0.95	1.053		0.830	1.205		0.788	1.270
TL00414	1.241	0.806		0.733	1.364		0.631	1.586	YES
TL00405	1.215	0.823		0.513	1.950	YES	0.537	1.861	YES
TL00402	1.251	0.8		0.538	1.860	YES	0.556	1.799	YES
TL00392	1.159	0.863		0.496	2.017	YES	0.516	1.939	YES
TL00379	0.987	1.013		0.469	2.130	YES	0.469	2.132	YES
TL00376	1.021	0.98		0.474	2.109	YES	0.472	2.119	YES
TL00373	1.088	0.92		0.475	2.107	YES	0.483	2.069	YES
TL00371	1.003	0.997		0.475	2.106	YES	0.437	2.287	YES
TL00370	1.148	0.871		0.511	1.959	YES	0.446	2.241	YES
TL00367	1.256	0.796		0.575	1.738	YES	0.491	2.035	YES
TL00365	1.215	0.823		0.593	1.687	YES	0.584	1.711	YES
TL00360	1.29	0.775		0.618	1.619	YES	0.575	1.739	YES
TL00761	1.312	0.762		0.605	1.653	YES	0.511	1.957	YES
TL00750	0.831	1.203		0.559	1.790	YES	0.421	2.376	YES
TL00725	1.148	0.871		0.591	1.693	YES	0.527	1.897	YES
TL00723	1.12	0.893		0.496	2.016	YES	0.463	2.158	YES
TL00717	1.014	0.987		0.646	1.548	YES	0.714	1.401
TL00715	0.986	1.014		0.408	2.449	YES	0.408	2.454	YES
TL00707	1.001	0.999		0.495	2.019	YES	0.452	2.211	YES
TL00687	0.976	1.025		0.475	2.104	YES	0.417	2.396	YES
TL01032	0.96	1.041		0.839	1.191		0.706	1.416
TL01020	0.828	1.207		0.322	3.106	YES	0.264	3.783	YES
TL00449	1.219	0.82		0.619	1.615	YES	0.585	1.711	YES
TL00445	0.804	1.243		0.638	1.566	YES	0.533	1.875	YES
TL00633	1.162	0.86		0.598	1.672	YES	0.584	1.714	YES
TL00274	1.21	0.826		0.528	1.894	YES	0.556	1.797	YES
TL00272	1.154	0.866		0.504	1.985	YES	0.540	1.853	YES
TL01038	1.198	0.835		0.531	1.883	YES	0.475	2.105	YES
TL01027	1.069	0.936		0.468	2.135	YES	0.423	2.363	YES
TL01015	1.017	0.984		0.461	2.168	YES	0.453	2.205	YES
TL00999	0.991	1.009		0.467	2.139	YES	0.467	2.143	YES
TL00998	0.988	1.012		0.476	2.102	YES	0.399	2.509	YES
TL00991	0.996	1.004		0.507	1.974	YES	0.407	2.459	YES
TL00977	1.108	0.902		0.555	1.801	YES	0.531	1.882	YES
TL00965	1.277	0.783		0.581	1.720	YES	0.506	1.978	YES
TL00793	1.209	0.827		0.604	1.655	YES	0.596	1.678	YES
TL00705	1.235	0.81		0.538	1.860	YES	0.546	1.831	YES
TL00662	1.176	0.85		0.566	1.766	YES	0.548	1.826	YES
TL00653	1.246	0.803		0.553	1.809	YES	0.509	1.965	YES
TL00641	1.086	0.921		0.579	1.726	YES	0.559	1.790	YES
TL00606	1.124	0.89		1.004	0.996		0.812	1.231
TL00550	1.117	0.895		0.467	2.141	YES	0.482	2.075	YES
TL00548	1.079	0.926		0.459	2.178	YES	0.470	2.126	YES
TL00547	1.072	0.933		0.545	1.836	YES	0.517	1.933	YES
TL00546	1.052	0.95		0.474	2.111	YES	0.469	2.133	YES
TL00543	1.164	0.859		0.544	1.839	YES	0.482	2.074	YES
TL00542	1.238	0.808		0.576	1.736	YES	0.544	1.838	YES
TL00541	1.261	0.793		0.578	1.731	YES	0.544	1.840	YES
TL00742	1.202	0.832		0.779	1.284		0.737	1.357
TL00736	1.266	0.79		0.557	1.794	YES	0.514	1.944	YES
TL00711	1.282	0.78		0.652	1.535	YES	0.546	1.831	YES
TL00707	1.117	0.895		0.532	1.880	YES	0.457	2.190	YES
TL00589	1.126	0.888		0.538	1.860	YES	0.452	2.214	YES
TL00588	1.073	0.932		0.495	2.020	YES	0.500	1.999	YES
TL00586	1.095	0.913		0.448	2.232	YES	0.423	2.363	YES
TL00585	1.076	0.929		0.508	1.968	YES	0.445	2.249	YES
TL00580	1.003	0.997		0.523	1.913	YES	0.455	2.197	YES
TL00577	1.063	0.941		0.503	1.987	YES	0.446	2.241	YES
TL00576	1.207	0.828		0.555	1.802	YES	0.487	2.052	YES
TL00572	1.184	0.845		0.707	1.415		0.893	1.119
	1	1		1.000	1.000		1.000	1.000
	1.364	0.733		1.021	0.979		1.167	0.857
TL00751	1.24	0.807		0.547	1.829	YES	0.516	1.936	YES
TL00566	1.148	0.871		1.378	0.726		1.373	0.728
TL00613	1.049	0.953		0.525	1.904	YES	0.472	2.119	YES
TL00612	1.079	0.926		0.496	2.016	YES	0.453	2.208	YES
TL00611	0.977	1.024		0.503	1.989	YES	0.476	2.099	YES
TL00609	1.096	0.912		0.549	1.822	YES	0.486	2.056	YES
TL00607	1.126	0.888		0.538	1.860	YES	0.476	2.099	YES
TL00605	1.266	0.79		0.660	1.515	YES	0.555	1.803	YES
TL00604	1.266	0.79		0.714	1.401		0.575	1.739	YES

