Species-specific oligonucleotides for bifidobacteria and a method of detection using the same

Abstract: Oligonucleotides which specifically hybridize to rRNAs of Bifidobacterium infantis , Bifidobacterium bifidum , Bifidobacterium adolescentis , Bifidobacterium breve , and Bifidobacterium longum represented by the sequences of formulae (I) to (V), respectively, or sequences complementary thereto: UAUCGGGGAGCAAGCGUGA (I) UCGGAUCGGAGCCUGC (II) CGCUUUUGACUGGGAGC (III) UGUGUUGAGUGUACCUU (IV) UAUCGGGGAGCAAGCGAGA (V) and a method of species-specifically detecting species of the genus Bifidobacterium of human origin comprising using these oligonucleotides as a labeled probe.

Description: FIELD OF THE INVENTION This invention relates to oligonucleotides having species specificity for various Bifidobacterium species, particularly those of human origin, and a species-specific method of detection using the same. BACKGROUND OF THE INVENTION Identification of species belonging to the genus Bifidobacterium has mainly been performed on the basis of phenotypic characteristics, such as carbohydrate fermentation patterns, gas-liquid chromatographic analyses of fatty acids, and cellular morphology. Recently, identification based on DNA-DNA homology has also been used (see Benno, Y., BISEIBUTSU , Vol. 6, pp. 1-12 (1990). Identification based on phenotypic characteristics requires a high degree of skill and takes a period of time before an identification can be made. The DNA-DNA homology approach, which requires extraction of DNA from microbial cells, is disadvantageous in that bifidobacteria are gram-positive bacteria which require more complicated procedures for bacteriolysis than those needed with gram-negative bacteria. In addition, the values for DNA-DNA homology between closely related species with no distinct difference are high. Hence, there has been keen demand for the development of a rapid, simple, and accurate method for detecting Bifidobacterium species, especially those found in humans, i.e., Bifidobacterium infantis , B . bifidum , B . adolescentis , B . breve , and B . longum . SUMMARY OF THE INVENTION In light of the demand for a better detection method, the present inventors have conducted extensive investigations. Studies were performed on detecting bifidobacteria using a labeled oligonucleotide having species specificity for a Bifidobacterium species as a probe and observing hybridization of the probe to the bacterium. This study was focused on the use of short oligonucleotides comprising about 20 bases, which would perform in situ hybridization without requiring extraction of nucleic acids, thereby making it feasible to detect even a 1-nucleotide difference. Species-specific portions of 16S rRNAs were chosen as the target site for assays because the 16S rRNA sequences have recently been accepted as a highly reliable indication of phylogenetic classification and also because 16S rRNAs have a much higher copy number per cell than chromosomal DNA and are expected to exhibit increased detection sensitivity. Standard strains of various bifidobacteria were subjected to enzymatic bacteriolysis, and crude high-molecular-weight RNAs were extracted by a conventional method. The 16S rRNA portion of the crude high-molecular weight RNA was partially sequenced according to a Sanger's [dideoxy chain termination] method using reverse transcriptase. After comparing the thus determined base sequences, it was found that the oligonucleotides having sequences represented by formulae (I) to (V)(SEQ ID NO:1, SEQ ID NO:4, SEQ ID NO:7, SEQ ID NO:10 and SEQ ID NO:13, respectively) shown below are specific to Bifidobacterium infantis, B. bifidum, B. adolescentis , B. breve, and B. longum , respectively, and are useful as primers for detecting bacteria in a polymerase chain reaction (PCR) method and that the oligonucleotides, when labeled, serve as a probe for species-specifically detecting bifidobacteria rapidly, simply, and accurately. The present invention has been completed based on these findings. The present invention relates to (1) an oligonucleotide which specifically hybridizes to Bifidobacterium infantis rRNA which has a sequence represented by formula (I)(SEQ ID NO:1) or a sequence complementary thereto: (2) an oligonucleotide which specifically hybridizes to Bifidobacterium bifidum rRNA which has a sequence represented by formula (II)(SEQ ID NO:4) or a sequence complementary thereto: (3) an oligonucleotide which specifically