Patent Publication Number: US-2011064761-A1

Title: Novel sequences of brachyspira, immunogenic compositions, methods for preparation and use thereof

Description:
FIELD 
     This invention relates to novel genes in  Brachyspira hyodysenteriae  and the proteins encoded therein. This invention further relates to use of these novel genes and proteins for diagnosis of  B. hyodysenteriae  disease, vaccines against  B. hyodysenteriae  and for screening for compounds that kill  B. hyodysenteriae  or block the pathogenic effects of  B. hyodysenteriae . These sequences may also be useful for diagnostic and therapeutic and/or prophylactic treatment of diseases in animals caused by other  Brachyspira  species, including  B. intermedia, B. alvinipulli, B. aalborgi, B. innocens, B. murdochii , and  B. pilosicoli.    
     BACKGROUND 
     Swine dysentery is a significant endemic disease of pigs in Australia and worldwide. Swine dysentery is a contagious mucohaemorrhagic diarrhoeal disease, characterised by extensive inflammation and necrosis of the epithelial surface of the large intestine. Economic losses due to swine dysentery result mainly from growth retardation, costs of medication and mortality. The causative agent of swine dysentery was first identified as an anaerobic spirochaete ( Treponema hyodysenteriae ) in 1971, and was recently reassigned to the genus  Brachyspira  as  B. hyodysenteriae . Where swine dysentery is established in a piggery, the disease spectrum can vary from being mild, transient or unapparent, to being severe and even fatal. Medication strategies on individual piggeries may mask clinical signs and on some piggeries the disease may go unnoticed, or may only be suspected. Whether or not obvious disease occurs,  B. hyodysenteriae  may persist in infected pigs, or in other reservoir hosts such as rodents, or in the environment. All these sources pose potential for transmission of the disease to uninfected herds. Commercial poultry may also be colonized by  B. hyodysenteriae , although it is not clear how commonly this occurs under field conditions. 
     Colonisation by  B. hyodysenteriae  elicits a strong immunological response against the spirochaete, hence indirect evidence of exposure to the spirochaete can be obtained by measuring circulating antibody titres in the blood of infected animals. These antibody titres have been reported to be maintained at low levels, even in animals that have recovered from swine dysentery. Serological tests for detection of antibodies therefore have considerable potential for detecting subclinical infections and recovered carrier pigs that have undetectable numbers of spirochaetes in their large intestines. These tests would be particularly valuable in an easy to use kit form, such as an enzyme-linked immunosorbent assay. A variety of techniques have been developed to demonstrate the presence of circulating antibodies against  B. hyodysenteriae , including indirect fluorescent antibody tests, haemagglutination tests, microtitration agglutination tests, complement fixation tests, and ELISA using either lipopolysaccharide or whole sonicated spirochaetes as antigen. All these tests have suffered from problems of specificity, as related non-pathogenic intestinal spirochaetes can induce cross-reactive antibodies. These tests are useful for detecting herds where there is obvious disease and high circulating antibody titres, but they are problematic for identifying sub-clinically infected herds and individual infected pigs. Consequently, to date, no completely sensitive and specific assays are available for the detection of antibodies against  B. hyodysenteriae . The lack of suitable diagnostic tests has hampered control of swine dysentery. 
     A number of methods are employed to control swine dysentery, varying from the prophylactic use of antimicrobial agents, to complete destocking of infected herds and prevention of re-entry of infected carrier pigs. All these options are expensive and, if they are to be fully effective, they require the use of sophisticated diagnostic tests to monitor progress. Currently, detection of swine dysentery in herds with sub-clinical infections, and individual healthy carrier animals, remains a major problem and is hampering implementation of effective control measures. A definitive diagnosis of swine dysentery traditionally has required the isolation and identification of  B. hyodysenteriae  from the faeces or mucosa of diseased pigs. Major problems involved include the slow growth and fastidious nutritional requirements of these anaerobic bacteria and confusion due to the presence of morphologically similar spirochaetes in the normal flora of the pig intestine. A significant improvement in the diagnosis of individual affected pigs was achieved with the development of polymerase chain reaction (PCR) assays for the detection of spirochaetes from faeces. Unfortunately in practical applications the limit of detection of PCRs rendered it unable to detect carrier animals with subclinical infections. As a consequence of these diagnostic problems, there is a clear need to develop a simple and effective diagnostic tool capable of detecting  B. hyodysenteriae  infection at the herd and individual pig level. 
     A strong immunological response is induced against the spirochaete following colonization with  B. hyodysenteriae , and pigs recovered from swine dysentery are protected from re-infection. Despite this, attempts to develop vaccines to control swine dysentery have met with very limited success, either because they have provided inadequate protection on a herd basis, or they have been too costly and difficult to produce to make them commercially viable. Bacterin vaccines provide some level of protection, but they tend to be lipopolysaccharide serogroup-specific, which then requires the use of multivalent bacterins. Furthermore they are difficult and costly to produce on a large scale because of the fastidious anaerobic growth requirements of the spirochaete. 
     Several attempts have been made to develop attenuated live vaccines for swine dysentery. This approach has the disadvantage that attenuated strains show reduced colonisation, and hence cause reduced immune stimulation. There also is reluctance on the part of producers and veterinarians to use live vaccines for swine dysentery because of the possibility of reversion to virulence, especially as very little is known about genetic regulation and organization in  B. hyodysenteriae.    
     The use of recombinant subunit vaccines is an attractive alternative, since the products would be well-defined (essential for registration purposes), and relatively easy to produce on a large scale. To date the first reported use of a recombinant protein from  B. hyodysenteriae  as a vaccine candidate (a 38-kilodalton flagellar protein) failed to prevent colonisation in pigs. This failure is likely to relate specifically to the particular recombinant protein used, as well as to other more down-stream issues of delivery systems and routes, dose rates, choice of adjuvants etc. (Gabe, J D, Chang, R J, Slomiany, R, Andrews, W H and McCaman, M T (1995) Isolation of extracytoplasmic proteins from  Serpulina hyodysenteriae  B204 and molecular cloning of the flaB1 gene encoding a 38-kilodalton flagellar protein. Infection and Immunity 63:142-148). The first reported partially protective recombinant  B. hyodysenteriae  protein used for vaccination was a 29.7 kDa outer membrane lipoprotein (Bhlp29.7, also referred to as BmpB and BlpA) which had homology with the methionine-binding lipoproteins of various pathogenic bacteria. The use of the his-tagged recombinant Bhlp29.7 protein for vaccination of pigs, followed by experimental challenge with  B. hyodysenteriae , resulted in 17-40% of vaccinated pigs developing disease compared to 50-70% of the unvaccinated control pigs developing disease. Since the incidence of disease for the Bhlp29.7 vaccinated pigs was significantly (P=0.047) less than for the control pigs, Bhlp29.7 appeared to have potential as a swine dysentery vaccine component (La, T, Phillips, N D, Reichel, M P and Hampson, D J (2004). Protection of pigs from swine dysentery by vaccination with recombinant BmpB, a 29.7 kDa outer-membrane lipoprotein of  Brachyspira hyodysenteriae . Veterinary Microbiology 102:97-109). A number of other attempts have been made to identify outer envelop proteins from  B. hyodysenteriae  that could be used as recombinant vaccine components, but again no successful vaccine has yet been made. A much more global approach is needed to the identification of potentially useful immunogenic recombinant proteins from  B. hyodysenteriae  is needed. 
     To date, only one study using DNA for vaccination has been reported. In this study, the  B. hyodysenteriae  ftnA gene, encoding a putative ferritin, was cloned into an  E. coli  plasmid and the plasmid DNA used to coat gold beads for ballistic vaccination. A murine model for swine dysentery was used to determine the protective nature of vaccination with DNA and/or recombinant protein. Vaccination with recombinant protein induced a good systemic response against ferritin however vaccination with DNA induced only a detectable systemic response. Vaccination with DNA followed a boost with recombinant protein induced a systemic immune response to ferritin only after boosting with protein. However, none of the vaccination regimes tested was able to provide the mice with protection against  B. hyodysenteriae  colonisation and the associated lesions. Interestingly, vaccination of the mice with DNA alone resulted in significant exacerbation of disease (Davis, A. J., Smith, S. C. and Moore, R. J. (2005). The  Brachyspira hyodysenteriae  ftnA gene: DNA vaccination and real-time PCR quantification of bacteria in a mouse model of disease. Current Microbiology 50: 285-291). 
     SUMMARY 
     Inventors have identified novel genes from  B. hyodysenteriae  and the proteins encoded by those genes. They have further identified that these novel genes and proteins can be used for therapeutic and diagnostic purposes. Moreover, the inventors have identified that these genes and/or the proteins can be used as a vaccine against  B. hyodysenteriae  and/or diagnose  B. hyodysenteriae  infections. 
     Accordingly, in a first aspect, the present invention provides novel  B. hyodysenteriae  polynucleotides having the nucleotide sequence contained in SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21 and 23. The present invention also provides nucleotide sequences that are homologous to SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21 and 23, where the homology can be 95%, 90%, 85%, 80%, 75% and 70%. This invention also includes a DNA vaccine or DNA immunogenic composition containing the nucleotide sequence of SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21 and 23 and sequences that are 95%, 90%, 85%, 80%, 75% and 70% homologous to these sequences. This invention further includes a diagnostic assay containing DNA having the nucleotide sequence of SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21 and 23 and sequences that are 95%, 90%, 85%, 80%, 75% and 70% homologous to these sequences. 
     In one aspect of the invention, the vaccine composition is a vaccine composition comprising at least two polynucleotides encoding protease molecules selected from the group consisting of SEQ ID No.1, 3, 5 and 7 for the treatment or prevention of swine dysentery associated with  Brachyspira hyodysenteriae.    
     In another aspect of the invention, the vaccine composition is a vaccine composition comprising at least three polynucleotides encoding protease molecules selected from the group consisting of SEQ ID No.1, 3, 5 and 7 for the treatment or prevention of swine dysentery associated with  Brachyspira hyodysenteriae.    
     In yet another aspect of the invention, the vaccine composition is a vaccine composition consisting of polynucleotides encoding protease molecules selected from the group consisting of: SEQ ID No.1, 3, 5 and 7 for the treatment or prevention of swine dysentery associated with  Brachyspira hyodysenteriae.    
     In a further aspect of the invention, the vaccine composition is a vaccine composition comprising at least two polynucleotides encoding lipase and/or peptidase molecules selected from the group consisting of SEQ ID No.9, 11, 13 and 15 for the treatment or prevention of swine dysentery associated with  Brachyspira hyodysenteriae.    
     In another aspect of the invention, the vaccine composition is a vaccine composition comprising at least three polynucleotides encoding lipase and/or peptidase molecules selected from the group consisting of SEQ ID No.9, 11, 13 and 15 for the treatment or prevention of swine dysentery associated with  Brachyspira hyodysenteriae.    
     In yet another aspect of the invention, the vaccine composition is a vaccine composition consisting of polynucleotides encoding lipase and/or peptidase molecules selected from the group consisting of: SEQ ID No.9, 11, 13 and 15 for the treatment or prevention of swine dysentery associated with  Brachyspira hyodysenteriae.    
     In a further aspect of the invention, the vaccine composition is a vaccine composition comprising at least two polynucleotides encoding toxin molecules selected from the group consisting of SEQ ID No.17, 19, 21 and 23 for the treatment or prevention of swine dysentery associated with  Brachyspira hyodysenteriae.    
     In another aspect of the invention, the vaccine composition is a vaccine composition comprising at least three polynucleotides encoding toxin molecules selected from the group consisting of SEQ ID No.17, 19, 21 and 23 for the treatment or prevention of swine dysentery associated with  Brachyspira hyodysenteriae.    
     In yet another aspect of the invention, the vaccine composition is a vaccine composition consisting of polynucleotides encoding toxin molecules selected from the group consisting of: SEQ ID No.17, 19, 21 and 23 for the treatment or prevention of swine dysentery associated with  Brachyspira hyodysenteriae.    
     In another aspect of the invention, the vaccine composition is vaccine composition comprising at least one polynucleotide encoding hemolysin molecules selected from the group consisting of SEQ ID No.25, 27, 29 and 31 together with at least one polynucleotide selected from the group consisting of SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21 and 23 for the treatment or prevention of swine dysentery associated with  Brachyspira hyodysenteriae.    
     In another aspect of the invention, the vaccine composition is a vaccine composition comprising: 
     (i) at least one polynucleotide encoding a protease molecule selected from the group of: SEQ ID No.1, 3, 5 and 7; and/or
 
(ii) at least one polynucleotide encoding a lipase and/or peptidase molecule selected from the group of: SEQ ID No. 9, 11, 13 and 15 and/or
 
(iii) at least one polynucleotide encoding a toxin molecule selected from the group of: SEQ ID No. 17, 19, 21 and 23 and/or
 
(iv) at least one polynucleotide encoding a hemolysin molecule selected from the group of: SEQ ID No. 25, 27, 29 and 31 and/or
 
for the treatment or prevention of swine dysentery associated with  Brachyspira.  
 