[0105] The group of genes selected were used as markers. The differences between the expression of the marker genes cultured with and without the lactic acid bacteria can be incorporated as markers.

EXAMPLE 2

A Method for Identifying an Unknown Microorganism as a Standardized and Recognized Lactic Acid Bacteria #7, #73 and #74

[0106] Detection system: Detection systems to the standardized and recognized lactic acid bacteria #7, #73 and #74 were provided in Example 1.

[0107] The cultures of the test cell line with and without an unknown microorganism: The conditions of an unknown microorganism cultured with and without Hep G2 were similar to the conditions of the co-culture of Hep G2 with and without lactic acid bacteria #7, #73 or #74 as described in Example 1.

[0108] Profiling the gene expression patterns: The gene expression patterns of the cultures of Hep G2 with and without the unknown microorganism were obtained as described in Example 1. The results were shown in Table 3 as listed below.

[0109] Selecting marker genes: According to Table 3, a group of genes having an expression ratio in Hep G2 cultured with the unknown microorganism to that cultured without the unknown microorganism larger than 1.5 were selected. The results were shown in Table 3.

[0110] Comparing the marker data: The marker data were compared with the marker data of the lactic acid bacteria #7, #73, or #74 obtained in Example 1. The result were shown in Table 3.

TABLE 3
		Unknown/	Cell/			#73	#74
Gene No.	unknown	cell	unknown	Selected	#7 marker	marker	marker
TL00356	0.113	0.581	1.72	YES		YES	YES
TL00348	0.082	0.423	2.365	YES		YES	YES
TL00340	0.106	0.563	1.775	YES		YES	YES
TL00334	0.109	0.561	1.783	YES		YES	YES
TL00578	0.830	1.198	0.835		YES
TL00556	0.101	0.518	1.931	YES		YES	YES
TL00555	0.093	0.493	2.028	YES		YES	YES
TL00554	0.111	0.549	1.822	YES		YES	YES
TL00553	0.111	0.552	1.81	YES		YES	YES
TL00552	0.250	0.631	1.584	YES		YES	YES
TL00551	0.131	0.6	1.666	YES		YES	YES
TL00549	0.114	0.534	1.874	YES		YES	YES
TL00545	0.089	0.442	2.264	YES		YES	YES
TL00544	0.094	0.418	2.393	YES		YES	YES
TL00593	0.092	0.399	2.507	YES		YES	YES
TL00592	0.099	0.388	2.577	YES		YES	YES
TL00591	0.094	0.406	2.464	YES		YES	YES
TL00587	0.094	0.417	2.4	YES		YES	YES
TL00584	0.158	0.563	1.775	YES		YES	YES
TL00583	0.095	0.458	2.185	YES		YES	YES
TL00582	0.200	0.561	1.782	YES		YES	YES