hybridizes to Bifidobacterium adolescentis rRNA which has a sequence represented by formula (III)(SEQ ID NO:7) or a sequence complementary thereto: (4) an oligonucleotide which specifically hybridizes to Bifidobacterium breve rRNA which has a sequence represented by formula (IV)(SEQ ID NO:10) or a sequence complementary thereto: (5) an oligonucleotide which specifically hybridizes to Bifidobacterium longum rRNA which has a sequence represented by formula (V)(SEQ ID NO:13) or a sequence complementary thereto: and (6) a species-specific method for detecting various species of the genus Bifidobacterium found in humans comprising using these oligonucleotides as a labeled probe. DETAILED DESCRIPTION OF THE INVENTION The oligonucleotide specific to Bifidobacterium infantis has a sequence represented by formula (I)(SEQ ID NO:1) or a sequence complementary thereto represented by formula (I')(SEQ ID NO:2) or (I")(SEQ ID NO:3): The oligonucleotide specific to Bifidobacterium bifidum has a sequence represented by formula (II)(SEQ ID NO:4) or a sequence complementary thereto represented by formula (II')(SEQ ID NO:5) or (II")(SEQ ID NO:6): The oligonucleotide specific to Bifidobacterium adolescentis has a sequence represented by formula (III)(SEQ ID NO:7) or a sequence complementary thereto represented by formula (III')(SEQ ID NO:8) or (III")(SEQ ID NO:9): The oligonucleotide specific to Bifidobacterium breve has a sequence represented by formula (IV)(SEQ ID NO:10) or a sequence complementary thereto represented by formula (IV')(SEQ ID NO:11) or (IV")(SEQ ID NO:12): The oligonucleotide specific to Bifidobacterium longum has a sequence represented by formula (V)(SEQ ID NO:13) or a sequence complementary thereto represented by formula (V')(SEQ ID NO:14) or (V")(SEQ ID NO:15): Each of the above-described sequences may have additional bases bonded to the 5'- or 3'-terminal thereof as long as it functions as a probe. These oligonucleotides can be prepared by conventional chemical synthesis means, for example by an automated DNA synthesizer. DNA fragments containing the above-mentioned sequences can be prepared by enzymatic cleavage of genes from the corresponding Bifidobacterium species. Species-specific detection of bifidobacteria using these oligonucleotides is carried out in a conventional manner using a labeled oligonucleotide as a probe. That is, any one of the species-specific probes is subjected to hybridization to a sample under assay, and the existence of a Bifidobacterium species corresponding to the probe is confirmed by examining whether or not hybrid cells are formed. Then, if desired, the same confirmations are successively made using the other oligonucleotide probes. The bifidobacteria found in humans present in the sample, i.e., Bifidobacterium infantis , B . bifidum , B . adolescentis , B . breve , and B . longum , can thus be detected with species specificity. Labeled preparations are prepared by labeling the oligonucleotide with a detectable marker by conventional means. Labeling markers which may be used include radioisotopes, fluorescent substances, enzymes, biotin and hapten. Hybridization between the labeled preparation and a sample can be performed in accordance with known techniques, such as dot blot hybridization and northern hybridization. The hybrid which are formed can be confirmed through the detection of the labeled preparation by known means, for example, autoradiography using radioisotopes, enzyme-labeled antibody techniques using enzyme or biotin, and the like. Further, of these oligonucleotides, the DNA fragments represented by formulae (I') to (V')(SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:8, SEQ ID NO:11 and SEQ ID NO:14, respectively) and (I'') to (V'')(SEQ ID NO:3, SEQ ID NO:6, SEQ ID NO:9, SEQ ID NO:12 and SEQ ID NO:15, respectively) can be used as a primer in the PCR method for identification of species. More specifically, microbial cells to be identified are subjected to bacteriolysis, and any of the DNA fragments of formulas (I') to (V')(SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:8, SEQ ID NO:11 and SEQ ID NO:14, respectively) and (I") to (V'')(SEQ ID NO:3, SEQ ID NO:6, SEQ ID NO:9, SEQ ID NO:12 and SEQ ID NO:15, respectively) is added thereto as a primer, followed by treatment with a DNA polymerase. If DNA amplification is observed using electrophoresis, etc., this means that the cells possess a gene portion which corresponds to the DNA fragment used, i.e., the