     The present invention also provides plasmids containing DNA having the sequence of SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, and 31; prokaryotic and/or eukaryotic expression vectors containing DNA having the sequence of SEQ ID NOs:1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, and 31; and a cell containing the plasmids which contain DNA having the sequence of SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, and 31. 
     The present invention also provides novel  B. hyodysenteriae  proteins having the amino acid sequence contained in SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30 and 32. This invention also provides proteins that are 95%, 90%, 85%, 80%, 75% and 70% homologous to the sequences contained in SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30 and 32. The present invention also provides a vaccine or immunogenic composition to contain the proteins having the amino acid sequence contained in SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30 and 32 or amino acid sequences that are 95%, 90%, 85%, 80%, 75% and 70% homologous to the sequences contained in SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30 and 32. 
     In one aspect of the invention, the vaccine composition is a vaccine composition comprising at least two protease polypeptides selected from the group consisting of SEQ ID No.2, 4, 6 and 8 for the treatment or prevention of swine dysentery associated with  Brachyspira hyodysenteriae.    
     In another aspect of the invention, the vaccine composition is a vaccine composition comprising at least three protease polypeptides selected from the group consisting of SEQ ID No.2, 4, 6 and 8 for the treatment or prevention of swine dysentery associated with  Brachyspira hyodysenteriae.    
     In yet another aspect of the invention, the vaccine composition is a vaccine composition consisting of protease polypeptides SEQ ID No.2, 4, 6 and 8 for the treatment or prevention of swine dysentery associated with  Brachyspira hyodysenteriae.    
     In one aspect of the invention, the vaccine composition is a vaccine composition comprising at least two lipase and/or peptidase polypeptides selected from the group consisting of SEQ ID No.10, 12, 14 and 16 for the treatment or prevention of swine dysentery associated with  Brachyspira hyodysenteriae.    
     In another aspect of the invention, the vaccine composition is a vaccine composition comprising at least three lipase and/or peptidase polypeptides selected from the group consisting of SEQ ID No.10, 12, 14 and 16 for the treatment or prevention of swine dysentery associated with  Brachyspira hyodysenteriae.    
     In yet another aspect of the invention, the vaccine composition is a vaccine composition consisting of lipase and/or peptidase polypeptides from the group consisting of: SEQ ID No.10, 12, 14 and 16 for the treatment or prevention of swine dysentery associated with  Brachyspira hyodysenteriae.    
     In one aspect of the invention, the vaccine composition is a vaccine composition comprising at least two toxin polypeptides selected from the group consisting of SEQ ID No.18, 20, 22 and 24 for the treatment or prevention of swine dysentery associated with  Brachyspira hyodysenteriae.    
     In another aspect of the invention, the vaccine composition is a vaccine composition comprising at least three toxin polypeptides selected from the group consisting of SEQ ID No.18, 20, 22 and 24 for the treatment or prevention of swine dysentery associated with  Brachyspira hyodysenteriae.    
     In yet another aspect of the invention, the vaccine composition is a vaccine composition consisting of toxin polypeptides selected from the group consisting of: SEQ ID No.18, 20, 22 and 24 for the treatment or prevention of swine dysentery associated with  Brachyspira hyodysenteriae.    
     In a further aspect of the invention, the vaccine composition is a vaccine composition comprising: 
     (i) at least one protease polypeptide selected from the group of: SEQ ID No.2, 4, 6, or 8 and/or
 
(ii) at least one lipase and/or peptidase polypeptide selected from the group of: SEQ ID No. 10, 12, 14, or 16 and/or
 
(iii) at least one toxin selected from the group of: SEQ ID No. 18, 20, 22 or 24 and/or
 
(iv) at least one hemolysin selected from the group of: SEQ ID No. 26, 28, 30 or 32
 
for the treatment or prevention of swine dysentery associated with  Brachyspira hyodysenteriae.  
 
     It is a further aspect of this invention to have a diagnostic kit containing one or more proteins having a sequence contained in SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30 and 32 or that are 95%, 90%, 85%, 80%, 75% and 70% homologous to the sequences contained in SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30 and 32. 
     It is another aspect of this invention to have nucleotide sequences which encode the proteins having the amino acid sequence contained in SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30 and 32. The invention also covers plasmids, eukaryotic and prokaryotic expression vectors, and DNA vaccines which contain DNA having a sequence which encodes a protein having the amino acid sequence contained in SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30 and 32. Cells which contain these plasmids and expression vectors are included in this invention. 
     This invention includes monoclonal antibodies that bind to proteins having an amino acid sequence contained in SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30 and 32 or bind to proteins that are 95%, 90%, 85%, 80%, 75% and 70% homologous to the sequences contained in SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30 and 32. Diagnostic kits containing the monoclonal antibodies that bind to proteins having an amino acid sequence contained in SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30 and 32 or bind to proteins that are 95%, 90%, 85%, 80%, 75% and 70% homologous to the sequences contained in SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30 and 32 are included in this invention. These diagnostic kits can detect the presence of  B. hyodysenteriae  in an animal. The animal is preferably a mammal or a bird; more preferably, chicken, goose, duck, turkey, parakeet, dog, cat, hamster, gerbil, rabbit, ferret, horse, cow, sheep, pig, monkey, and human. 
     The invention also contemplates the method of preventing or treating an infection of  B. hyodysenteriae  in an animal by administering to an animal a DNA vaccine containing one or more nucleotide sequences listed in SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, and 31 or sequences that are 95%, 90%, 85%, 80%, 75% and 70% homologous to these sequences. This invention also covers a method of preventing or treating an infection of  B. hyodysenteriae  in an animal by administering to an animal a vaccine containing one or more proteins having the amino acid sequence containing in SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30 and 32 or sequences that are 95%, 90%, 85%, 80%, 75% and 70% homologous to these sequences. 
     The invention also contemplates the method of generating an immune response in an animal by administering to an animal an immunogenic composition containing one or more nucleotide sequences listed in SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, and 31 or sequences that are 95%, 90%, 85%, 80%, 75% and 70% homologous to these sequences. This invention also covers a method of generating an immune response in an animal by administering to an animal an immunogenic composition containing one or more proteins having the amino acid sequence containing in SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30 and 32 or sequences that are 95%, 90%, 85%, 80%, 75% and 70% homologous to these sequences. 
    