TL00581	0.479	0.943	1.061				YES
TL00579	0.365	0.978	1.022
TL00578	1.042	0.96	1.042
TL00438	0.156	0.706	1.416		YES		YES
TL00437	0.215	0.664	1.506	YES		YES
TL00428	0.126	0.578	1.731	YES		YES
TL00417	0.769	1.018	0.982		YES
TL00594	0.332	0.775	1.291
TL00918	0.100	0.497	2.012	YES		YES	YES
TL00915	0.108	0.537	1.862	YES	YES	YES	YES
TL00610	0.098	0.521	1.92	YES		YES	YES
TL00608	0.101	0.538	1.859	YES		YES	YES
TL00603	0.096	0.512	1.952	YES		YES	YES
TL00601	0.103	0.511	1.958	YES		YES	YES
TL00598	0.113	0.57	1.754	YES		YES	YES
TL00575	0.367	0.726	1.377				YES
TL00574	0.333	1.159	0.863				YES
TL00573	0.142	0.608	1.646	YES		YES	YES
TL00571	0.097	0.409	2.444	YES		YES	YES
TL00564	0.094	0.407	2.458	YES		YES	YES
TL00563	0.120	0.454	2.204	YES		YES	YES
TL00561	0.100	0.447	2.235	YES		YES	YES
TL00560	0.091	0.443	2.255	YES		YES	YES
TL00559	0.097	0.475	2.105	YES		YES	YES
TL00558	0.158	0.717	1.395
TL00557	0.157	0.806	1.241
TL00596	1.149	0.866	1.155
TL00788	0.105	0.532	1.881	YES		YES	YES
TL00775	0.100	0.549	1.821	YES		YES	YES
TL00765	0.114	0.577	1.734	YES		YES	YES
TL00762	0.113	0.559	1.788	YES		YES	YES
TL00798	0.105	0.566	1.768	YES		YES	YES
TL00668	0.109	0.543	1.841	YES		YES	YES
TL00666	0.111	0.58	1.725	YES		YES	YES
TL00655	0.173	0.795	1.258
TL00650	0.357	0.604	1.655	YES		YES
TL00635	0.097	0.517	1.932	YES		YES	YES
TL00632	0.105	0.515	1.941	YES		YES	YES
TL00631	0.105	0.541	1.847	YES		YES	YES
TL00630	0.118	0.512	1.953	YES		YES	YES
TL00626	0.099	0.454	2.201	YES		YES	YES
TL00625	0.126	0.461	2.167	YES		YES	YES
TL00535	0.113	0.447	2.239	YES		YES	YES
TL00534	0.094	0.396	2.525	YES		YES	YES
TL00508	0.098	0.469	2.131	YES		YES	YES
TL00495	0.106	0.432	2.312	YES		YES	YES
TL00484	0.265	0.893	1.12
TL00459	0.120	0.587	1.703	YES		YES	YES
TL00458	0.135	0.609	1.642	YES		YES
TL00457	0.101	0.536	1.866	YES		YES	YES
TL00456	0.498	2.25	0.444	YES		YES	YES
TL01081	0.101	0.526	1.901	YES		YES	YES
TL01071	0.097	0.509	1.964	YES		YES	YES
TL01068	0.094	0.484	2.066	YES		YES	YES
TL01066	0.104	0.525	1.905	YES		YES	YES
TL00064	0.097	0.509	1.964	YES		YES	YES
TL00060	0.264	0.74	1.352
TL00059	0.123	0.613	1.63	YES		YES	YES
TL00054	0.219	0.514	1.947	YES		YES	YES
TL00047	0.204	0.52	1.924	YES		YES	YES
TL00046	0.103	0.545	1.835	YES		YES	YES
TL00036	0.412	0.918	1.089				YES
TL00031	0.149	0.611	1.636	YES		YES
TL00028	0.256	0.231	4.323	YES		YES	YES
TL00027	0.104	0.517	1.933	YES		YES	YES
TL00022	0.345	0.725	1.379				YES
