La1 - the genome of a lactobacillus strain

Abstract

The present invention pertains to the use of the DNA sequence of a Lactobacillus johnsonii strain, in particular to its genomic sequence for elucidating interactions of micro-organism with hosts they colonize, and moreover for elucidating the basis of probiotic properties exhibited by such strain. In addition, the present invention also relates to methods of detecting nucleic acids or polypeptides of Lactobacilli and related species, respectively. A data carrier is provided comprising nucleotide sequences and/or polypeptide sequences of La1.

1 . A method for elucidating an interaction between a host and a bacteria which comprises providing a DNA sequence as identified by SEQ ID. No. 1 or part thereof or sequences homologous thereto and contacting the sequence with the host and bacteria in order to elucidate the interaction.  
     
     
         2 . The method according to  claim 1 , wherein the interaction is based on one or more of probiotic properties, anti-pathogenic properties or anti-viral properties of bacterial strains.  
     
     
         3 . The method according to  claim 1 , wherein the interaction is based on probiotic properties of bacterial strains for stimulating the immune system,  
     
     
         4 . The method according to  claim 1 , wherein the sequence is a fragment of SEQ. ID. No. 1 selected from the group consisting of from nucleotide 1-54596, from 56070-77430, from 81302-308537, from 309588-342757, from 378458-389217, from 389779-404510, from 405561-501116, from 503873-558194, from 563262-696518, from 697569-721736, from 722787-756845, from 761682-860446, from 860723-865550, from 867260-867490, from 868541-1448288, from 1463851-1526077, from 1527278-1552024, from 1563147-1809115, from 1810166-1858190, from 1863258-1872871, from 1877939-1930430, from 1932063-1983043, based on the numbering of SEQ ID. No. 1.  
     
     
         5 . The method according to  claim 1 , for the detection, identification or selection of a  Lactobacillus  strain in a biological sample, comprising: 
 (a) contacting the sample with a nucleotide sequence derived from a polynucleotide sequence as identified by SEQ ID. No. 1 in the presence of a polymerase enzyme and nucleotides under conditions which permit extension of the nucleotide; and    (b) detecting the presence of extension products in the sample in which the detection of primer extension products indicates the presence of a  Lactobacillus  strain in the sample.    
     
     
         6 . The method according to  claim 5  wherein the strain is  Lactobacillus johnsonii.    
     
     
         7 . The method according to  claim 1 , for the detection, identification or selection of a  Lactobacillus  strain in a biological sample, comprising: 
 (a) contacting the sample with a nucleotide sequence derived from a polynucleotide sequence as identified by SEQ ID. NO. 1 under conditions which permit hybridization of complementary base pairs; and    (b) detecting the presence of hybridization complexes in the sample in which the detection of hybridization complexes indicates the presence of a  Lactobacillus  strain in the sample.    
     
     
         8 . The method according to  claim 7  wherein the strain is  Lactobacillus johnsonii.    
     
     
         9 . The method according to  claim 1 , for the detection, identification or selection of a  Lactobacillus  strain in a biological sample, comprising: 
 (a) contacting the sample with an antibody raised against a polypeptide derived from SEQ ID. No. 1 under conditions suitable for the formation of immune complexes; and    (b) detecting the presence of immune complexes in the sample, in which the detection of immune complexes indicates the presence of a  Lactobacillus  strain in the sample.    
     
     
         10 . The method according to  claim 9  wherein the strain is  Lactobacillus johnsonii.    
     
     
         11 . The method according to  claim 1 , for the detection, identification or selection of antibodies directed to  Lactobacillus  polypeptides in a biological sample, comprising: 
 (a) contacting the sample with a polypeptide produced according to  claim 4  under conditions suitable for the formation of immune complexes; and    (b) detecting the presence of immune complexes in the sample, in which the detection of immune complexes indicates the presence of  Lactobacillus  polypeptides in the sample.    
     
     
         12 . A DNA array/chip containing an array of polynucleotides comprising at least a polynucleotide derived from SEQ ID. No. 1.  
     
     
         13 . A protein array/chip containing an array of polypeptides comprising at least one of the polypeptides obtainable by expressing a polypeptide as identified by an open reading frame derived from SEQ. ID. No. 1.  
     
     
         14 . An antibody chip containing an array of antibodies comprising at least one antibody directed to a polypeptide obtainable by expressing an open reading frame in SEQ ID. No.  
     
     
         15 . The method according to  claim 1 , for screening, comprising: 
 (a) contacting a test compound with a polynucleotide as identified by SEQ ID. No. 1 or with a part thereof; and    (b) detecting whether binding occurs.    
     
     
         16 . The method according to  claim 1 , for screening, comprising: 
 (a) contacting a test compound with a polypeptide obtainable by expressing an open reading frame derived from SEQ ID. No. 1; and    (b) detecting whether binding occurs.    
     
     
         17 . The method according to  claim 1 , for screening, comprising: 
 (a) contacting a test compound with an antibody raised against a polypeptide obtainable by expressing an open reading frame derived from SEQ ID. No. 1; and    (b) detecting whether binding occurs.    
     
     
         18 . A kit comprising a polynucleotide as identified by SEQ. ID. No. 1 or parts thereof.  
     
     
         19 . The kit according to  claim 18 , wherein the polynucleotide is a primer or a probe and wherein the kit optionally contains a polymerase and deoxynucleotide triphosphates.  
     
     
         20 . A kit comprising containing an antibody raised against a polypeptide obtainable by expressing an open reading frame in SEQ ID. No. 1.  
     
     
         21 . A computer readable medium having recorded thereon a nucleic acid sequence as identified by SEQ ID. No. 1 or parts thereof or a polypeptide sequence derived from the nucleotide sequence as identified by SQE ID. No. 1.  
     
     
         22 . The computer readable medium according to  claim 21 , wherein said medium is selected from the group consisting of: 
 (a) a floppy disc;    (b) a hard disc;    (c) random access memory (RAM);    (d) read only memory (ROM); and    (e) CD-ROM.    
     
     
         23 . A computer-based system for identifying fragments of the  Lactobacillus johnsonii  genome comprising the following elements: 
 (a) a data storage means comprising a nucleic acid sequence as identified by SEQ ID. No. 1;    (b) search means for comparing a target sequence to the nucleotide sequence of the data storage means of step (a) to identify homologous sequence (s); and    (c) retrieval means for obtaining said homologous sequence (s) of step (b).