    
     DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS OF THE INVENTION 
     Before describing the present invention in detail, it is to be understood that this invention is not limited to particularly exemplified methods and may, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments of the invention only, and is not intended to be limiting which will be limited only by the appended claims. 
     All publications, patents and patent applications cited herein, whether supra or infra, are hereby incorporated by reference in their entirety. However, publications mentioned herein are cited for the purpose of describing and disclosing the protocols, reagents and vectors which are reported in the publications and which might be used in connection with the invention. Nothing herein is to be construed as an admission that the invention is not entitled to antedate such disclosure by virtue of prior invention. 
     Furthermore, the practice of the present invention employs, unless otherwise indicated, conventional immunological and molecular biological techniques and pharmacology within the skill of the art. Such techniques are well known to the skilled worker, and are explained fully in the literature. See, eg., Coligan, Dunn, Ploegh, Speicher and Wingfield “Current protocols in Protein Science” (1999) Volume I and II (John Wiley &amp; Sons Inc.); Sambrook et al., “Molecular Cloning: A Laboratory Manual” (1989), 2 nd  Edition (Cold Spring Harbor Laboratory press); and Prescott, Harley and Klein “Microbiology” (1999), 4 th  Edition (WBC McGraw-Hill). 
     It must be noted that as used herein and in the appended claims, the singular forms “a,” “an,” and “the” include plural reference unless the context clearly dictates otherwise. Thus, for example, a reference to “a gene” includes a plurality of such genes, and a reference to “an animal” is a reference to one or more animals, and so forth. Unless defined otherwise, all technical and scientific terms used herein have the same meanings as commonly understood by one of ordinary skill in the art to which this invention belongs. Although any materials and methods similar or equivalent to those described herein can be used to practice or test the present invention, the preferred materials and methods are now described. 
     In the broadest aspect of the invention there is provided a novel  B. hyodysenteriae  polynucleotide having the nucleotide sequence contained in SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21 and 23 or an amino acid sequence (polypeptide) encoded by these polynucleotides. 
     The term “amino acid” is intended to embrace all molecules, whether natural or synthetic, which include both an amino functionality and an acid functionality and capable of being included in a polymer of naturally-occurring amino acids. Exemplary amino acids include naturally-occurring amino acids; analogs, derivatives and congeners thereof; amino acid analogs having variant side chains; and all stereoisomers of any of any of the foregoing. 
     An animal can be a mammal or a bird that can be infected with  Brachyspira , especially  B. hyodysenteriae . Examples of mammals include dog, cat, hamster, gerbil, rabbit, ferret, horse, cow, sheep, pig, monkey, and human. Examples of birds include chicken, goose, duck, turkey, and parakeet. It is appreciated by those skilled in the art that certain  Brachyspira  species are capable of infecting a broad host range (see, for example, Hampson et al., 2006, Emerging Infectious diseases, Vol. 12(5), p 869-870, incorporated herein in its entirety by reference). Accordingly the term “animal” as used herein encompasses a range of animals, but especially pigs and poultry. 
     The term “conserved residue” refers to an amino acid that is a member of a group of amino acids having certain common properties. The term “conservative amino acid substitution” refers to the substitution (conceptually or otherwise) of an amino acid from one such group with a different amino acid from the same group. A functional way to define common properties between individual amino acids is to analyze the normalized frequencies of amino acid changes between corresponding proteins of homologous organisms (Schulz, G. E. and R. H. Schinner, Principles of Protein Structure, Springer-Verlag). According to such analyses, groups of amino acids may be defined where amino acids within a group exchange preferentially with each other, and therefore resemble each other most in their impact on the overall protein structure (Schulz, G. E. and R. H. Schirmer, Principles of Protein Structure, Springer-Verlag). Examples of amino acid groups defined in this manner include: (i) a positively-charged group containing Lys, Arg and His, (ii) a negatively-charged group containing Glu and Asp, (iii) an aromatic group containing Phe, Tyr and Trp, (iv) a nitrogen ring group containing His and Trp, (v) a large aliphatic nonpolar group containing Val, Leu and De, (vi) a slightly-polar group containing Met and Cys, (vii) a small-residue group containing Ser Thr, Asp, Asn, Gly, Ala, Glu, Gln and Pro, (viii) an aliphatic group containing Val, Leu, Ile, Met and Cys, and (ix) a small, hydroxyl group containing Ser and Thr. 
     A “fusion protein” or “fusion polypeptide” refers to a chimeric protein as that term is known in the art and may be constructed using methods known in the art. In many examples of fusion proteins, there are two different polypeptide sequences, and in certain cases, there may be more. The polynucleotide sequences encoding the fusion protein may be operably linked in frame so that the fusion protein may be translated correctly. A fusion protein may include polypeptide sequences from the same species or from different species. In various embodiments, the fusion polypeptide may contain one or more amino acid sequences linked to a first polypeptide. In the case where more than one amino acid sequence is fused to a first polypeptide, the fusion sequences may be multiple copies of the same sequence, or alternatively, may be different amino acid sequences. The fusion polypeptides may be fused to the N-terminus, the C-terminus, or the N- and C-terminus of the first polypeptide. Exemplary fusion proteins include polypeptides containing a glutathione S-transferase tag (GST-tag), histidine tag (His-tag), an immunoglobulin domain or an immunoglobulin binding domain. 
     The term “isolated polypeptide” refers to a polypeptide, in certain embodiments prepared from recombinant DNA or RNA, or of synthetic origin or natural origin, or some combination thereof, which (1) is not associated with proteins that it is normally found with in nature, (2) is separated from the cell in which it normally occurs, (3) is free of other proteins from the same cellular source, (4) is expressed by a cell from a different species, or (5) does not occur in nature. It is possible for an isolated polypeptide to exist, but not qualify as a purified polypeptide. 
     The term “isolated nucleic acid” and “isolated polynucleotide” refers to a polynucleotide whether genomic DNA, cDNA, mRNA, tRNA, rRNA, iRNA, or a polynucleotide obtained from a cellular organelle (such as mitochondria and chloroplast), or whether from synthetic origin, which (1) is not associated with the cell in which the “isolated nucleic acid” is found in nature, or (2) is operably linked to a polynucleotide to which it is not linked in nature. It is possible for an isolated polynucleotide to exist, but not qualify as a purified polynucleotide. 
     The term “nucleic acid” and “polynucleotide” refers to a polymeric form of nucleotides, either ribonucleotides or deoxyribonucleotides or a modified form of either type of nucleotide. The terms should also be understood to include, as equivalents, analogs of either RNA or DNA made from nucleotide analogs, and, as applicable to the embodiment being described, single-stranded (such as sense or antisense) and double-stranded polynucleotides. 
     The term “nucleic acid of the invention” and “polynucleotide of the invention” refers to a nucleic acid encoding a polypeptide of the invention. A polynucleotide of the invention may comprise all, or a portion of, a subject nucleic acid sequence; a nucleotide sequence at least 60%, 70%, 80%, 90%, 95%, 96%, 97%, 98% or 99% identical to a subject nucleic acid sequence; a nucleotide sequence that hybridizes under stringent conditions to a subject nucleic acid sequence; nucleotide sequences encoding polypeptides that are functionally equivalent to polypeptides of the invention; nucleotide sequences encoding polypeptides at least about 60%, 70%, 80%, 85%, 90%, 95%, 98%, 99% homologous or identical with a subject amino acid sequence; nucleotide sequences encoding polypeptides having an activity of a polypeptide of the invention and having at least about 60%, 70%, 80%, 85%, 90%, 95%, 98%, 99% or more homology or identity with a subject amino acid sequence; nucleotide sequences that differ by 1 to about 2, 3, 5, 7, 10, 15, 20, 30, 50, 75 or more nucleotide substitutions, additions or deletions, such as allelic variants, of a subject nucleic acid sequence; nucleic acids derived from and evolutionarily related to a subject nucleic acid sequence; and complements of, and nucleotide sequences resulting from the degeneracy of the genetic code, for all of the foregoing and other nucleic acids of the invention. Nucleic acids of the invention also include homologs, e.g., orthologs and paralogs, of a subject nucleic acid sequence and also variants of a subject nucleic acid sequence which have been codon optimized for expression in a particular organism (e.g., host cell). 
     The term “operably linked”, when describing the relationship between two nucleic acid regions, refers to a juxtaposition wherein the regions are in a relationship permitting them to function in their intended manner. For example, a control sequence “operably linked” to a coding sequence is ligated in such a way that expression of the coding sequence is achieved under conditions compatible with the control sequences, such as when the appropriate molecules (e.g., inducers and polymerases) are bound to the control or regulatory sequence(s). 
     The term “polypeptide”, and the terms “protein” and “peptide” which are used interchangeably herein, refers to a polymer of amino acids. Exemplary polypeptides include gene products, naturally-occurring proteins, homologs, orthologs, paralogs, fragments, and other equivalents, variants and analogs of the foregoing. 
     The terms “polypeptide fragment” or “fragment”, when used in reference to a reference polypeptide, refers to a polypeptide in which amino acid residues are deleted as compared to the reference polypeptide itself, but where the remaining amino acid sequence is usually identical to the corresponding positions in the reference polypeptide. Such deletions may occur at the amino-terminus or carboxy-terminus of the reference polypeptide, or alternatively both. Fragments typically are at least 5, 6, 8 or 10 amino acids long, at least 14 amino acids long, at least 20, 30, 40 or 50 amino acids long, at least 75 amino acids long, or at least 100, 150, 200, 300, 500 or more amino acids long. A fragment can retain one or more of the biological activities of the reference polypeptide. In certain embodiments, a fragment may comprise a domain having the desired biological activity, and optionally additional amino acids on one or both sides of the domain, which additional amino acids may number from 5, 10, 15, 20, 30, 40, 50, or up to 100 or more residues. Further, fragments can include a sub-fragment of a specific region, which sub-fragment retains a function of the region from which it is derived. In another embodiment, a fragment may have immunogenic properties. 
     The term “polypeptide of the invention” refers to a polypeptide containing a subject amino acid sequence, or an equivalent or fragment thereof. Polypeptides of the invention include polypeptides containing all or a portion of a subject amino acid sequence; a subject amino acid sequence with 1 to about 2, 3, 5, 7, 10, 15, 20, 30, 50, 75 or more conservative amino acid substitutions; an amino acid sequence that is at least 60%, 70%, 80%, 90%, 95%, 96%, 97%, 98%, or 99% identical to a subject amino acid sequence; and functional fragments thereof. Polypeptides of the invention also include homologs, e.g., orthologs and paralogs, of a subject amino acid sequence. 
     It is also possible to modify the structure of the polypeptides of the invention for such purposes as enhancing therapeutic or prophylactic efficacy, or stability (e.g., ex vivo shelf life, resistance to proteolytic degradation in vivo, etc.). Such modified polypeptides, when designed to retain at least one activity of the naturally-occurring form of the protein, are considered “functional equivalents” of the polypeptides described in more detail herein. Such modified polypeptides may be produced, for instance, by amino acid substitution, deletion, or addition, which substitutions may consist in whole or part by conservative amino acid substitutions. 
     For instance, it is reasonable to expect that an isolated conservative amino acid substitution, such as replacement of a leucine with an isoleucine or valine, an aspartate with a glutamate, a threonine with a serine, will not have a major affect on the biological activity of the resulting molecule. Whether a change in the amino acid sequence of a polypeptide results in a functional homolog may be readily determined by assessing the ability of the variant polypeptide to produce a response similar to that of the wild-type protein. Polypeptides in which more than one replacement has taken place may readily be tested in the same manner. 
     The term “purified” refers to an object species that is the predominant species present (i.e., on a molar basis it is more abundant than any other individual species in the composition). A “purified fraction” is a composition wherein the object species is at least about 50 percent (on a molar basis) of all species present. In making the determination of the purity or a species in solution or dispersion, the solvent or matrix in which the species is dissolved or dispersed is usually not included in such determination; instead, only the species (including the one of interest) dissolved or dispersed are taken into account. Generally, a purified composition will have one species that is more than about 80% of all species present in the composition, more than about 85%, 90%, 95%, 99% or more of all species present. The object species may be purified to essential homogeneity (contaminant species cannot be detected in the composition by conventional detection methods) wherein the composition is essentially a single species. A skilled artisan may purify a polypeptide of the invention using standard techniques for protein purification in light of the teachings herein. Purity of a polypeptide may be determined by a number of methods known to those of skill in the art, including for example, amino-terminal amino acid sequence analysis, gel electrophoresis, mass-spectrometry analysis and the methods described herein. 
     The terms “recombinant protein” or “recombinant polypeptide” refer to a polypeptide which is produced by recombinant DNA techniques. An example of such techniques includes the case when DNA encoding the expressed protein is inserted into a suitable expression vector which is in turn used to transform a host cell to produce the protein or polypeptide encoded by the DNA. 
     The term “regulatory sequence” is a generic term used throughout the specification to refer to polynucleotide sequences, such as initiation signals, enhancers, regulators and promoters, that are necessary or desirable to affect the expression of coding and non-coding sequences to which they are operably linked. Exemplary regulatory sequences are described in Goeddel;  Gene Expression Technology: Methods in Enzymology , Academic Press, San Diego, Calif. (1990), and include, for example, the early and late promoters of SV40, adenovirus or cytomegalovirus immediate early promoter, the lac system, the trp system, the TAC or TRC system, T7 promoter whose expression is directed by T7 RNA polymerase, the major operator and promoter regions of phage lambda, the control regions for fd coat protein, the promoter for 3-phosphoglycerate kinase or other glycolytic enzymes, the promoters of acid phosphatase (e.g., Pho5), the promoters of the yeast α-mating factors, the polyhedron promoter of the baculovirus system and other sequences known to control the expression of genes of prokaryotic or eukaryotic cells or their viruses, and various combinations thereof. The nature and use of such control sequences may differ depending upon the host organism. In prokaryotes, such regulatory sequences generally include promoter, ribosomal binding site, and transcription termination sequences. The term “regulatory sequence” is intended to include, at a minimum, components whose presence may influence expression, and may also include additional components whose presence is advantageous, for example, leader sequences and fusion partner sequences. In certain embodiments, transcription of a polynucleotide sequence is under the control of a promoter sequence (or other regulatory sequence) which controls the expression of the polynucleotide in a cell-type in which expression is intended. It will also be understood that the polynucleotide can be under the control of regulatory sequences which are the same or different from those sequences which control expression of the naturally-occurring form of the polynucleotide. 
     The term “sequence homology” refers to the proportion of base matches between two nucleic acid sequences or the proportion of amino acid matches between two amino acid sequences. When sequence homology is expressed as a percentage, e.g., 50%, the percentage denotes the proportion of matches over the length of sequence from a desired sequence that is compared to some other sequence. Gaps (in either of the two sequences) are permitted to maximize matching; gap lengths of 15 bases or less are usually used, 6 bases or less are used more frequently, with 2 bases or less used even more frequently. The term “sequence identity” means that sequences are identical (i.e., on a nucleotide-by-nucleotide basis for nucleic acids or amino acid-by-amino acid basis for polypeptides) over a window of comparison. The term “percentage of sequence identity” is calculated by comparing two optimally aligned sequences over the comparison window, determining the number of positions at which the identical amino acids or nucleotides occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the comparison window, and multiplying the result by 100 to yield the percentage of sequence identity. Methods to calculate sequence identity are known to those of skill in the art and described in further detail below. 