TL00018	0.119	0.545	1.834	YES		YES	YES
TL00015	0.411	0.98	1.02
TL00900	0.108	0.407	2.456	YES		YES	YES
TL00894	1.191	2.777	0.36	YES	YES	YES	YES
TL00888	0.961	1.179	0.849
TL00885	0.122	0.528	1.893	YES		YES	YES
TL00737	0.116	0.594	1.685	YES		YES	YES
TL00873	0.127	0.663	1.509	YES		YES	YES
TL00801	0.541	0.863	1.159
TL00570	0.104	0.542	1.844	YES		YES	YES
TL00569	0.101	0.535	1.87	YES		YES	YES
TL00568	0.102	0.553	1.808	YES		YES	YES
TL00567	0.115	0.581	1.72	YES		YES	YES
TL00194	0.129	0.602	1.662	YES		YES	YES
TL00182	0.100	0.514	1.947	YES		YES	YES
TL00177	0.110	0.573	1.745	YES		YES	YES
TL00165	0.106	0.538	1.86	YES		YES	YES
TL00161	0.106	0.553	1.807	YES		YES	YES
TL00159	0.108	0.552	1.811	YES		YES	YES
TL00150	0.104	0.564	1.772	YES		YES	YES
TL00146	0.101	0.547	1.828	YES		YES	YES
TL00140	0.096	0.503	1.989	YES		YES	YES
TL00136	0.099	0.494	2.024	YES		YES	YES
TL00132	0.125	0.575	1.739	YES		YES	YES
TL00119	0.106	0.445	2.248	YES		YES	YES
TL00109	0.096	0.448	2.234	YES		YES	YES
TL00098	0.144	0.527	1.897	YES		YES	YES
TL00096	0.104	0.42	2.378	YES		YES	YES
TL00084	0.123	0.467	2.139	YES		YES	YES
TL00082	0.125	0.541	1.848	YES		YES	YES
TL00079	0.107	0.53	1.888	YES		YES	YES
TL00071	0.087	0.481	2.08	YES		YES	YES
TL00070	0.099	0.553	1.808	YES		YES	YES
TL00602	0.102	0.532	1.88	YES		YES	YES
TL00599	0.103	0.54	1.851	YES		YES	YES
TL00597	0.311	0.737	1.356
TL00595	0.102	0.521	1.918	YES		YES	YES
TL00672	0.102	0.559	1.788	YES		YES	YES
TL00323	0.118	0.615	1.627	YES		YES	YES
TL00656	0.127	0.654	1.529	YES		YES	YES
TL00319	0.135	0.684	1.462				YES
TL00309	0.148	0.633	1.58	YES		YES	YES
TL00307	0.099	0.547	1.828	YES		YES	YES
TL00302	0.101	0.577	1.734	YES		YES	YES
TL00299	0.098	0.528	1.892	YES		YES	YES
TL00290	0.096	0.52	1.924	YES		YES	YES
TL00287	0.185	0.523	1.911	YES		YES	YES
TL00280	0.086	0.46	2.176	YES		YES	YES
TL00278	0.095	0.462	2.165	YES		YES	YES
TL00276	0.128	0.548	1.825	YES		YES	YES
TL00263	0.098	0.442	2.262	YES		YES	YES
TL00244	0.095	0.434	2.305	YES		YES	YES
TL00240	0.143	0.515	1.941	YES		YES	YES
TL00239	0.111	0.532	1.88	YES		YES	YES
TL00236	0.127	0.6	1.667	YES		YES	YES
TL00233	0.136	0.656	1.525	YES		YES	YES
TL00231	0.401	0.832	1.202
TL00414	0.151	0.737	1.356				YES
TL00405	0.104	0.517	1.934	YES		YES	YES
TL00402	0.106	0.533	1.875	YES		YES	YES
TL00392	0.110	0.492	2.032	YES		YES	YES
TL00379	0.117	0.466	2.146	YES		YES	YES
TL00376	0.104	0.47	2.126	YES		YES	YES