cells are identified to be of the same species as the origin of the DNA fragment primer. The present invention will now be illustrated in greater detail with reference to Examples, but it should be understood that the present invention is not construed as being limited thereto. EXAMPLE 1 16S rRNA Sequence Determination (1) Cultivation and Preparation of Crude High-Molecular-Weight RNA: The standard Bifidobacterium strain shown in Table 1 below were cultivated for one day in 100 mℓ of GAM broth (referred to the following formula, produced by Nissui Seiyaku Co., Ltd.) supplemented with 1% glucose. After incubation, the cells were collected by centrifugation, washed three times with a washing solution (50 mM Tris, 1 mM EDTA; pH=7.4) and suspended in 7.3 mℓ of the same washing solution. To the cell suspension were added 2.3 mℓ of 2M sucrose, 0.33 µℓ of 0.5 mg/mℓ M1 enzyme (N-acethylmuramidase, produced by Seikagaku Kogyo Co., Ltd.), and 0.07 mℓ of 50 mg/mℓ lysozyme, followed by incubating at 37°C for 30 minutes for bacteriolysis. To the solution were added 925 µℓ of an EDTA solution (50 mM Tris, 250 mM EDTA; pH=8.0) and 575 µℓ of an SDS solution (20% sodium dodecylsulfate, 50 mM Tris, 20 mM EDTA; pH=8.0), followed by shaking at 60°C until the mixture became clear. Deproteination of the solution was conducted using a TE solution (10 mM Tris, 1 mM EDTA; pH=7.4)-saturated phenol and then a 24:1 mixture of chloroform/isoamyl alcohol. Nucleic acids were then precipitated in ethanol. The precipitate was dissolved in an adequate amount of a TE solution (10 mM Tris, 1 mM EDTA; pH=7.4), and an equal amount of 4M NaCℓ was added thereto, followed by allowing the resulting solution to stand on ice overnight to precipitate crude high-molecular-weight RNA. The high-molecular-weight RNA was collected by centrifugation, again dissolved in a TE solution, and ethanol precipitated to remove salts. The resulting RNA was stored in 70% ethanol at -70°C or was dissolved in a TE solution at an appropriate concentration. Formula of GAM broth (1ℓ) Peptone 10.0 g Soybean peptone 3.0 g Proteose peptone 10.0 g Digestive serum powder 13.5 g Yeast extract 5.0 g Meat extract 2.2 g Liver extract 1.2 g Glucose 3.0 g Potassium dihydrogenphosphate 2.6 g Sodium chloride 3.0 g Soluble starch 5.0 g L-cysteine hydrochloride 0.3 g Sodium thioglycolic acid 0.3 g pH 7.3 ± 0.1 Species Strain No. B. adolescentis ATCC 15703 B. bifidum ATCC 29521 B. breve ATCC 15700 B. infantis ATCC 15697 B. longum ATCC 15707 B. angulatum ATCC 27535 B. dentium ATCC 27534 B. pseudolongum ATCC 25526 (2) Partial Sequence of 16S rRNA: The 16S rRNA was directly sequenced from RNA using AMV reverse transcriptase (RNA sequencing kit, produced by Boehringer Mannheim) according to a Sanger's dideoxy chain termination method. The universal primer [G(A or T)ATTACCGCGGC(G or T)GCTG](SEQ ID NO:16) described in Lane et al., Proc. Natl. Acd. Sci. USA , Vol. 82, pp. 6955-6969 (1985) (hereinafter referred to as "PPR") was used as a primer for sequencing. The hybridization site of this primer corresponds to the position of from 519 to 536 of E . coli 16S rRNA. In the sequencing, a mixture of 4 µℓ of a 2.0 mg/mℓ solution of the high-molecular-weight RNA prepared in (1) above, 1.5 µℓ of 20 µg/mℓ primer, and 1.5 µℓ of distilled water was used as an annealing solution. Electrophoresis of the reaction mixture was carried out using a 6% polyacrylamide gel containing 8 M urea. (3) Selection of Species-Specific Sequences for Bifidobacterium infantis, B. bifidum, B. adolescentis, B. breve, and B. longum : By comparing the sequences obtained in (2) above, partial sequences specific to Bifidobacterium infantis , B . bifidum , B . adolescentis , B . breve , and B . longum were selected. The partial sequences selected and the results of sequencing of other Bifidobacterium species are shown below. In the above sequences, the underlined region is a target site for the species-specific probe of the respective Bifidobacterium species. The numbers correspond to the positions from the 5'-terminal of the base sequence of the E . coli 16S rRNA (refer to Noller, H.F. and C.R. Woese, Science , Vol. 212, pp. 403-411 (1981)). EXAMPLE 2 (1) Synthesis of Probe and Labeling: An oligonucleotide having a sequence complementary to each of the underlined species-specific sequences of the Bifidobacterium species shown in Example 1 was synthesized with a DNA synthesizer (Model 380B, produced by Applied Biosystems) and purified