     The term “soluble” as used herein with reference to a polypeptide of the invention or other protein, means that upon expression in cell culture, at least some portion of the polypeptide or protein expressed remains in the cytoplasmic fraction of the cell and does not fractionate with the cellular debris upon lysis and centrifugation of the lysate. Solubility of a polypeptide may be increased by a variety of art recognized methods, including fusion to a heterologous amino acid sequence, deletion of amino acid residues, amino acid substitution (e.g., enriching the sequence with amino acid residues having hydrophilic side chains), and chemical modification (e.g., addition of hydrophilic groups). 
     The solubility of polypeptides may be measured using a variety of art recognized techniques, including, dynamic light scattering to determine aggregation state, UV absorption, centrifugation to separate aggregated from non-aggregated material, and SDS gel electrophoresis (e.g., the amount of protein in the soluble fraction is compared to the amount of protein in the soluble and insoluble fractions combined). When expressed in a host cell, the polypeptides of the invention may be at least about 1%, 2%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or more soluble, e.g., at least about 1%, 2%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or more of the total amount of protein expressed in the cell is found in the cytoplasmic fraction. In certain embodiments, a one liter culture of cells expressing a polypeptide of the invention will produce at least about 0.1, 0.2, 0.5, 1, 2, 5, 10, 20, 30, 40, 50 milligrams of more of soluble protein. In an exemplary embodiment, a polypeptide of the invention is at least about 10% soluble and will produce at least about 1 milligram of protein from a one liter cell culture. 
     The term “specifically hybridizes” refers to detectable and specific nucleic acid binding. Polynucleotides, oligonucleotides and nucleic acids of the invention selectively hybridize to nucleic acid strands under hybridization and wash conditions that minimize appreciable amounts of detectable binding to nonspecific nucleic acids. Stringent conditions may be used to achieve selective hybridization conditions as known in the art and discussed herein. Generally, the nucleic acid sequence homology between the polynucleotides, oligonucleotides, and nucleic acids of the invention and a nucleic acid sequence of interest will be at least 30%, 40%, 50%, 60%, 70%, 80%, 85%, 90%, 95%, 98%, 99%, or more. In certain instances, hybridization and washing conditions are performed under stringent conditions according to conventional hybridization procedures and as described further herein. 
     The terms “stringent conditions” or “stringent hybridization conditions” refer to conditions which promote specific hybridization between two complementary polynucleotide strands so as to form a duplex. Stringent conditions may be selected to be about 5° C. lower than the thermal melting point (Tm) for a given polynucleotide duplex at a defined ionic strength and pH. The length of the complementary polynucleotide strands and their GC content will determine the Tm of the duplex, and thus the hybridization conditions necessary for obtaining a desired specificity of hybridization. The Tm is the temperature (under defined ionic strength and pH) at which 50% of a polynucleotide sequence hybridizes to a perfectly matched complementary strand. In certain cases it may be desirable to increase the stringency of the hybridization conditions to be about equal to the Tm for a particular duplex. 
     A variety of techniques for estimating the Tm are available. Typically, G-C base pairs in a duplex are estimated to contribute about 3° C. to the Tm, while A-T base pairs are estimated to contribute about 2° C., up to a theoretical maximum of about 80-100° C. 
     However, more sophisticated models of Tm are available in which G-C stacking interactions, solvent effects, the desired assay temperature and the like are taken into account. For example, probes can be designed to have a dissociation temperature (Td) of approximately 60° C., using the formula: Td=(((3×#GC)+(2×#AT))×37)−562)/#bp)-5; where #GC, #AT, and #bp are the number of guanine-cytosine base pairs, the number of adenine-thymine base pairs, and the number of total base pairs, respectively, involved in the formation of the duplex. 
     Hybridization may be carried out in 5×SSC, 4×SSC, 3×SSC, 2×SSC, 1×SSC or 0.2×SSC for at least about 1 hour, 2 hours, 5 hours, 12 hours, or 24 hours. The temperature of the hybridization may be increased to adjust the stringency of the reaction, for example, from about 25° C. (room temperature), to about 45° C., 50° C., 55° C., 60° C., or 65° C. The hybridization reaction may also include another agent affecting the stringency, for example, hybridization conducted in the presence of 50% formamide increases the stringency of hybridization at a defined temperature. 
     The hybridization reaction may be followed by a single wash step, or two or more wash steps, which may be at the same or a different salinity and temperature. For example, the temperature of the wash may be increased to adjust the stringency from about 25° C. (room temperature), to about 45° C., 50° C., 55° C., 60° C., 65° C., or higher. The wash step may be conducted in the presence of a detergent, e.g., 0.1 or 0.2% SDS. For example, hybridization may be followed by two wash steps at 65° C. each for about 20 minutes in 2×SSC, 0.1% SDS, and optionally two additional wash steps at 65° C. each for about 20 minutes in 0.2×SSC, 0.1% SDS. 
     Exemplary stringent hybridization conditions include overnight hybridization at 65° C. in a solution containing 50% formamide, 10×Denhardt (0.2% Ficoll, 0.2% polyvinylpyrrolidone, 0.2% bovine serum albumin) and 200 μg/ml of denatured carrier DNA, e.g., sheared salmon sperm DNA, followed by two wash steps at 65° C. each for about 20 minutes in 2×SSC, 0.1% SDS, and two wash steps at 65° C. each for about 20 minutes in 0.2×SSC, 0.1% SDS. 
     Hybridization may consist of hybridizing two nucleic acids in solution, or a nucleic acid in solution to a nucleic acid attached to a solid support, e.g., a filter. When one nucleic acid is on a solid support, a prehybridization step may be conducted prior to hybridization. Prehybridization may be carried out for at least about 1 hour, 3 hours or 10 hours in the same solution and at the same temperature as the hybridization solution (without the complementary polynucleotide strand). 
     Appropriate stringency conditions are known to those skilled in the art or may be determined experimentally by the skilled artisan. See, for example, Current Protocols in Molecular Biology, John Wiley &amp; Sons, N.Y. (1989), 6.3.1-12.3.6; Sambrook et al., 1989, Molecular Cloning, A Laboratory Manual, Cold Spring Harbor Press, N.Y.; S. Agrawal (ed.) Methods in Molecular Biology, volume 20; Tijssen (1993) Laboratory Techniques in Biochemistry and Molecular Biology—Hybridization With Nucleic Acid Probes, e.g., part I chapter 2 “Overview of principles of hybridization and the strategy of nucleic acid probe assays”, Elsevier, N.Y.; and Tibanyenda, N. et al., Eur. J. Biochem. 139:19 (1984) and Ebel, S. et al., Biochem. 31:12083 (1992). 
     The term “vector” refers to a nucleic acid capable of transporting another nucleic acid to which it has been linked. One type of vector which may be used in accord with the invention is an episome, i.e., a nucleic acid capable of extra-chromosomal replication. Other vectors include those capable of autonomous replication and expression of nucleic acids to which they are linked. Vectors capable of directing the expression of genes to which they are operatively linked are referred to herein as “expression vectors”. In general, expression vectors of utility in recombinant DNA techniques are often in the form of “plasmids” which refer to circular double stranded DNA molecules which, in their vector form are not bound to the chromosome. In the present specification, “plasmid” and “vector” are used interchangeably as the plasmid is the most commonly used form of vector. However, the invention is intended to include such other forms of expression vectors which serve equivalent functions and which become known in the art subsequently hereto. 
     The nucleic acids of the invention may be used as diagnostic reagents to detect the presence or absence of the target DNA or RNA sequences to which they specifically bind, such as for determining the level of expression of a nucleic acid of the invention. In one aspect, the present invention contemplates a method for detecting the presence of a nucleic acid of the invention or a portion thereof in a sample, the method of the steps of: (a) providing an oligonucleotide at least eight nucleotides in length, the oligonucleotide being complementary to a portion of a nucleic acid of the invention; (b) contacting the oligonucleotide with a sample containing at least one nucleic acid under conditions that permit hybridization of the oligonucleotide with a nucleic acid of the invention or a portion thereof; and (c) detecting hybridization of the oligonucleotide to a nucleic acid in the sample, thereby detecting the presence of a nucleic acid of the invention or a portion thereof in the sample. In another aspect, the present invention contemplates a method for detecting the presence of a nucleic acid of the invention or a portion thereof in a sample, by (a) providing a pair of single stranded oligonucleotides, each of which is at least eight nucleotides in length, complementary to sequences of a nucleic acid of the invention, and wherein the sequences to which the oligonucleotides are complementary are at least ten nucleotides apart; and (b) contacting the oligonucleotides with a sample containing at least one nucleic acid under hybridization conditions; (c) amplifying the nucleotide sequence between the two oligonucleotide primers; and (d) detecting the presence of the amplified sequence, thereby detecting the presence of a nucleic acid of the invention or a portion thereof in the sample. 
     In another aspect of the invention, the polynucleotide of the invention is provided in an expression vector containing a nucleotide sequence encoding a polypeptide of the invention and operably linked to at least one regulatory sequence. It should be understood that the design of the expression vector may depend on such factors as the choice of the host cell to be transformed and/or the type of protein desired to be expressed. The vector&#39;s copy number, the ability to control that copy number and the expression of any other protein encoded by the vector, such as antibiotic markers, should be considered. 
     An expression vector containing the polynucleotide of the invention can then be used as a pharmaceutical agent to treat an animal infected with  B. hyodysenteriae  or as a vaccine (also a pharmaceutical agent) to prevent an animal from being infected with  B. hyodysenteriae , or to reduce the symptoms and course of the disease if the animal does become infected. One manner of using an expression vector as a pharmaceutical agent is to administer a nucleic acid vaccine to the animal at risk of being infected or to the animal after being infected. Nucleic acid vaccine technology is well-described in the art. Some descriptions can be found in U.S. Pat. No. 6,562,376 (Hooper et al.); U.S. Pat. No. 5,589,466 (Feigner, et al.); U.S. Pat. No. 6,673,776 (Feigner, et al.); and U.S. Pat. No. 6,710,035 (Feigner, et al.). Nucleic acid vaccines can be injected into muscle or intradermally, can be electroporated into the animal (see WO 01/23537, King et al.; and WO 01/68889, Malone et al.), via lipid compositions (see U.S. Pat. No. 5,703,055, Feigner, et al), or other mechanisms known in the art field. 
     Expression vectors can also be transfected into bacteria which can be administered to the target animal to induce an immune response to the protein encoded by the nucleotides of this invention contained on the expression vector. The expression vector can contain eukaryotic expression sequences such that the nucleotides of this invention are transcribed and translated in the host animal. Alternatively, the expression vector can be transcribed in the bacteria and then translated in the host animal. The bacteria used as a carrier of the expression vector should be attenuated but still invasive. One can use  Shigella  spp.,  Salmonella  spp.,  Escherichia  spp., and  Aeromonas  spp., just to name a few, that have been attenuated but still invasive. Examples of these methods can be found in U.S. Pat. No. 5,824,538 (Branstrom et al); U.S. Pat. No. 5,877,159 (Powell, et al.); U.S. Pat. No. 6,150,170 (Powell, et al.); U.S. Pat. No. 6,500,419 (Hone, et al.); and U.S. Pat. No. 6,682,729 (Powell, et al.). 
     Alternatively, the polynucleotides of this invention can be placed in certain viruses which act a vector. Viral vectors can either express the proteins of this invention on the surface of the virus, or carry polynucleotides of this invention into an animal cell where the polynucleotide is transcribed and translated into a protein. The animal infected with the viral vectors can develop an immune response to the proteins encoded by the polynucleotides of this invention. Thereby one can alleviate or prevent an infection by  B. hyodysenteriae  in the animal which received the viral vectors. Examples of viral vectors can be found U.S. Pat. No. 5,283,191 (Morgan et al.); U.S. Pat. No. 5,554,525 (Sondermeijer et al) and U.S. Pat. No. 5,712,118 (Murphy). 
     The polynucleotide of the invention may be used to cause expression and over-expression of a polypeptide of the invention in cells propagated in culture, e.g. to produce proteins or polypeptides, including fusion proteins or polypeptides. 
     This invention pertains to a host cell transfected with a recombinant gene in order to express a polypeptide of the invention. The host cell may be any prokaryotic or eukaryotic cell. For example, a polypeptide of the invention may be expressed in bacterial cells, such as  E. coli , insect cells (baculovirus), yeast, plant, or mammalian cells. In those instances when the host cell is human, it may or may not be in a live subject. Other suitable host cells are known to those skilled in the art. Additionally, the host cell may be supplemented with tRNA molecules not typically found in the host so as to optimize expression of the polypeptide. Alternatively, the nucleotide sequence may be altered to optimize expression in the host cell, yet the protein produced would have high homology to the originally encoded protein. Other methods suitable for maximizing expression of the polypeptide will be known to those in the art. 
     The present invention further pertains to methods of producing the polypeptides of the invention. For example, a host cell transfected with an expression vector encoding a polypeptide of the invention may be cultured under appropriate conditions to allow expression of the polypeptide to occur. The polypeptide may be secreted and isolated from a mixture of cells and medium containing the polypeptide. Alternatively, the polypeptide may be retained cytoplasmically and the cells harvested, lysed and the protein isolated. 
     A cell culture includes host cells, media and other byproducts. Suitable media for cell culture are well known in the art. The polypeptide may be isolated from cell culture medium, host cells, or both using techniques known in the art for purifying proteins, including ion-exchange chromatography, gel filtration chromatography, ultrafiltration, electrophoresis, and immunoaffinity purification with antibodies specific for particular epitopes of a polypeptide of the invention. 
     Thus, a nucleotide sequence encoding all or a selected portion of polypeptide of the invention, may be used to produce a recombinant form of the protein via microbial or eukaryotic cellular processes. Ligating the sequence into a polynucleotide construct, such as an expression vector, and transforming or transfecting into hosts, either eukaryotic (yeast, avian, insect or mammalian) or prokaryotic (bacterial cells), are standard procedures. Similar procedures, or modifications thereof, may be employed to prepare recombinant polypeptides of the invention by microbial means or tissue-culture technology. 
     Suitable vectors for the expression of a polypeptide of the invention include plasmids of the types: pTrcHis-derived plasmids, pET-derived plasmids, pBR322-derived plasmids, pEMBL-derived plasmids, pEX-derived plasmids, pBTac-derived plasmids and pUC-derived plasmids for expression in prokaryotic cells, such as  E. coli . The various methods employed in the preparation of the plasmids and transformation of host organisms are well known in the art. For other suitable expression systems for both prokaryotic and eukaryotic cells, as well as general recombinant procedures, see  Molecular Cloning, A Laboratory Manual,  2nd Ed., ed. by Sambrook, Fritsch and Maniatis (Cold Spring Harbor Laboratory Press, 1989) Chapters 16 and 17. 