TL00373	0.107	0.471	2.124	YES		YES	YES
TL00371	0.110	0.471	2.122	YES		YES	YES
TL00370	0.112	0.507	1.973	YES		YES	YES
TL00367	0.117	0.571	1.751	YES		YES	YES
TL00365	0.120	0.598	1.673	YES		YES	YES
TL00360	0.109	0.623	1.604	YES		YES	YES
TL00761	0.127	0.61	1.64	YES		YES	YES
TL00750	0.207	0.561	1.782	YES		YES	YES
TL00725	0.141	0.595	1.682	YES		YES	YES
TL00723	0.111	0.5	1.998	YES		YES	YES
TL00717	0.319	0.648	1.543	YES		YES
TL00715	0.107	0.412	2.427	YES		YES	YES
TL00707	0.121	0.488	2.05	YES		YES	YES
TL00687	0.113	0.468	2.139	YES		YES	YES
TL01032	0.253	0.833	1.2
TL01020	0.222	0.319	3.132	YES		YES	YES
TL00449	0.121	0.61	1.64	YES		YES	YES
TL00445	0.259	0.634	1.577	YES		YES	YES
TL00633	0.130	0.59	1.696	YES		YES	YES
TL00274	0.106	0.519	1.927	YES		YES	YES
TL00272	0.105	0.492	2.034	YES		YES	YES
TL01038	0.118	0.52	1.924	YES		YES	YES
TL01027	0.109	0.457	2.186	YES		YES	YES
TL01015	0.105	0.45	2.222	YES		YES	YES
TL00999	0.104	0.456	2.193	YES		YES	YES
TL00998	0.115	0.465	2.15	YES		YES	YES
TL00991	0.134	0.497	2.012	YES		YES	YES
TL00977	0.118	0.543	1.84	YES		YES	YES
TL00965	0.112	0.587	1.705	YES		YES	YES
TL00793	0.111	0.61	1.64	YES		YES	YES
TL00705	0.107	0.543	1.843	YES		YES	YES
TL00662	0.119	0.571	1.751	YES		YES	YES
TL00653	0.112	0.558	1.793	YES		YES	YES
TL00641	0.135	0.584	1.713	YES		YES	YES
TL00606	0.362	1.007	0.993
TL00550	0.106	0.472	2.121	YES		YES	YES
TL00548	0.101	0.464	2.157	YES		YES	YES
TL00547	0.125	0.542	1.845	YES		YES	YES
TL00546	0.101	0.471	2.123	YES		YES	YES
TL00543	0.111	0.541	1.848	YES		YES	YES
TL00542	0.106	0.573	1.745	YES		YES	YES
TL00541	0.104	0.574	1.741	YES		YES	YES
TL00742	0.164	0.776	1.288
TL00736	0.104	0.554	1.804	YES		YES	YES
TL00711	0.128	0.649	1.541	YES		YES	YES
TL00707	0.119	0.529	1.889	YES		YES	YES
TL00589	0.125	0.541	1.85	YES		YES	YES
TL00588	0.126	0.498	2.009	YES		YES	YES
TL00586	0.107	0.451	2.218	YES		YES	YES
TL00585	0.126	0.511	1.957	YES		YES	YES
TL00580	0.125	0.526	1.903	YES		YES	YES
TL00577	0.112	0.506	1.975	YES		YES	YES
TL00576	0.109	0.558	1.791	YES		YES	YES
TL00572	0.152	0.71	1.409
	1.001	1.001	1
	0.341	1.022	0.978
TL00751	0.107	0.549	1.821	YES		YES	YES
TL00566	0.633	1.379	0.725
TL00613	0.117	0.527	1.896	YES		YES	YES
TL00612	0.109	0.498	2.006	YES		YES	YES
TL00611	0.117	0.505	1.981	YES		YES	YES
TL00609	0.118	0.551	1.814	YES		YES	YES
TL00607	0.125	0.54	1.852	YES		YES	YES
TL00605	0.125	0.663	1.508	YES		YES	YES
TL00604	0.149	0.716	1.396				YES