in the usual manner. The resulting oligonucleotides corresponding to Bifidobacterium infantis , B . bifidum , B . adolescentis , B . breve , and B . longum will hereinafter be referred to as probes "PIN", "PBI", "PAD", "PBR", and "PLO", respectively. These oligonucleotide probes and probe PPR (the Universal primer used for sequencing in Example 1-(2)) were 5'-end labeled with 32 P by using Megalabel (produced by Takara Shuzo Co., Ltd.). (2) Dot Blotting of High-Molecular-Weight RNA to Membrane: An appropriate amount of a high-molecular-weight RNA from each of the microorganisms shown in Table 3 below was extracted in the same manner as in Example 1-(1), and the resulting extracts were dissolved 10 µℓ in of distilled water, and 20 µℓ of 100% formamide, 7 µℓ of formaldehyde, and 2 µℓ of 20x SSC (3 M NaCℓ, 0.3 M sodium citrate) were added thereto. The solution was incubated at 68°C for 15 minutes to denature the RNA. A double amount of 20x SSC was added to the solution, and the resulting solution was applied to a nylon membrane (Gene Screen Plus, produced by E.I. Du Pont) set in a microfiltration apparatus (Bio-Dot, produced by Bio-Rad Laboratories). The membrane was dried at room temperature and heated at 80°C for 30 minutes to remove formaldehyde. (3) Hybridization: The resulting high-molecular-weight RNA-blotted membrane was soaked in 6x SSC (0.9 M NaCℓ, 0.09 M sodium citrate) and then put in a plastic bag. A prehybridization solution (6x SSC, 2x Denhardt's solution, 1% SDS, 0.1 mg/mℓ salmon sperm DNA, 10% dextran sulfate) was added thereto, followed by incubating at a temperature selected from 40 to 55°C, as shown in Table 2 below, for 1 hour. The prehybridization solution was replaced by a hybridization solution (6x SSC, 2x Denhardt's solution, 1% SDS, 10% dextran sulfate, about 10 6 cpm labeled probe), and incubation was continued at the temperature shown in Table 2 for an additional period of 2 hours. The membrane was taken out of the bag and washed three times with 6x SSC at room temperature for 5 minutes each time. As a more stringent wash, the membrane was further washed at a temperature selected from 50 to 70°C, as shown in Table 2, for at least 30 minutes. Hybridization was examined by autoradiography or observation under a Betascope 603 blot analyzer (manufactured by Betagen Corp.). Treating Temperature (°C) PPR PIN PBI PAD PBR PLO Prehybridization and Hybridization 55 55 55 50 40 55 Washing 65 70 65 60 50 70 The results of dot blot hybridization between each probe and each high-molecular-weight RNA are shown in Table 3. + ... Hybridization was observed. - ... No hybridization was observed. Species (Strain No.) PPR PIN PBI PAD PBR PLO Escherichia coli (ATCC 11775) + - - - - - Actinomyces israelii (ATCC 10048) + - - - - - Eubacterium aerofaciens (ATCC 25986) + - - - - - Peptostreptococcus productus (ATCC 27340) + - - - - - Bifidobacterium adolescentis (ATCC 15703) + - - + - - B . angulatum (ATCC 27535) + - - - - - B . animalis (ATCC 25527) + - - - - - B . bifidum (ATCC 29521) + - + - - - B . breve (ATCC 15700) + - - - + - B . dentium (ATCC 27534) + - - - - - B . globosum (ATCC 25864) + - - - - - B . infantis (ATCC 15697) + + - - - - B . longum (ATCC 15707) + - - - - + B . pseudolongum (ATCC 25526) + - - - - - As is apparent from the results in Table 3, probe PPR hybridized to RNA from all of the strains tested. This accurately reflects the fact that the sequence of probe PPR is complementary to the common portion in the 16S rRNAs of all bacteria. Probe PPR is used as a positive control for detecting the presence of target RNAs for this very reason. To the contrary, probe PIN hybridized to the RNA extracted from B . infantis , but not to those from other Bifidobacterium species or non- Bifidobacterium reference microorganisms including Actinomyces israelii , which is believed to be phylogenetically close to Bifidobacterium species. In other words, probe PIN was confirmed to be species-specific to B . infantis . Likewise, probes PBI, PAD, PBR and PLO hybridized specifically to the RNA extracted from the respective target strains but not to those from other Bifidobacterium species or non- Bifidobacterium reference microorganisms, including Actinomyces israelii , which is believed phylogenetically close to Bifidobacterium species, and thus also proved specific to the respective species. EXAMPLE 3 Dot blot hybridization was conducted between each probe and fixed cells of the microorganisms shown in Table 