     Coding sequences for a polypeptide of interest may be incorporated as a part of a fusion gene including a nucleotide sequence encoding a different polypeptide. The present invention contemplates an isolated polynucleotide containing a nucleic acid of the invention and at least one heterologous sequence encoding a heterologous peptide linked in frame to the nucleotide sequence of the nucleic acid of the invention so as to encode a fusion protein containing the heterologous polypeptide. The heterologous polypeptide may be fused to (a) the C-terminus of the polypeptide of the invention, (b) the N-terminus of the polypeptide of the invention, or (c) the C-terminus and the N-terminus of the polypeptide of the invention. In certain instances, the heterologous sequence encodes a polypeptide permitting the detection, isolation, solubilization and/or stabilization of the polypeptide to which it is fused. In still other embodiments, the heterologous sequence encodes a polypeptide such as a poly His tag, myc, HA, GST, protein A, protein G, calmodulin-binding peptide, thioredoxin, maltose-binding protein, poly arginine, poly His-Asp, FLAG, a portion of an immunoglobulin protein, and a transcytosis peptide. 
     Fusion expression systems can be useful when it is desirable to produce an immunogenic fragment of a polypeptide of the invention. For example, the VP6 capsid protein of rotavirus may be used as an immunologic carrier protein for portions of polypeptide, either in the monomeric form or in the form of a viral particle. The nucleic acid sequences corresponding to the portion of a polypeptide of the invention to which antibodies are to be raised may be incorporated into a fusion gene construct which includes coding sequences for a late vaccinia virus structural protein to produce a set of recombinant viruses expressing fusion proteins comprising a portion of the protein as part of the virion. The Hepatitis B surface antigen may also be utilized in this role as well. Similarly, chimeric constructs coding for fusion proteins containing a portion of a polypeptide of the invention and the poliovirus capsid protein may be created to enhance immunogenicity (see, for example, EP Publication NO: 0259149; and Evans et al., (1989)  Nature  339:385; Huang et al., (1988)  J. Virol.  62:3855; and Schlienger et al., (1992)  J. Virol.  66:2). 
     Fusion proteins may facilitate the expression and/or purification of proteins. For example, a polypeptide of the invention may be generated as a glutathione-S-transferase (GST) fusion protein. Such GST fusion proteins may be used to simplify purification of a polypeptide of the invention, such as through the use of glutathione-derivatized matrices (see, for example,  Current Protocols in Molecular Biology , eds. Ausubel et al., (N.Y.: John Wiley &amp; Sons, 1991)). In another embodiment, a fusion gene coding for a purification leader sequence, such as a poly-(His)/enterokinase cleavage site sequence at the N-terminus of the desired portion of the recombinant protein, may allow purification of the expressed fusion protein by affinity chromatography using a Ni 2+  metal resin. The purification leader sequence may then be subsequently removed by treatment with enterokinase to provide the purified protein (e.g., see Hochuli et al., (1987)  J. Chromatography  411: 177; and Janknecht et al.,  PNAS USA  88:8972). 
     Techniques for making fusion genes are well known. Essentially, the joining of various DNA fragments coding for different polypeptide sequences is performed in accordance with conventional techniques, employing blunt-ended or stagger-ended termini for ligation, restriction enzyme digestion to provide for appropriate termini, filling-in of cohesive ends as appropriate, alkaline phosphatase treatment to avoid undesirable joining, and enzymatic ligation. In another embodiment, the fusion gene may be synthesized by conventional techniques including automated DNA synthesizers. Alternatively, PCR amplification of gene fragments may be carried out using anchor primers which give rise to complementary overhangs between two consecutive gene fragments which may subsequently be annealed to generate a chimeric gene sequence (see, for example,  Current Protocols in Molecular Biology , eds. Ausubel et al., John Wiley &amp; Sons: 1992). 
     In other embodiments, the invention provides for nucleic acids of the invention immobilized onto a solid surface, including, plates, microtiter plates, slides, beads, particles, spheres, films, strands, precipitates, gels, sheets, tubing, containers, capillaries, pads, slices, etc. The nucleic acids of the invention may be immobilized onto a chip as part of an array. The array may contain one or more polynucleotides of the invention as described herein. In one embodiment, the chip contains one or more polynucleotides of the invention as part of an array of polynucleotide sequences from the same pathogenic species as such polynucleotide(s). 
     In a preferred form of the invention there is provided isolated  B. hyodysenteriae  polypeptides as herein described, and also the polynucleotide sequences encoding these polypeptides. More desirably the  B. hyodysenteriae  polypeptides are provided in substantially purified form. 
     Preferred polypeptides of the invention will have one or more biological properties (e.g., in vivo, in vitro or immunological properties) of the native full-length polypeptide. Non-functional polypeptides are also included within the scope of the invention because they may be useful, for example, as antagonists of the functional polypeptides. The biological properties of analogues, fragments, or derivatives relative to wild type may be determined, for example, by means of biological assays. 
     Polypeptides, including analogues, fragments and derivatives, can be prepared synthetically (e.g., using the well known techniques of solid phase or solution phase peptide synthesis). Preferably, solid phase synthetic techniques are employed. Alternatively, the polypeptides of the invention can be prepared using well known genetic engineering techniques, as described infra. In yet another embodiment, the polypeptides can be purified (e.g., by immunoaffinity purification) from a biological fluid, such as but not limited to plasma, faeces, serum, or urine from animals, including, but not limited to, pig, chicken, goose, duck, turkey, parakeet, human, monkey, dog, cat, horse, hamster, gerbil, rabbit, ferret, horse, cattle, and sheep. 
     The  B. hyodysenteriae  polypeptide analogues include those polypeptides having the amino acid sequence, wherein one or more of the amino acids are substituted with another amino acid which substitutions do not substantially alter the biological activity of the molecule. 
     According to the invention, the polypeptides of the invention produced recombinantly or by chemical synthesis and fragments or other derivatives or analogues thereof, including fusion proteins, may be used as an immunogen to generate antibodies that recognize the polypeptides. 
     A molecule is “antigenic” when it is capable of specifically interacting with an antigen recognition molecule of the immune system, such as an immunoglobulin (antibody) or T cell antigen receptor. An antigenic amino acid sequence contains at least about 5, and preferably at least about 10, amino acids. An antigenic portion of a molecule can be the portion that is immunodominant for antibody or T cell receptor recognition, or it can be a portion used to generate an antibody to the molecule by conjugating the antigenic portion to a carrier molecule for immunization. A molecule that is antigenic need not be itself immunogenic, i.e., capable of eliciting an immune response without a carrier. 
     An “antibody” is any immunoglobulin, including antibodies and fragments thereof, that binds a specific epitope. The term encompasses polyclonal, monoclonal, and chimeric antibodies, the last mentioned described in further detail in U.S. Pat. Nos. 4,816,397 and 4,816,567, as well as antigen binding portions of antibodies, including Fab, F(ab′) 2  and F(v) (including single chain antibodies). Accordingly, the phrase “antibody molecule” in its various grammatical forms as used herein contemplates both an intact immunoglobulin molecule and an immunologically active portion of an immunoglobulin molecule containing the antibody combining site. An “antibody combining site” is that structural portion of an antibody molecule comprised of heavy and light chain variable and hypervariable regions that specifically binds an antigen. 
     Exemplary antibody molecules are intact immunoglobulin molecules, substantially intact immunoglobulin molecules and those portions of an immunoglobulin molecule that contain the paratope, including those portions known in the art as Fab, Fab′, F(ab′) 2  and F(v), which portions are preferred for use in the therapeutic methods described herein. 
     Fab and F(ab′) 2  portions of antibody molecules are prepared by the proteolytic reaction of papain and pepsin, respectively, on substantially intact antibody molecules by methods that are well-known. See for example, U.S. Pat. No. 4,342,566 to Theofilopolous et al. Fab′ antibody molecule portions are also well-known and are produced from F(ab′) 2  portions followed by reduction with mercaptoethanol of the disulfide bonds linking the two heavy chain portions, and followed by alkylation of the resulting protein mercaptan with a reagent such as iodoacetamide. An antibody containing intact antibody molecules is preferred herein. 
     The phrase “monoclonal antibody” in its various grammatical forms refers to an antibody having only one species of antibody combining site capable of immunoreacting with a particular antigen. A monoclonal antibody thus typically displays a single binding affinity for any antigen with which it immunoreacts. A monoclonal antibody may therefore contain an antibody molecule having a plurality of antibody combining sites, each immunospecific for a different antigen; e.g., a bispecific (chimeric) monoclonal antibody. 
     The term “adjuvant” refers to a compound or mixture that enhances the immune response to an antigen. An adjuvant can serve as a tissue depot that slowly releases the antigen and also as a lymphoid system activator that non-specifically enhances the immune response [Hood et al., in  Immunology , p. 384, Second Ed., Benjamin/Cummings, Menlo Park, Calif. (1984)]. Often, a primary challenge with an antigen alone, in the absence of an adjuvant, will fail to elicit a humoral or cellular immune response. Adjuvants include, but are not limited to, complete Freund&#39;s adjuvant, incomplete Freund&#39;s adjuvant, saponin, mineral gels such as aluminium hydroxide, surface active substances such as lysolecithin, pluronic polyols, polyanions, peptides, oil or hydrocarbon emulsions, keyhole limpet hemocyanins, dinitrophenol, and potentially useful human adjuvants such as BCG ( bacille Calmette - Guerin ) and  Corynebacterium parvum . Preferably, the adjuvant is pharmaceutically acceptable. 
     Various procedures known in the art may be used for the production of polyclonal antibodies to the polypeptides of the invention. For the production of antibody, various host animals can be immunised by injection with the polypeptide of the invention, including but not limited to rabbits, mice, rats, sheep, goats, etc. In one embodiment, a polypeptide of the invention can be conjugated to an immunogenic carrier, e.g., bovine serum albumin (BSA) or keyhole limpet hemocyanin (KLH). Various adjuvants may be used to increase the immunological response, depending on the host species, including but not limited to Freund&#39;s (complete and incomplete), mineral gels such as aluminum hydroxide, surface active substances such as lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, keyhole limpet hemocyanins, dinitrophenol, and potentially useful human adjuvants such as BCG ( bacille Calmette - Guerin ) and  Corynebacterium parvum.    
     For preparation of monoclonal antibodies directed toward a polypeptide of the invention, any technique that provides for the production of antibody molecules by continuous cell lines in culture may be used. These include but are not limited to the hybridoma technique originally developed by Kohler et al., (1975)  Nature,  256:495-497, the trioma technique, the human B-cell hybridoma technique [Kozbor et al., (1983)  Immunology Today,  4:72], and the EBV-hybridoma technique to produce human monoclonal antibodies [Cole et al., (1985) in  Monoclonal Antibodies and Cancer Therapy , pp. 77-96, Alan R. Liss, Inc.]. Immortal, antibody-producing cell lines can be created by techniques other than fusion, such as direct transformation of B lymphocytes with oncogenic DNA, or transfection with Epstein-Barr virus. See, e.g., U.S. Pat. Nos. 4,341,761; 4,399,121; 4,427,783; 4,444,887; 4,451,570; 4,466,917; 4,472,500; 4,491,632; and 4,493,890. 
     In an additional embodiment of the invention, monoclonal antibodies can be produced in germ-free animals utilising recent technology. According to the invention, chicken or swine antibodies may be used and can be obtained by using chicken or swine hybridomas or by transforming B cells with EBV virus in vitro. In fact, according to the invention, techniques developed for the production of “chimeric antibodies” [Morrison et al., (1984)  J. Bacteriol.,  159-870; Neuberger et al., (1984)  Nature,  312:604-608; Takeda et al., (1985)  Nature,  314:452-454] by splicing the genes from a mouse antibody molecule specific for a polypeptide of the invention together with genes from an antibody molecule of appropriate biological activity can be used; such antibodies are within the scope of this invention. Such chimeric antibodies are preferred for use in therapy of intestinal diseases or disorders (described infra), since the antibodies are much less likely than xenogenic antibodies to induce an immune response, in particular an allergic response, themselves. 
     According to the invention, techniques described for the production of single chain antibodies (U.S. Pat. No. 4,946,778) can be adapted to produce single chain antibodies specific for an polypeptide of the invention. An additional embodiment of the invention utilises the techniques described for the construction of Fab expression libraries [Huse et al., (1989)  Science,  246:1275-1281] to allow rapid and easy identification of monoclonal Fab fragments with the desired specificity for a polypeptide of the invention. 
     Antibody fragments, which contain the idiotype of the antibody molecule, can be generated by known techniques. For example, such fragments include but are not limited to: the F(ab′) 2  fragment which can be produced by pepsin digestion of the antibody molecule; the Fab′ fragments which can be generated by reducing the disulfide bridges of the F(ab′) 2  fragment, and the Fab fragments which can be generated by treating the antibody molecule with papain and a reducing agent. 
     In the production of antibodies, screening for the desired antibody can be accomplished by techniques known in the art, e.g., radioimmunoassay, ELISA, “sandwich” immunoassays, immunoradiometric assays, gel diffusion precipitin reactions, immunodiffusion assays, in situ immunoassays (using colloidal gold, enzyme or radioisotope labels, for example), Western blots, precipitation reactions, agglutination assays (e.g., gel agglutination assays, hemagglutination assays), complement fixation assays, immunofluorescence assays, protein A assays, immunoelectrophoresis assays, etc. In one embodiment, antibody binding is detected by detecting a label on the primary antibody. In another embodiment, the primary antibody is detected by detecting binding of a secondary antibody or reagent to the primary antibody. In a further embodiment, the secondary antibody is labelled. Many means are known in the art for detecting binding in an immunoassay and are within the scope of the present invention. For example, to select antibodies that recognise a specific epitope of a polypeptide of the invention, one may assay generated hybridomas for a product that binds to a fragment of a polypeptide of the invention containing such epitope. 
     The invention also covers diagnostic and prognostic methods to detect the presence of  B. hyodysenteriae  using a polypeptide of the invention and/or antibodies which bind to the polypeptide of the invention and kits useful for diagnosis and prognosis of  B. hyodysenteriae  infections. 
     Diagnostic and prognostic methods will generally be conducted using a biological sample obtained from an animal, such as chicken or swine. A “sample” refers to an animal&#39;s tissue or fluid suspected of containing a  Brachyspira  species, such as  B. hyodysenteriae , or its polynucleotides or its polypeptides. Examples of such tissue or fluids include, but not limited to, plasma, serum, faecal material, urine, lung, heart, skeletal muscle, stomach, intestines, and in vitro cell culture constituents. 
     The invention provides methods for detecting the presence of a polypeptide of the invention in a sample, with the following steps: (a) contacting a sample suspected of containing a polypeptide of the invention with an antibody (preferably bound to a solid support) that specifically binds to the polypeptide of the invention under conditions which allow for the formation of reaction complexes comprising the antibody and the polypeptide of the invention; and (b) detecting the formation of reaction complexes comprising the antibody and polypeptide of the invention in the sample, wherein detection of the formation of reaction complexes indicates the presence of the polypeptide of the invention in the sample. 
     Preferably, the antibody used in this method is derived from an affinity-purified polyclonal antibody, and more preferably a monoclonal antibody. In addition, it is preferable for the antibody molecules used herein be in the form of Fab, Fab′, F(ab′) 2  or F(v) portions or whole antibody molecules. 
     Particularly preferred methods for detecting  B. hyodysenteriae  based on the above method include enzyme linked immunosorbent assays, radioimmunoassays, immunoradiometric assays and immunoenzymatic assays, including sandwich assays using monoclonal and/or polyclonal antibodies. 
     Three such procedures that are especially useful utilise either polypeptide of the invention (or a fragment thereof) labelled with a detectable label, antibody Ab 1  labelled with a detectable label, or antibody Ab 2  labelled with a detectable label. The procedures may be summarized by the following equations wherein the asterisk indicates that the particle is labelled and “AA” stands for the polypeptide of the invention: 
         AA*+Ab   1   =AA*Ab   1   A.
 