[0111] Result: According to Table 3, the marker data of the unknown microorganism was the same as the marker data of the lactic acid bacteria #73. The unknown microorganism was identified as the lactic acid bacteria #73.

[0112] While embodiments of the present invention have been illustrated and described, various modifications and improvements can be made by persons skilled in the art. The embodiments of the present invention are therefore described in an illustrative but not restrictive sense. It is intended that the present invention is not limited to the particular forms as illustrated, and that all the modifications not departing from the spirit and scope of the present invention are within the scope as defined in the appended claims.

Claims

1. A method for establishing a standardized detection system for identifying a microorganism, which comprises: (i) providing a test cell line; (ii) culturing the test cell line with and without the microorganism; (iii) determining gene expression values in the test cell line cultured with and without the microorganism; (iv) selecting a group of genes, whose gene expression values in the test cell line cultured without the microorganism is significantly different from that cultured with the microorganism as markers; and (v) storing the marker data obtained as the standardized detection system.

2. The method according to claim 1, wherein the gene expression values are determined in a microarray.

3. The method according to claim 1, wherein the test cell line in step (i) is provided to show significantly different gene expression values of the test cell line cultured with and without the microorganism.

4. The method according to claim 1, wherein the gene expression values in step (iii) are determined by determining individual gene expression values of the test cell line.

5. The method according to claim 1, wherein the group of genes of step (iv) have an expression value ratio of the test cell line cultured with the microorganism to that cultured without the microorganism larger than 0.2.

6. The method according to claim 1, wherein the group of genes of step (iv) have an expression value ratio of the test cell line cultured with the microorganism to that cultured without the microorganism larger than 1.5.

7. The method according to claim 1, wherein the expression difference between the group of genes in step (iv) in the test cell line cultured with and without the microorganism is incorporated into the marker data.

8. The method according to claim 1, wherein more than one cell line is used in step (i); wherein the more than one cell line are derived from the same species.

9. A method for identifying an unknown microorganism as a standardized and recognized microorganism, which comprises: (a) providing a standardized detection system for a standardized and recognized microorganism, wherein the detection system is prepared by the steps of: (i) providing a test cell line; (ii) culturing the test cell line with and without the standardized and recognized microorganism; (iii) determining gene expression values in the test cell line cultured with and without the microorganism; (iv) selecting a group of genes, whose gene expression values in the test cell line cultured without the microorganism is significantly different from that cultured with the microorganism as markers; and (v) storing the marker data obtained as the standardized detection system; (b) culturing the test cell line with and without the unknown microorganism; (c) determining gene expression values in the test cell line cultured with and without the unknown microorganism; (d) selecting a group of genes, whose expression in the test cell line cultured without the unknown microorganism is significantly different from that cultured with the unknown microorganism as markers; (e) comparing the marker data obtained in step (d) with the marker data obtained in step (a), whereby the unknown microorganism is identified as the standardized and recognized microorganism if the marker data obtained in step (d) is similar to the marker data obtained in step (a) within an acceptable level.

10. The method according to claim 9, wherein the gene expression values are determined in a microarray.

11. The method according to claim 9, wherein the test cell line in step (i) of step (a) is provided to show significantly different gene expression values of the test cell line cultured with and without the standardized and recognized microorganism.

12. The method according to claim 9, wherein the gene expression values in step (iii) of step (a) and in step (c) are determined by determining individual gene expression values of the test cell line.

13. The method according to claim 9, wherein the group of genes in step (iv) of step (a) have an expression value ratio of the test cell line cultured with the standardized and recognized to that cultured without the standardized and recognized microorganism larger than 0.2.