4 below. (1) Cell Fixation with Formaldehyde: After having been cultured overnight, about 3 mℓ of microbial cells were collected by centrifugation, washed with a phosphate buffer (145 mM NaCℓ, 100 mM sodium phosphate; pH=7.4), and suspended in 5 mℓ of the same phosphate buffer. Formaldehyde was added thereto to a concentration of 1%, and the mixture was left on ice for 30 minutes with occasional shaking. Centrifugal collection of the cells, followed by washing with a phosphate buffer were repeated twice, and the finally obtained cells were suspended in an adequate amount of a Tris buffer solution (145 mM NaCℓ, 10 mM Tris; pH=7.4). (2) Dot Blot Hybridization: The fixed cells were applied to Gene Screen Plus set on Bio-Dot, and the membrane was heated at 80°C for 1 hour. Hybridization was carried out in the same manner as in Example 2-(3). The results observed are shown in Table 4, in which symbols + and - have the same meaning as in Table 3. The results in Table 4 show hybridization of probe PPR to RNA from all of the cells tested, irrespective of the genus or species, similar to the results of Example 2, revealing that all the cells were sufficiently fixed. To the contrary, probes PAD, PBR, and PLO hybridized exclusively with the corresponding species, irrespective of the strain sources, but not with any of the other species, tested. The probes PAD, PBR and PLO were thus proved specific to the respective species. Probe PIN hybridized exclusively with the corresponding species, B . infantis , irrespective of the strain sources, but not with other species except Bifidobacterium suis , proving specific to B . infantis . Although probe PIN cross-reacted with the standard B . suis strain, because this species is only found in swine feces, such a cross-reaction is considered to be of no importance because B . suis would not be present the samples tested for Bifidobacterium infantis , such as foodstuffs or human feces. Probe PBI hybridized exclusively with the corresponding species, B . bifidum , irrespective of the strain sources, but not with other species except for a few strains of other species, thus proving specific to B . bifidum . That is, although probe PBI showed hybridization with the standard strains of Bifidobacterium asteroides , B . indicum , and B . thermophilum , because these Bifidobacterium strains are of animal origin, such as bees, swine and cattle, such a cross-reaction is not considered to be important because these species would not be present in samples being tested for B. bifidum, such as foodstuffs or human feces. The oligonucleotides according to the present invention are species-specific to Bifidobacterium bacteria found in humans, i.e., B. infantis, B. bifidum, B. adolescentis, B. breve, and B. longum, and are useful as probes for rapidly, simply and accurately detecting Bifidobacterium bacteria which are found in humans. SEQUENCE LISTING (1) GENERAL INFORMATION: (i) APPLICANT: (A) NAME: KABUSHIKI KAISHA YAKULT HONSHA (B) STREET: 1-19, HIGASHISHINBASHI 1-CHOME (C) CITY: MINATO-KU (D) STATE: TOKYO (E) COUNTRY: JAPAN (F) POSTAL CODE (ZIP): 105 (G) TELEPHONE: 03-3574-8960 (H) TELEFAX: 03-3574-7049 (ii) TITLE OF INVENTION: SPECIES-SPECIFIC OLIGONUCLEOTIDES FOR BIFIDOBACTERIA AND A METHOD OF DETECTION USING THE SAME (iii) NUMBER OF SEQUENCES: 39 (iv) COMPUTER READABLE FORM: (A) MEDIUM TYPE: Floppy disk (B) COMPUTER: IBM PC compatible (C) OPERATING SYSTEM: PC-DOS/MS-DOS (D) SOFTWARE: PatentIn Release #1.0, Version #1.25 (EPO) (2) INFORMATION FOR SEQ ID NO:1: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 19 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: rRNA (vi) ORIGINAL SOURCE: (A) ORGANISM: Bifidobacterium infantis (xi) SEQUENCE DESCRIPTION: SEQ ID NO:1: (2) INFORMATION FOR SEQ ID NO:2: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 19 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: cDNA to rRNA (vi) ORIGINAL SOURCE: (A) ORGANISM: Bifidobacterium infantis (xi) SEQUENCE DESCRIPTION: SEQ ID NO:2: (2) INFORMATION FOR SEQ ID NO:3: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 19 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA complementary to cDNA (vi) ORIGINAL SOURCE: (A) ORGANISM: Bifidobacterium infantis (xi) SEQUENCE DESCRIPTION: SEQ ID NO:3: (2) INFORMATION FOR SEQ ID NO:4: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 16 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: rRNA (vi) ORIGINAL SOURCE: (A) ORGANISM: Bifidobacterium bifidum (xi) SEQUENCE DESCRIPTION: SEQ ID NO:4: (2) INFORMATION FOR SEQ ID NO:5: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 16 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: cDNA to rRNA (vi) ORIGINAL SOURCE: (A) ORGANISM: Bifidobacterium bifidum (xi) SEQUENCE DESCRIPTION: SEQ ID NO:5: (2) INFORMATION FOR SEQ ID NO:6: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 16 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA complementary to cDNA (vi) ORIGINAL SOURCE: (A) ORGANISM: Bifidobacterium bifidum (xi) SEQUENCE DESCRIPTION: SEQ ID NO:6: (2) INFORMATION FOR SEQ ID NO:7: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 17 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: rRNA (vi) ORIGINAL SOURCE: (A) ORGANISM: Bifidobacterium adolescentis (xi) SEQUENCE DESCRIPTION: SEQ ID NO:7: . (2) INFORMATION FOR SEQ ID NO:8: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 17 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: cDNA to rRNA (vi) ORIGINAL SOURCE: (A) ORGANISM: Bifidobacterium adolescentis (xi) SEQUENCE DESCRIPTION: SEQ ID NO:8: (2) INFORMATION FOR SEQ ID NO:9: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 17 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA complementary to cDNA (vi) ORIGINAL SOURCE: (A) ORGANISM: Bifidobacterium adolescentis (xi) SEQUENCE DESCRIPTION: SEQ ID NO:9: (2) INFORMATION FOR SEQ ID NO:10: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 17 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: rRNA (vi) ORIGINAL SOURCE: (A) ORGANISM: Bifidobacterium breve (xi) SEQUENCE DESCRIPTION: SEQ ID NO:10: (2) INFORMATION FOR SEQ ID NO:11: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 17 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: cDNA to rRNA (vi) ORIGINAL SOURCE: (A) ORGANISM: Bifidobacterium breve (xi) SEQUENCE DESCRIPTION: SEQ ID NO:11: (2) INFORMATION FOR SEQ ID NO:12: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 17 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA complementary to cDNA (vi) ORIGINAL SOURCE: (A) ORGANISM: Bifidobacterium breve (xi) SEQUENCE DESCRIPTION: SEQ ID NO:12: (2) INFORMATION FOR SEQ ID NO:13: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 19 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: rRNA (vi) ORIGINAL SOURCE: (A) ORGANISM: Bifidobacterium longum (xi) SEQUENCE DESCRIPTION: SEQ ID NO:13: (2) INFORMATION FOR SEQ ID NO:14: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 19 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: cDNA to rRNA (vi) ORIGINAL SOURCE: (A) ORGANISM: Bifidobacterium longum (xi) SEQUENCE DESCRIPTION: SEQ ID NO:14: (2) INFORMATION FOR SEQ ID NO:15: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 19 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA complementary to cDNA (vi) ORIGINAL SOURCE: (A) ORGANISM: Bifidobacterium longum (xi) SEQUENCE DESCRIPTION: SEQ ID NO:15: (2) INFORMATION FOR SEQ ID NO:16: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 18 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: synthetic DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:16: (2) INFORMATION FOR SEQ ID NO:17: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 24 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: rRNA (vi) ORIGINAL SOURCE: (A) ORGANISM: Bifidobacterium infantis (xi) SEQUENCE DESCRIPTION: SEQ ID NO:17: (2) INFORMATION FOR SEQ ID NO:18: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 14 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: rRNA (vi) ORIGINAL SOURCE: (A) ORGANISM: Bifidobacterium infantis (xi) SEQUENCE DESCRIPTION: SEQ ID NO:18: (2) INFORMATION FOR SEQ ID NO:19: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 25 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: rRNA (vi) ORIGINAL SOURCE: (A) ORGANISM: Bifidobacterium adolescentis (xi) SEQUENCE DESCRIPTION: SEQ ID NO:19: (2) INFORMATION FOR SEQ ID NO:20: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 14 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: rRNA (vi) ORIGINAL SOURCE: (A) ORGANISM: Bifidobacterium adolescentis (xi) SEQUENCE DESCRIPTION: SEQ ID NO:20: (2) INFORMATION FOR SEQ ID NO:21: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 25 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: rRNA (vi) ORIGINAL SOURCE: (A) ORGANISM: Bifidobacterium angulatum (xi) SEQUENCE DESCRIPTION: SEQ ID NO:21: (2) INFORMATION FOR SEQ ID NO:22: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 14 