         AA+Ab*   1   =AA Ab   1 *  B.
 
         AA+Ab   1   +Ab   2   *=Ab   1    AA Ab   2 *  C.
 
     The procedures and their application are all familiar to those skilled in the art and accordingly may be utilised within the scope of the present invention. The “competitive” procedure, Procedure A, is described in U.S. Pat. Nos. 3,654,090 and 3,850,752. Procedure B is representative of well-known competitive assay techniques. Procedure C, the “sandwich” procedure, is described in U.S. Pat. Nos. RE 31,006 and 4,016,043. Still other procedures are known, such as the “double antibody” or “DASP” procedure, and can be used. 
     In each instance, the polypeptide of the invention form complexes with one or more antibody(ies) or binding partners and one member of the complex is labelled with a detectable label. The fact that a complex has formed and, if desired, the amount thereof, can be determined by known methods applicable to the detection of labels. 
     It will be seen from the above, that a characteristic property of Ab 2  is that it will react with Ab 1 . This reaction is because Ab 1 , raised in one mammalian species, has been used in another species as an antigen to raise the antibody, Ab 2 . For example, Ab 2  may be raised in goats using rabbit antibodies as antigens. Ab 2  therefore would be anti-rabbit antibody raised in goats. For purposes of this description and claims, Ab 1  will be referred to as a primary antibody, and Ab 2  will be referred to as a secondary or anti-Ab 1  antibody. 
     The labels most commonly employed for these studies are radioactive elements, enzymes, chemicals that fluoresce when exposed to ultraviolet light, and others. Examples of fluorescent materials capable of being utilised as labels include fluorescein, rhodamine and auramine. A particular detecting material is anti-rabbit antibody prepared in goats and conjugated with fluorescein through an isothiocyanate. Examples of preferred isotope include  3 H,  14 C,  32 P,  35 S,  36 Cl,  51 Cr,  57 Co,  58 Co,  59 Fe,  90 Y,  125 I,  131 I, and  186 Re. The radioactive label can be detected by any of the currently available counting procedures. While many enzymes can be used, examples of preferred enzymes are peroxidase, β-glucuronidase, β-D-glucosidase, β-D-galactosidase, urease, glucose oxidase plus peroxidase and alkaline phosphatase. Enzyme are conjugated to the selected particle by reaction with bridging molecules such as carbodiimides, diisocyanates, glutaraldehyde and the like. Enzyme labels can be detected by any of the presently utilized colorimetric, spectrophotometric, fluorospectrophotometric, amperometric or gasometric techniques. U.S. Pat. Nos. 3,654,090; 3,850,752; and 4,016,043 are referred to by way of example for their disclosure of alternate labelling material and methods. 
     The invention also provides a method of detecting antibodies to a polypeptide of the invention in biological samples, using the following steps: (a) providing a polypeptide of the invention or a fragment thereof; (b) incubating a biological sample with said polypeptide of the invention under conditions which allow for the formation of an antibody-antigen complex; and (c) determining whether an antibody-antigen complex with the polypeptide of the invention is formed. 
     In another embodiment of the invention there are provided in vitro methods for evaluating the level of antibodies to a polypeptide of the invention in a biological sample using the following steps: (a) detecting the formation of reaction complexes in a biological sample according to the method noted above; and (b) evaluating the amount of reaction complexes formed, which amount of reaction complexes corresponds to the level of polypeptide of the invention in the biological sample. 
     Further there are provided in vitro methods for monitoring therapeutic treatment of a disease associated with  B. hyodysenteriae  in an animal host by evaluating, as describe above, the levels of antibodies to a polypeptide of the invention in a series of biological samples obtained at different time points from an animal host undergoing such therapeutic treatment. 
     The present invention further provides methods for detecting the presence or absence of  B. hyodysenteriae  in a biological sample by: (a) bringing the biological sample into contact with a polynucleotide probe or primer of polynucleotide of the invention under suitable hybridizing conditions; and (b) detecting any duplex formed between the probe or primer and nucleic acid in the sample. 
     According to one embodiment of the invention, detection of  B. hyodysenteriae  may be accomplished by directly amplifying polynucleotide sequences from biological sample, using known techniques and then detecting the presence of polynucleotide of the invention sequences. 
     In one form of the invention, the target nucleic acid sequence is amplified by PCR and then detected using any of the specific methods mentioned above. Other useful diagnostic techniques for detecting the presence of polynucleotide sequences include, but are not limited to: 1) allele-specific PCR; 2) single stranded conformation analysis; 3) denaturing gradient gel electrophoresis; 4) RNase protection assays; 5) the use of proteins which recognize nucleotide mismatches, such as the  E. coli  mutS protein; 6) allele-specific oligonucleotides; and 7) fluorescent in situ hybridisation. 
     In addition to the above methods polynucleotide sequences may be detected using conventional probe technology. When probes are used to detect the presence of the desired polynucleotide sequences, the biological sample to be analysed, such as blood or serum, may be treated, if desired, to extract the nucleic acids. The sample polynucleotide sequences may be prepared in various ways to facilitate detection of the target sequence; e.g. denaturation, restriction digestion, electrophoresis or dot blotting. The targeted region of the sample polynucleotide sequence usually must be at least partially single-stranded to form hybrids with the targeting sequence of the probe. If the sequence is naturally single-stranded, denaturation will not be required. However, if the sequence is double-stranded, the sequence will probably need to be denatured. Denaturation can be carried out by various techniques known in the art. 
     Sample polynucleotide sequences and probes are incubated under conditions that promote stable hybrid formation of the target sequence in the probe with the putative desired polynucleotide sequence in the sample. Preferably, high stringency conditions are used in order to prevent false positives. 
     Detection, if any, of the resulting hybrid is usually accomplished by the use of labelled probes. Alternatively, the probe may be unlabeled, but may be detectable by specific binding with a ligand that is labelled, either directly or indirectly. Suitable labels and methods for labelling probes and ligands are known in the art, and include, for example, radioactive labels which may be incorporated by known methods (e.g., nick translation, random priming or kinasing), biotin, fluorescent groups, chemiluminescent groups (e.g., dioxetanes, particularly triggered dioxetanes), enzymes, antibodies and the like. Variations of this basic scheme are known in the art, and include those variations that facilitate separation of the hybrids to be detected from extraneous materials and/or that amplify the signal from the labelled moiety. 
     It is also contemplated within the scope of this invention that the nucleic acid probe assays of this invention may employ a cocktail of nucleic acid probes capable of detecting the desired polynucleotide sequences of this invention. Thus, in one example to detect the presence of polynucleotide sequences of this invention in a cell sample, more than one probe complementary to a polynucleotide sequences is employed and in particular the number of different probes is alternatively 2, 3, or 5 different nucleic acid probe sequences. 
     The polynucleotide sequences described herein (preferably in the form of probes) may also be immobilised to a solid phase support for the detection of  Brachyspira  species, including but not limited to  B. hyodysenteriae, B. intermedia, B. alvinipulli, B. aalborgi, B. innocens, B. murdochii , and  B. pilosicoli . Alternatively the polynucleotide sequences described herein will form part of a library of DNA molecules that may be used to detect simultaneously a number of different genes from  Brachyspira  species, such as  B. hyodysenteriae . In a further alternate form of the invention polynucleotide sequences described herein together with other polynucleotide sequences (such as from other bacteria or viruses) may be immobilised on a solid support in such a manner permitting identification of the presence of a  Brachyspira  species, such as  B. hyodysenteriae  and/or any of the other polynucleotide sequences bound onto the solid support. 
     Techniques for producing immobilised libraries of DNA molecules have been described in the art. Generally, most prior art methods describe the synthesis of single-stranded nucleic acid molecule libraries, using for example masking techniques to build up various permutations of sequences at the various discrete positions on the solid substrate. U.S. Pat. No. 5,837,832 describes an improved method for producing DNA arrays immobilised to silicon substrates based on very large scale integration technology. In particular, U.S. Pat. No. 5,837,832 describes a strategy called “tiling” to synthesize specific sets of probes at spatially defined locations on a substrate that may be used to produced the immobilised DNA libraries of the present invention. U.S. Pat. No. 5,837,832 also provides references for earlier techniques that may also be used. Thus polynucleotide sequence probes may be synthesised in situ on the surface of the substrate. 
     Alternatively, single-stranded molecules may be synthesised off the solid substrate and each pre-formed sequence applied to a discrete position on the solid substrate. For example, polynucleotide sequences may be printed directly onto the substrate using robotic devices equipped with either pins or pizo electric devices. 
     The library sequences are typically immobilised onto or in discrete regions of a solid substrate. The substrate may be porous to allow immobilisation within the substrate or substantially non-porous, in which case the library sequences are typically immobilised on the surface of the substrate. The solid substrate may be made of any material to which polypeptides can bind, either directly or indirectly. Examples of suitable solid substrates include flat glass, silicon wafers, mica, ceramics and organic polymers such as plastics, including polystyrene and polymethacrylate. It may also be possible to use semi-permeable membranes such as nitrocellulose or nylon membranes, which are widely available. The semi-permeable membranes may be mounted on a more robust solid surface such as glass. The surfaces may optionally be coated with a layer of metal, such as gold, platinum or other transition metal. 
     Preferably, the solid substrate is generally a material having a rigid or semi-rigid surface. In preferred embodiments, at least one surface of the substrate will be substantially flat, although in some embodiments it may be desirable to physically separate synthesis regions for different polymers with, for example, raised regions or etched trenches. It is also preferred that the solid substrate is suitable for the high density application of DNA sequences in discrete areas of typically from 50 to 100 μm, giving a density of 10000 to 40000 dots/cm −2 . 
     The solid substrate is conveniently divided up into sections. This may be achieved by techniques such as photoetching, or by the application of hydrophobic inks, for example teflon-based inks (Cel-line, USA). 
     Discrete positions, in which each different member of the library is located may have any convenient shape, e.g., circular, rectangular, elliptical, wedge-shaped, etc. 
     Attachment of the polynucleotide sequences to the substrate may be by covalent or non-covalent means. The polynucleotide sequences may be attached to the substrate via a layer of molecules to which the library sequences bind. For example, the polynucleotide sequences may be labelled with biotin and the substrate coated with avidin and/or streptavidin. A convenient feature of using biotinylated polynucleotide sequences is that the efficiency of coupling to the solid substrate can be determined easily. Since the polynucleotide sequences may bind only poorly to some solid substrates, it is often necessary to provide a chemical interface between the solid substrate (such as in the case of glass) and the nucleic acid sequences. Examples of suitable chemical interfaces include hexaethylene glycol. Another example is the use of polylysine coated glass, the polylysine then being chemically modified using standard procedures to introduce an affinity ligand. Other methods for attaching molecules to the surfaces of solid substrate by the use of coupling agents are known in the art, see for example WO98/49557. 
     Binding of complementary polynucleotide sequences to the immobilised nucleic acid library may be determined by a variety of means such as changes in the optical characteristics of the bound polynucleotide sequence (i.e. by the use of ethidium bromide) or by the use of labelled nucleic acids, such as polypeptides labelled with fluorophores. Other detection techniques that do not require the use of labels include optical techniques such as optoacoustics, reflectometry, ellipsometry and surface plasmon resonance (see WO97/49989). 
     Thus, the present invention provides a solid substrate having immobilized thereon at least one polynucleotide of the present invention, preferably two or more different polynucleotide sequences of the present invention. 
     The present invention also can be used as a prophylactic or therapeutic, which may be utilised for the purpose of stimulating humoral and cell mediated responses in animals, such as chickens and swine, thereby providing protection against colonisation with  Brachyspira  species, including but not limited to  B. hyodysenteriae, B. intermedia, B. alvimpulli, B. aalborgi, B. innocens, B. murdochii , and  B. pilosicoli . Natural infection with a  Brachyspira  species, such as  B. hyodysenteriae  induces circulating antibody titres against the proteins described herein. Therefore, the amino acid sequences described herein or parts thereof, have the potential to form the basis of a systemically or orally administered prophylactic or therapeutic to provide protection against intestinal spirochaetosis. 
     It is well appreciated by those skilled in the art there is a high degree of sequence conservation between species of  Brachyspira . For example, as shown below  B. hyodysenteriae  toxin (H46) and outer membrane protein (H114) have a high degree of similarity between a number of  Brachyspira  species. Cross-species nucleotide similarity for  B. hyodysenteriae  lipase (H46) 
     
       
         
           
               
               
               
             
               
                   
                   
               
               
                   
                   
                 Similarity at nucleotide level (%) 
               
               
                   
                   Brachyspira  species 
                 H46 
               
               
                   
                   
               
             
            
               
                   
               
            
           
           
               
               
               
            
               
                   
                 
                   Brachyspira hyodysenteriae 
                 
                 100 
               
               
                   
                 
                   Brachyspira pilosicoli 
                 
                 81.9 
               
               
                   
                 
                   Brachyspira intermedia 
                 
                 95.5 
               
               
                   
                 
                   Brachyspira murdochii 
                 
                 85.9 
               
               
                   
                 
                   Brachyspira alvinipulli 
                 
                 84.8 
               
               
                   
                   
               
            
           
         
       
     
     Cross-species nucleotide similarity for  B. hyodysenteriae  toxin (H72) 
     
       
         
           
               
               
             
               
                   
               
               
                   
                 Similarity at nucleotide level (%) 
               
               
                   Brachyspira  species 
                 H72 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
            
               
                 
                   Brachyspira hyodysenteriae 
                 
                 100 
               
               
                 
                   Brachyspira pilosicoli 
                 
                 83.3 
               
               
                   Brachyspira  intermedia 
                 95.0 
               
               
                   Brachyspira  murdochii 
                 87.3 
               
               
                 
                   Brachyspira alvinipulli 
                 
                 85.8 
               
               
                   
               
            
           
         
       
     
     Also as shown in Example 22, the nucleotide and amino acid sequences of the present invention are capable of producing cross-reactivity over a range of  Brachyspira  species not just  B. hyodysenteriae . Accordingly, polypeptides used in the present invention are capable of use against other species of  Brachyspira  species not just  B. hyodysenteriae.    
     Accordingly, in one embodiment the present invention provides the amino acid sequences described herein or fragments thereof or antibodies that bind the amino acid sequences or the polynucleotide sequences described herein in a therapeutically effective amount admixed with a pharmaceutically acceptable carrier, diluent, or excipient. 
     The phrase “therapeutically effective amount” is used herein to mean an amount sufficient to reduce by at least about 15%, preferably by at least 50%, more preferably by at least 90%, and most preferably prevent, a clinically significant deficit in the activity, function and response of the animal host. Alternatively, a therapeutically effective amount is sufficient to cause an improvement in a clinically significant condition in the animal host. 
     The phrase “pharmaceutically acceptable” refers to molecular entities and compositions that are physiologically tolerable and do not typically produce an allergic or similarly untoward reaction, such as gastric upset and the like, when administered to an animal. The term “carrier” refers to a diluent, adjuvant, excipient, or vehicle with which the compound is administered. Such pharmaceutical carriers can be sterile liquids, such as water and oils, including those of petroleum, animal, vegetable or synthetic origin, such as peanut oil, soybean oil, mineral oil, sesame oil and the like. Water or saline solutions and aqueous dextrose and glycerol solutions are preferably employed as carriers, particularly for injectable solutions. Suitable pharmaceutical carriers are described in Martin,  Remington&#39;s Pharmaceutical Sciences,  18th Ed., Mack Publishing Co., Easton, Pa., (1990). 
     In a more specific form of the invention there are provided pharmaceutical compositions comprising therapeutically effective amounts of the amino acid sequences described herein or an analogue, fragment or derivative product thereof or antibodies thereto together with pharmaceutically acceptable diluents, preservatives, solubilizes, emulsifiers, adjuvants and/or carriers. Such compositions include diluents of various buffer content (e.g., Tris-HCl, acetate, phosphate), pH and ionic strength and additives such as detergents and solubilizing agents (e.g., Tween 80, Polysorbate 80), anti-oxidants (e.g., ascorbic acid, sodium metabisulfite), preservatives (e.g., Thimersol, benzyl alcohol) and bulking substances (e.g., lactose, mannitol). The material may be incorporated into particulate preparations of polymeric compounds such as polylactic acid, polyglycolic acid, etc. or into liposomes. Hylauronic acid may also be used. Such compositions may influence the physical state, stability, rate of in vivo release, and rate of in vivo clearance of the present proteins and derivatives. See, e.g., Martin,  Remington&#39;s Pharmaceutical Sciences,  18th Ed. (1990, Mack Publishing Co., Easton, Pa. 18042) pages 1435-1712 that are herein incorporated by reference. The compositions may be prepared in liquid form, or may be in dried powder, such as lyophilised form. 
     Alternatively, the polynucleotides of the invention can be optimized for expression in plants (e.g., corn). The plant may be transformed with plasmids containing the optimized polynucleotides. Then the plant is grown, and the proteins of the invention are expressed in the plant, or the plant-optimized version is expressed. The plant is later harvested, and the section of the plant containing the proteins of the invention is processed into feed for the animal. This animal feed will impart immunity against  B. hyodysenteriae  when eaten by the animal. Examples of prior art detailing these methods can be found in U.S. Pat. No. 5,914,123 (Arntzen, et al.); U.S. Pat. No. 6,034,298 (Lam, et al.); and U.S. Pat. No. 6,136,320 (Arntzen, et al.). 
     It will be appreciated that pharmaceutical compositions provided accordingly to the invention may be administered by any means known in the art. Preferably, the pharmaceutical compositions for administration are administered by injection, orally, or by the pulmonary, or nasal route. The amino acid sequences described herein or antibodies derived therefrom are more preferably delivered by intravenous, intraarterial, intraperitoneal, intramuscular, or subcutaneous routes of administration. Alternatively, the amino acid sequence described herein or antibodies derived therefrom, properly formulated, can be administered by nasal or oral administration. 
     In a specific embodiment of the invention, a vaccine composition may be a “combination vaccine” with one or more polynucleotide or polypeptide sequences of the invention which have a similar functional role that are combined in a vaccine. For example, the following four different functional groups can be combined as identified in the following tables: 
     