14. The method according to claim 9, wherein the group of genes in step (iv) of step (a) have an expression value ratio of the test cell line cultured with the standardized and recognized microorganism to that cultured without the standardized and recognized microorganism larger than 1.5.

15. The method according to claim 9, wherein the expression difference between the group of genes in step (iv) in the test cell line cultured with and without the standardized and recognized microorganism is incorporated into the marker data.

16. The method according to claim 9, which is applied in quality control for manufacturing a microorganism composition.

17. The method according to claim 9, wherein more than one cell line is used in step (i); wherein the more than one cell line are derived from the same species.

18. A method for establishing a standardized detection system for detecting a specific function in a microorganism, which comprises: (i) providing a test cell line; (ii) culturing the test cell line with and without a reference microorganism having a specific function; (iii) determining gene expression values in the test cell line cultured with and without the microorganism; (iv) selecting a group of genes, whose gene expression values in the test cell line cultured without the microorganism is significantly different from that cultured with the microorganism as markers; and (v) storing the marker data obtained as the standardized detection system.

19. The method according to claim 18, wherein the gene expression values are determined in a microarray.

20. The method according to claim 18, wherein the test cell line in step (i) is provided to show significantly different gene expression values of the test cell line cultured with and without the reference microorganism.

21. The method according to claim 18, wherein the gene expression values in step (iii) are determined by determining individual gene expression values related to the specific function of the test cell line.

22. The method according to claim 18, wherein the group of genes of step (iv) have an expression value ratio of the test cell line cultured with the reference microorganism to that cultured without the reference microorganism larger than 0.2.

23. The method according to claim 18, wherein the group of genes of step (iv) have an expression value ratio of the test cell line cultured with the reference microorganism to that cultured without the reference microorganism larger than 1.5.

24. The method according to claim 18, wherein the expression difference between the group of genes in step (iv) in the test cell line cultured with and without the reference microorganism is incorporated into the marker data.

25. The method according to claim 18, wherein more than one cell line is used in step (i); wherein the more than one cell line are derived from the same species.

26. A method for detecting a test microorganism having a specific function, which comprises: (a) providing a standardized detection system for identifying the specific function in a reference microorganism, wherein the detection system is prepared by the steps of: (i) providing a test cell line; (ii) culturing the test cell line with and without the reference microorganism; (iii) determining gene expression values in the test cell line cultured with and without the microorganism; (iv) selecting a group of genes, whose gene expression values in the test cell line cultured without the microorganism is significantly different from that cultured with the microorganism as markers; and (v) storing the marker data obtained as the standardized detection system; (b) culturing the test cell line with and without the test microorganism; (c) determining gene expression values related to the specific function of the test cell line cultured with and without the test microorganism; (d) selecting a group of genes, whose expression in the test cell line cultured without the test microorganism is significantly different from that with the test microorganism as markers; (e) comparing the marker data obtained in step (d) with the marker data obtained in step (a), whereby the test microorganism is identified to have the specific function if the marker data obtained in step (d) is similar to the maker data obtained in step (a) within an acceptable level.

27. The method according to claim 26, wherein the gene expression values are determined in a microarray.

28. The method according to claim 26, wherein the test cell line in step (i) of step (a) is provided to show significantly different gene expression values of the test cell line cultured with and without the reference microorganism.

29. The method according to claim 26, wherein the gene expression values in step (iii) of step (a) and in step (c) are determined by determining individual gene expression values related to the specific function of the test cell line.

30. The method according to claim 26, wherein the group of genes in step (iv) of step (a) have an expression value ratio of the test cell line cultured with the reference microorganism to that cultured without the reference microorganism larger than 0.2.

31. The method according to claim 26, wherein the group of genes in step (iv) of step (a) have an expression value ratio of the test cell line cultured with the reference microorganism to that cultured without the reference microorganism larger than 1.5.

32. The method according to claim 26, wherein the expression difference between the group of genes in step (iv) in the test cell line cultured with and without the reference microorganism is incorporated into the marker data.

33. The method according to claim 26, wherein more than one cell line is used in step (i); wherein the more than one cell line are derived from the same species.