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: rRNA (vi) ORIGINAL SOURCE: (A) ORGANISM: Bifidobacterium angulatum (xi) SEQUENCE DESCRIPTION: SEQ ID NO:22: (2) INFORMATION FOR SEQ ID NO:23: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 25 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: rRNA (vi) ORIGINAL SOURCE: (A) ORGANISM: Bifidobacterium bifidum (xi) SEQUENCE DESCRIPTION: SEQ ID NO:23: (2) INFORMATION FOR SEQ ID NO:24: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 14 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: rRNA (vi) ORIGINAL SOURCE: (A) ORGANISM: Bifidobacterium bifidum (xi) SEQUENCE DESCRIPTION: SEQ ID NO:24: (2) INFORMATION FOR SEQ ID NO:25: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 29 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: rRNA (vi) ORIGINAL SOURCE: (A) ORGANISM: Bifidobacterium breve (xi) SEQUENCE DESCRIPTION: SEQ ID NO:25: (2) INFORMATION FOR SEQ ID NO:26: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 14 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: rRNA (vi) ORIGINAL SOURCE: (A) ORGANISM: Bifidobacterium breve (xi) SEQUENCE DESCRIPTION: SEQ ID NO:26: (2) INFORMATION FOR SEQ ID NO:27: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 25 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: rRNA (vi) ORIGINAL SOURCE: (A) ORGANISM: Bifidobacterium dentium (xi) SEQUENCE DESCRIPTION: SEQ ID NO:27: (2) INFORMATION FOR SEQ ID NO:28: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 14 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: rRNA (vi) ORIGINAL SOURCE: (A) ORGANISM: Bifidobacterium dentium (xi) SEQUENCE DESCRIPTION: SEQ ID NO:28: (2) INFORMATION FOR SEQ ID NO:29: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 24 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: rRNA (vi) ORIGINAL SOURCE: (A) ORGANISM: Bifidobacterium longum (xi) SEQUENCE DESCRIPTION: SEQ ID NO:29: (2) INFORMATION FOR SEQ ID NO:30: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 14 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: rRNA (vi) ORIGINAL SOURCE: (A) ORGANISM: Bifidobacterium longum (xi) SEQUENCE DESCRIPTION: SEQ ID NO:30: (2) INFORMATION FOR SEQ ID NO:31: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 47 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: rRNA (vi) ORIGINAL SOURCE: (A) ORGANISM: Bifidobacterium pseudolongum (xi) SEQUENCE DESCRIPTION: SEQ ID NO:31: (2) INFORMATION FOR SEQ ID NO:32: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 16 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: rRNA (vi) ORIGINAL SOURCE: (A) ORGANISM: Bifidobacterium bifidum (xi) SEQUENCE DESCRIPTION: SEQ ID NO:32: (2) INFORMATION FOR SEQ ID NO:33: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 16 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: rRNA (vi) ORIGINAL SOURCE: (A) ORGANISM: Bifidobacterium adoloescentis (xi) SEQUENCE DESCRIPTION: SEQ ID NO:33: (2) INFORMATION FOR SEQ ID NO:34: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 16 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: rRNA (vi) ORIGINAL SOURCE: (A) ORGANISM: Bifidobacterium angulatum (xi) SEQUENCE DESCRIPTION: SEQ ID NO:34: (2) INFORMATION FOR SEQ ID NO:35: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 16 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: rRNA (vi) ORIGINAL SOURCE: (A) ORGANISM: Bifidobacterium animalis (xi) SEQUENCE DESCRIPTION: SEQ ID NO:35: (2) INFORMATION FOR SEQ ID NO:36: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 16 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: rRNA (vi) ORIGINAL SOURCE: (A) ORGANISM: Bifidobacterium breve (xi) SEQUENCE DESCRIPTION: SEQ ID NO:36: (2) INFORMATION FOR SEQ ID NO:37: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 16 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: rRNA (vi) ORIGINAL SOURCE: (A) ORGANISM: Bifidobacterium dentium (xi) SEQUENCE DESCRIPTION: SEQ ID NO:37: (2) INFORMATION FOR SEQ ID NO:38: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 16 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: rRNA (vi) ORIGINAL SOURCE: (A) ORGANISM: Bifidobacterium infantis (xi) SEQUENCE DESCRIPTION: SEQ ID NO:38: (2) INFORMATION FOR SEQ ID NO:39: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 16 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: rRNA (vi) ORIGINAL SOURCE: (A) ORGANISM: Bifidobacterium longum (xi) SEQUENCE DESCRIPTION: SEQ ID NO:39:

Claims: An oligonucleotide which specifically hybridizes to Bifidobacterium infantis rRNA represented by the sequence of formula (I) or a sequence complementary thereto: The oligonucleotide as claimed in Claim 1, wherein said oligonucleotide having a sequence complementary to the sequence represented by formula (I) has a DNA sequence represented by formula (I'): The oligonucleotide as claimed in Claim 1, wherein said oligonucleotide has a DNA sequence represented by formula (I"): An oligonucleotide which specifically hybridizes to Bifidobacterium bifidum rRNA represented by the sequence of formula (II) or a sequence complementary thereto: The oligonucleotide as claimed in Claim 4, wherein said oligonucleotide having a sequence complementary to the sequence represented by formula (II) has a DNA sequence represented by formula (II'): The oligonucleotide as claimed in Claim 4, wherein said oligonucleotide has a DNA sequence represented by formula (II"): An oligonucleotide which specifically hybridizes to Bifidobacterium adolescentis rRNA represented by the sequence of formula (III) or a sequence complementary thereto: The oligonucleotide as claimed in Claim 7, wherein said oligonucleotide having a sequence complementary to the sequence represented by formula (III) has a DNA sequence represented by formula (III'): The oligonucleotide as claimed in Claim 7, wherein said oligonucleotide has a DNA sequence represented by formula (III"): An oligonucleotide which specifically hybridizes to Bifidobacterium breve rRNA represented by the sequence of formula (IV) or a sequence complementary thereto: The oligonucleotide as claimed in Claim 10, wherein said oligonucleotide having a sequence complementary to the sequence represented by formula (IV) has a DNA sequence represented by formula (IV'): The oligonucleotide as claimed in Claim 10, wherein said oligonucleotide has a DNA sequence represented by formula (IV"): An oligonucleotide which specifically hybridizes to Bifidobacterium longum rRNA represented by the sequence of formula (V) or a sequence complementary thereto: The oligonucleotide as claimed in Claim 13, wherein said oligonucleotide having a sequence complementary to the sequence represented by formula (V) has a DNA sequence represented by formula (V'): The oligonucleotide as claimed in Claim 13, wherein said oligonucleotide has a DNA sequence represented by formula (V"): A method of species-specifically detecting species of the genus Bifidobacterium found in humans comprising the steps of: (A) contacting a sample with an oligonucleotide probe in a hybridizing solution, wherein said probe is selected from the group consisting of: (1) a labeled oligonucleotide which specifically hybridizes to Bifidobacterium infantis rRNA represented by the sequence of formula (I): or a sequence complementary thereto; (2) a labeled oligonucleotide which specifically hybridizes to Bifidobacterium bifidum rRNA represented by the sequence of formula (II): or a sequence complementary thereto; (3) a labeled oligonucleotide which specifically hybridizes to Bifidobacterium adolescentis rRNA represented by the sequence of formula (III): or a sequence complementary thereto; (4) a labeled oligonucleotide which specifically hybridizes to Bifidobacterium breve rRNA represented by the sequence of formula (IV): or a sequence complementary thereto; and (5) a labeled oligonucleotide which specifically hybridizes to Bifidobacterium longum rRNA represented by the sequence of formula (V): or a sequence complementary thereto, and (B) determining whether said probe hybridizes to nucleic acids in said sample so as to detect whether said species of said genus is present in said sample. The method as claimed in Claim 16, wherein said labeled oligonucleotide is an oligonucleotide labeled with a radioisotope. The method as claimed in Claim 16, wherein said labeled oligonucleotide is an oligonucleotide labeled with fluorescent molecules. The method as claimed in Claim 16, wherein said labeled oligonucleotide is an oligonucleotide labeled with an enzyme. The method as claimed in Claim 16, wherein said labeled oligonucleotide is an oligonucleotide labeled with a biotin.

Inventors: MOROTOMI MASAMI, TANAKA RYUICHIRO, YAMAMOTO TAKAHARU, MOROTOMI, MASAMI, TANAKA, RYUICHIRO, YAMAMOTO, TAKAHARU, Morotomi, Masami, c/o K.K. Yakult Honsha, Tanaka, Ryuichiro, c/o K.K. Yakult Honsha, Yamamoto, Takaharu, c/o K.K. Yakult Honsha
Applicants: YAKULT HONSHA KK, KABUSHIKI KAISHA YAKULT HONSHA
Application year: 1993
Main classification: C12Q1
IPC codes: C12Q1