       
         
           
               
               
               
               
             
               
                   
                   
               
               
                   
                 Gene 
                 Polynucleotide sequence 
                 Polypeptide sequence 
               
               
                   
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 Group: Proteases 
               
            
           
           
               
               
               
               
            
               
                   
                 NAV-H197 
                 SEQ ID No. 1 
                 SEQ ID No. 2 
               
               
                   
                 NAV-H188 
                 SEQ ID No. 3 
                 SEQ ID No. 4 
               
               
                   
                 NAV-H185 
                 SEQ ID No. 5 
                 SEQ ID No. 6 
               
               
                   
                 NAV-H179 
                 SEQ ID No. 7 
                 SEQ ID No. 8 
               
            
           
           
               
            
               
                 Group: Lipases/Peptidases 
               
            
           
           
               
               
               
               
            
               
                   
                 NAV-H191 
                 SEQ ID No. 9 
                 SEQ ID No. 10 
               
               
                   
                 NAV-H186 
                 SEQ ID No. 11 
                 SEQ ID No. 12 
               
               
                   
                 NAV-H184 
                 SEQ ID No. 13 
                 SEQ ID No. 14 
               
               
                   
                 NAV-H46 
                 SEQ ID No. 15 
                 SEQ ID No. 16 
               
            
           
           
               
            
               
                 Group: Toxins 
               
            
           
           
               
               
               
               
            
               
                   
                 NAV-H177 
                 SEQ ID No. 17 
                 SEQ ID No. 18 
               
               
                   
                 NAV-H72 
                 SEQ ID No. 19 
                 SEQ ID No. 20 
               
               
                   
                 NAV-H66 
                 SEQ ID No. 21 
                 SEQ ID No. 22 
               
               
                   
                 NAV-H40 
                 SEQ ID No. 23 
                 SEQ ID No. 24 
               
            
           
           
               
            
               
                 Group: Hemolysins 
               
            
           
           
               
               
               
               
            
               
                   
                 NAV-H68 
                 SEQ ID No. 25 
                 SEQ ID No. 26 
               
               
                   
                 NAV-H43 
                 SEQ ID No. 27 
                 SEQ ID No. 28 
               
               
                   
                 NAV-H33 
                 SEQ ID No. 29 
                 SEQ ID No. 30 
               
               
                   
                 NAV-H32 
                 SEQ ID No. 31 
                 SEQ ID No. 32 
               
               
                   
                   
               
            
           
         
       
     
     A prerequisite for combination vaccines is a lack of competition (i.e. between antigens) and a high compatibility with respect to the subject to be immunized. According to international standard applied in connection with immunization, a combination vaccine should confer a protection which is comparable to that achieved by separate vaccinations. However, the combination of antigens is a complicated process which is associated with a number of problems and uncertainties. 
     As the individual components of a combination vaccine are not inert substances, the combination of various components into one mixture can negatively influence the immunogenicity of the individual antigenic components. For example, interactions between the different antigens or between the antigens and other components typically used in such vaccines can occur due to differences in charge, chemical residues, detergents, formaldehyde, concentration of ions etc. These changes can occur instantaneously after contacting the different antigens with each other or with other substances usually present in vaccine formulations. Moreover, these changes can also occur with a significant delay after mixing, for example during storage, shipping, etc. However, it cannot be predicted to which extent the immunogenicity of individual antigens may be influenced by mixing them to one combination. As a consequence, a situation can occur in which one or more antigens of the vaccine only confer an insufficient seroprotection against one or more of diseases which renders the product unsuitable for medical practice. 
     The production of effective combination vaccines is a complex matter which depends on multidimensional interactions between the individual components of the vaccine and does not allow to extrapolate any effect of the components observed when administered separately. 
     It has been found that the combination vaccines according to the present invention may be combined with one or more further antigens and remain effective and stable. 
     The term “stable” as used in the context of the present invention means that the combination vaccine formulation can be kept for a period of eight days or more preferably 14 days at room temperature without any substantial loss with respect to immunogenity and stability of its distinct antigen compounds. In order to enhance stability, stabilizing agents such as saccharose can be added to the vaccine composition. Instead of saccharose or in addition thereto, other stabilizers, e.g. human serum albumin, mannose, trehalose, mannite, or polygeline can also be added as stabilizing agents. The vaccines of the present invention exhibit a pH value of preferably between 5.0 to 8.0, more preferably between 6.0 to 7.0, wherein a pH value of 6.8 to 7.8 is most preferred. 
     The term “effective” as used herein, refers to the fact that the sequence of the invention upon single or repeated administration to a subject (for example, a mammal) confers protection against a specific disease. 
     As used herein the term “conferring protection” means that the sequence of the invention, upon administration, induces an immunological response in the vaccinated subject which response is capable to protect said subject from the symptoms of subsequent infection. 
     Also encompassed by the present invention is the use of polynucleotide sequences of the invention, as well as antisense and ribozyme polynucleotide sequences hybridisable to a polynucleotide sequence encoding an amino acid sequence according to the invention, for manufacture of a medicament for modulation of a disease associated  B. hyodysenteriae.    
     Polynucleotide sequences encoding antisense constructs or ribozymes for use in therapeutic methods are desirably administered directly as a naked nucleic acid construct. Uptake of naked nucleic acid constructs by bacterial cells is enhanced by several known transfection techniques, for example those including the use of transfection agents. Example of these agents include cationic agents (for example calcium phosphate and DEAE-dextran) and lipofectants. Typically, nucleic acid constructs are mixed with the transfection agent to produce a composition. 
     Alternatively the antisense construct or ribozymes may be combined with a pharmaceutically acceptable carrier or diluent to produce a pharmaceutical composition. Suitable carriers and diluents include isotonic saline solutions, for example phosphate-buffered saline. The composition may be formulated for parenteral, intramuscular, intravenous, subcutaneous, intraocular, oral or transdermal administration. The routes of administration described are intended only as a guide since a skilled practitioner will be able to determine readily the optimum route of administration and any dosage for any particular animal and condition. 
     The invention also includes kits for screening animals suspected of being infected with a  Brachyspira  species, such as  B. hyodysenteriae  or to confirm that an animal is infected with a  Brachyspira  species, such as  B. hyodysenteriae . In a further embodiment of this invention, kits suitable for use by a specialist may be prepared to determine the presence or absence of  Brachyspira  species, including but not limited to  B. hyodysenteriae, B. intermedia, B. alvinipulli, B. aalborgi, B. innocens, B. murdochii , and  B. pilosicoli  in suspected infected animals or to quantitatively measure a  Brachyspira  species, including but not limited to  B. hyodysenteriae, B. intermedia, B. alvinipulli, B. aalborgi  and  B. pilosicoli  infection. In accordance with the testing techniques discussed above, such kits can contain at least a labelled version of one of the amino acid sequences described herein or its binding partner, for instance an antibody specific thereto, and directions depending upon the method selected, e.g., “competitive,” “sandwich,” “DASP” and the like. Alternatively, such kits can contain at least a polynucleotide sequence complementary to a portion of one of the polynucleotide sequences described herein together with instructions for its use. The kits may also contain peripheral reagents such as buffers, stabilizers, etc. 
     Accordingly, a test kit for the demonstration of the presence of a  Brachyspira  species, including but not limited to  B. hyodysenteriae, B. intermedia, B. alvinipulli, B. aalborgi, B. innocens, B. murdochii , and  B. pilosicoli , may contain the following: 
     (a) a predetermined amount of at least one labelled immunochemically reactive component obtained by the direct or indirect attachment of one of the amino acid sequences described herein or a specific binding partner thereto, to a detectable label; 
     (b) other reagents; and 
     (c) directions for use of said kit. 
     More specifically, the diagnostic test kit may contain: 
     (a) a known amount of one of the amino acid sequences described herein as described above (or a binding partner) generally bound to a solid phase to form an immunosorbent, or in the alternative, bound to a suitable tag, or there are a plural of such end products, etc; 
     (b) if necessary, other reagents; and 
     (c) directions for use of said test kit. 
     In a further variation, the test kit may contain: 
     (a) a labelled component which has been obtained by coupling one of the amino acid sequences described herein to a detectable label; 
     (b) one or more additional immunochemical reagents of which at least one reagent is a ligand or an immobilized ligand, which ligand is selected from the group consisting of:
         (i) a ligand capable of binding with the labelled component (a);   (ii) a ligand capable of binding with a binding partner of the labelled component (a);   (iii) a ligand capable of binding with at least one of the component(s) to be determined; or   (iv) a ligand capable of binding with at least one of the binding partners of at least one of the component(s) to be determined; and       

     (c) directions for the performance of a protocol for the detection and/or determination of one or more components of an immunochemical reaction between one of the amino acid sequences described herein and a specific binding partner thereto. 
     In one embodiment, the present invention provides simple point-of-care kit that uses principles similar to the widely-used serum testing kits, for the rapid detection of the circulating antibodies in the animal to the polypeptides of the invention will allow the healthcare professional or veterinarian to rapidly diagnose  Brachyspira  infection, and to rapidly institute proven and effective therapeutic and preventive measures. The use of the kit can represent the standard of care for all animals that are at risk of developing  Brachyspira  infection. 
     The methods and kits of the present invention can also provide a means for detecting or monitoring  Brachyspira  infection including the change in status. It can be especially useful in detecting early stage  Brachyspira  infection. Thus, the invention also provides a means for a healthcare professional or veterinarian to monitor the progression of  Brachyspira  infection (worsening, improving, or remaining the same) during and following treatment. Typically, the healthcare professional or veterinarian would establish a protocol of collecting and analysing a quantity of biological sample from the animal at selected intervals. Typically the sample is obtained intermittently during a prescribed period. The period of time between intermittent sampling may be dictated by the condition of the animal, and can range from a sample each 24 hours to a sample taken days, weeks or even months apart. 
     A point-of-care kit for use in the method typically comprises a media having affixed thereto one or more capture polypeptides, whereby the sample is contacted with the media to expose the capture polypeptides to the circulating antibodies contained in the sample. The kit includes an acquiring means that can comprise an implement, such as a needle or vacutainer, having a surface comprising the media. The acquiring means can also comprise a container for accepting the sample, where the container has a serum-contacting surface that comprises the media. In another typical embodiment, the assay for detecting the complex of the circulating antibodies and the capture polypeptides can comprise an ELISA, and can be used to quantitate the amount of circulating antibodies to the polypeptides of the invention in a sample. In an alternative embodiment, the acquiring means can comprise an implement comprising a cassette containing the media. 
     A method and kit of the present invention for detecting the circulating antibodies to the polypeptides of the invention can be made by adapting the methods and kits known in the art for the rapid detection of other proteins and ligands in a biological sample. Examples of methods and kits that can be adapted to the present invention are described in U.S. Pat. No. 5,656,503, issued to May et al. on Aug. 12, 1997, U.S. Pat. No. 6,500,627, issued to O&#39;Conner et al. on Dec. 31, 2002, U.S. Pat. No. 4,870,007, issued to Smith-Lewis on Sep. 26, 1989, U.S. Pat. No. 5,273,743, issued to Ahlem et al. on Dec. 28, 1993, and U.S. Pat. No. 4,632,901, issued to Valkers et al. on Dec. 30, 1986, all such references being hereby incorporated by reference. 
     A rapid one-step method of detecting the circulating antibodies to the polypeptides of the present invention can reduce the time for detecting the development of  Brachyspira  infection. A typical method can comprise the steps of: obtaining a sample from an animal at risk of or suspected of having a  Brachyspira  infection; mixing a portion of the sample with one or more detecting polypeptides which specifically bind to one of the circulating antibodies, so as to initiate the binding of the detecting polypeptides to the circulating antibodies in the sample; contacting the mixture of sample and detecting polypeptides with an immobilized capture antibody which specifically binds to the detecting polypeptides, which capture antibody does not cross-react with the detecting polypeptide, so as to bind the detecting polypeptide to the circulating antibodies, and the circulating antibodies to the capture antibody, to form a detectable complex; removing unbound detecting polypeptide and any unbound sample from the complex; and detecting the detecting polypeptide of the complex. The detectable polypeptide can be labelled with a detectable marker, such as a radioactive label, enzyme, biological dye, magnetic bead, or biotin, as is well known in the art. 
     The following examples are provided for the purposes of illustration and are not intended to limit the scope of the invention. 
     Example 1 
     Genome Sequencing 
     An Australian porcine field isolate of  B. hyodysenteriae  (strain WA1) is shotgun sequenced. This strain has been well-characterised and shown to be virulent following experimental challenge of pigs. The spirochaete is grown in anaerobic trypticase soy broth culture and 100 μg DNA was extracted using a cetyltrimethylammonium bromide (CTAB) method to prepare high quality chromosomal DNA suitable for preparation of genomic DNA libraries. The genomic DNA is sheared using a GeneMachines Hydroshear, and the fragmented DNA processed for cloning as per the protocol recommended by the suppliers of the pSMART vector system (Lucigen). A small insert (2-3 kb) library and a medium insert (3-10 kb) library are constructed into the low copy version of the pSMART vector. 
     Example 2 
     Annotation 
     Partial genome sequences for  B. hyodysenteriae  are assembled and annotated by the Australian Genome Research Facility (AGRF) in Queensland and at Murdoch University by the Centre for Bioinformatics and Biological Computing (CBBC). The CBBC uses up-to-date mirrors of the major international databases and have developed leading edge bioinformatics software and strategies for annotation of features in large genome sequences. A range of public domain bioinformatics tools are used to analyse and re-analyse the sequences as part of a quality assurance procedure on data analysis. Open reading frames (ORFs) are predicted using a variety of programs including GeneMark, GLIMMER, ORPHEUS, SELFID and GetORF. Putative ORFs are examined for homology (DNA and protein) with existing international databases using searches including BLAST and FASTA. All the predicted ORFs are analysed to determine their cellular localisation using programs such as PSI-BLAST, FASTA, MOTIFS, FINDPATTERNS, PHD, SIGNALP and PSORT. Databases including Interpro, Prosite, Propom, Pfam and Blocks are used to predict surface associated proteins such as transmembrane domains, leader peptides, homologies to know surface proteins, lipoprotein signature, outer membrane anchoring motifs and host cell binding domains. Phylogenetic and other molecular evolution analysis is conducted with the identified genes and with other species to assist in the assignment of function. The in silico analysis of both partially sequenced genomes has produced a comprehensive list of all the predicted ORFs present in the sequence data available. Each ORF is interrogated for descriptive information such as predicted molecular weight, isoelectric point, hydrophobicity, and subcellular localisation to enable correlation with the in vitro properties of the native gene product. Predicted genes which encode proteins similar to surface localized components and virulence factors in other pathogenic bacteria are selected as potential vaccine targets. 
     Example 3 
     Analysis of Gene Distribution Using PCR 
     One or two primer pairs which anneal to different regions of the target gene coding region are designed and optimised for PCR detection. Distribution analysis of the  B. hyodysenteriae  target genes is performed on 23 strains of  B. hyodysenteriae , including two strains which have been shown to be avirulent. Primer sets used in the distribution analysis are shown in Table 1. PCR analysis is performed in a 25 μl total volume using Taq DNA polymerase. The amplification mixture consisted of 1×PCR buffer (containing 1.5 mM of MgCl2), 1 U of Taq DNA polymerase, 0.2 mM of each dNTP, 0.5 μM of the primer pair, and 1 μl purified chromosomal template DNA. Cycling conditions involved an initial template denaturation step of 5 min at 94° C., followed by 30 cycles of denaturation at 94° C. for 30 s, annealing at 50° C. for 15 s, and primer extension at 72° C. for 1 min. The PCR products are subjected to electrophoresis in 1% (w/v) agarose gels in 1×TAE buffer (40 mM Tris-acetate, 1 mM EDTA), stained with a 1 μg/ml ethidium bromide solution and viewed over ultraviolet (UV) light. 
     
       
         
           
               
             
               
                 TABLE 1 
               
             
            
               
                   
               
               
                 OLIGONUCLEOTIDE PRIMERS USED IN THE PCR 
               
               
                 DISTRIBUTION ANALYSIS OF THE  B. HYODYSENTERIAE   
               
               
                  VACCINE CANDIDATE GENES 
               
            
           
           
               
               
               
               
            
               
                   
                 Primer 
                 Primer 
                   
               
               
                 Gene 
                 name 
                 Sequence (5′-3′) 
                 SEQ ID No. 
               
               
                   
               
               
                 NAV-H32 
                 H32-F4 
                 CATATTTCTGGTGATT 
                 SEQ ID No. 33 
               
               
                   
                   
                 CTC 
                   
               
               
                   
               
               
                   
                 H32-R564 
                 TTTTTTGATAAATAAG 
                 SEQ ID No. 34 
               
               
                   
                   
                 TTTTTTATTTG 
                   
               
               
                   
               
               
                 NAV-H33 
                 H33-F4 
                 TTTAATACTCCTATAT 
                 SEQ ID No. 35 
               
               
                   
                   
                 TATTAATTATTT 
                   
               
               
                   
               
               
                   
                 H33-R396 
                 AAGGAGAATCACCAGA 
                 SEQ ID No. 36 
               
               
                   
                   
                 AA 
                   
               
               
                   
               
               
                 NAV-H40 
                 H40-F16 
                 AAATATGCTTCCATTA 
                 SEQ ID No. 37 
               
               
                   
                   
                 TAGG 
                   
               
               
                   
               
               
                   
                 H40-R1815 
                 ACTTTTAGGAAGAAGT 
                 SEQ ID No. 38 
               
               
                   
                   
                 TTAAC 
                   
               
               
                   
               
               
                 NAV-H43 
                 H43-F4 
                 GATATAATTATAATAA 
                 SEQ ID No. 39 
               
               
                   
                   
                 TAGTGTTAATAC 
                   
               
               
                   
               
               
                   
                 H43-R1296 
                 TTCAGTGTCTGAATCA 
                 SEQ ID No. 40 
               
               
                   
                   
                 TTC 
                   
               
               
                   
               
               
                 NAV-H46 
                 H46-F327 
                 TATGATGGGGCATAGT 
                 SEQ ID No. 41 
               
               
                   
                   
                 ATGG 
                   
               
               
                   
               
               
                   
                 H46-R769 
                 TATCTCCTACAGGGTC 
                 SEQ ID No. 42 
               
               
                   
                   
                 TTTCG 
                   
               
               
                   
               
               
                 NAV-H66 
                 H66-F17 
                 ATGATAAAGCTTGGGA 
                 SEQ ID No. 43 
               
               
                   
                   
                 AGATTATC 
                   
               
               
                   
               
               
                   
                 H66-R255 
                 ATAATGTGTTTTACAT 
                 SEQ ID No. 44 
               
               
                   
                   
                 CCAAC 
                   
               
               
                   
               
               
                 NAV-H68 
                 H68-F53 
                 TTATGCTCTCTGCTTT 
                 SEQ ID No. 45 
               
               
                   
                   
                 ATTTTCTGG 
                   
               
               
                   
               
               
                   
                 H68-R596 
                 TCTTTTATTATTCCTT 
                 SEQ ID No. 46 
               
               
                   
                   
                 CTTTATGCC 
                   
               
               
                   
               
               
                 NAV-H72 
                 H72-F128 
                 CTATGGCAGAAAACAA 
                 SEQ ID No. 47 
               
               
                   
                   
                 AGTC 
                   
               
               
                   
               
               
                   
                 H72-R614 
                 GCAGATAAAGATAAAT 
                 SEQ ID No. 48 
               
               
                   
                   
                 CAAGTC 
                   
               
               
                   
               
               
                 NAV-H177 
                 H177-F20 
                 AAAGAGCTTGGCAG 
                 SEQ ID No. 49 
               
               
                   
               
               
                   
                 H177-R258 
                 CTTATCATAATGGTAT 
                 SEQ ID No. 50 
               
               
                   
                   
                 TTACAAGATG 
                   
               
               
                   
               
               
                 NAV-H179 
                 H179-F420 
                 TGCTATTGCTGATGCT 
                 SEQ ID No. 51 
               
               
                   
                   
                 ACTAC 
                   
               
               
                   
               
               
                   
                 H179-R705 
                 ATTATCTTGATGAGGA 
                 SEQ ID No. 52 
               
               
                   
                   
                 TGCTTTC 
                   
               
               
                   
               
               
                 NAV-H184 
                 H184-F314 
                 TAGATAAAGATGATGA 
                 SEQ ID No. 53 
               
               
                   
                   
                 TGAAAAAAG 
                   
               
               
                   
               
               
                   
                 H184-R762 
                 AAATAAACCTAAATAA 
                 SEQ ID No. 54 
               
               
                   
                   
                 GCACC 
                   
               
               
                   
               
               
                 NAV-H185 
                 H185-F294 
                 TGGGTTTAGAATAGGT 
                 SEQ ID No. 55 
               
               
                   
                   
                 GCAGG 
                   
               
               
                   
               
               
                   
                 H185-R796 
                 ATTTTAATGTTTGTCT 
                 SEQ ID No. 56 
               
               
                   
                   
                 TTTTGC 
                   
               
               
                   
               
               
                 NAV-H186 
                 H186-F44 
                 TAGAAAAGATGCCTAT 
                 SEQ ID No. 57 
               
               
                   
                   
                 GCTG 
                   
               
               
                   
               
               
                   
                 H186-R718 
                 TTACAAGAGAAAAATA 
                 SEQ ID No. 58 
               
               
                   
                   
                 AACCTG 
                   
               
               
                   
               
               
                 NAV-H188 
                 H188-F293 
                 TGGGGAATCATACAAA 
                 SEQ ID No. 59 
               
               
                   
                   
                 TAGAAG 
                   
               
               
                   
               
               
                   
                 H188-R565 
                 GGCTCATCAAAGGAAG 
                 SEQ ID No. 60 
               
               
                   
                   
                 AACC 
                   
               
               
                   
               
               
                 NAV-H191 
                 H191-F8 
                 ATAATAAAAAAGAAGA 
                 SEQ ID No. 61 
               
               
                   
                   
                 AAAAGAG 
                   
               
               
                   
               
               
                   
                 H191-R403 
                 GTCTGTATCCTAATAA 
                 SEQ ID No. 62 
               
               
                   
                   
                 AATAGTATG 
                   
               
               
                   
               
               
                 NAV-H197 
                 H197-F39 
                 TCTTGGGCTTACATTT 
                 SEQ ID No. 63 
               
               
                   
                   
                 ACTTTG 
                   
               
               
                   
               
               
                   
                 H197-R354 
                 TGATTTCTGACTTCTT 
                 SEQ ID No. 64 
               
               
                   
                   
                 TTTTG 
               
               
                   
               
            
           
         
       
     
     Example 4 
     Bioinformatics 
     Shot-gun sequencing of the  B. hyodysenteriae  genome resulted in 73% (2,347.8 kb out of a predicted 2,300 kb) of the genome to be sequenced. These sequences are comprised of 171 contigs with an average contig size of 13.7 kb. From the 171 contigs, 1,860 open-reading frames (ORFs) are predicted. Comparison of the predicted ORFs with genes present in the nucleic acid and protein databases indicated that approximately 70% in each species have homology with genes contained in the databases. The remaining 30% of the predicted ORFs from each genome have no known identity. 
     Example 5 
     Vaccine candidates 
     ORFs showing strong homology with putative virulence-associated proteins present in the public databases are selected as vaccine targets. Table 2 shows the genes selected as vaccine targets and their similarity with other known genes. 
     
       
         
           
               
             
               
                 TABLE 2 
               
             
            
               
                   
               
               
                 FUNCTION OF  B. Hyodysenteriae  GENES BASED ON SIMILARITY WITH THE AMINO 
               
               
                 ACID SEQUENCE OF SIMILAR BACTERIAL PROTEINS OBTAINED FROM THE SWISS- 
               
               
                 PROT DATABASE 
               
            
           
           
               
               
               
               
            
               
                   
                   
                 Identity 
                   
               
               
                   
                   
                 (amino 
                 Similarity 
               
               
                 Gene 
                 Function 
                 acids) 
                 (amino acids) 
               
               
                   
               
               
                 NAV-H32 
                 Hemolysin 
                  49/137 
                  77/137 
               
               
                   
                 hemolytic protein (HlpA) of  Nostoc  sp. 
                 (35%) 
                 (56%) 
               
               
                   
                 Nucleotide seq. SEQ ID No. 25 
               
               
                   
                 Amino acid seq. SEQ ID No. 26 
               
               
                 NAV-H33 
                 Hemolysin 
                  64/117 
                  83/117 
               
               
                   
                 hemolytic protein of  Prevotella intermedia   
                 (54%) 
                 (70%) 
               
               
                   
                 Nucleotide seq. SEQ ID No. 27 
               
               
                   
                 Amino acid seq. SEQ ID No. 28 
               
               
                 NAV-H40 
                 Toxin 
                 120/449 
                 185/449 
               
               
                   
                 lytic murein transglycosylase (contains LysM/invasin domains) 
                 (26%) 
                 (41%) 
               
               
                   
                 Nucleotide seq. SEQ ID No. 19 
               
               
                   
                 Amino acid seq. SEQ ID No. 20 
               
               
                 NAV-H43 
                 Hemolysin 
                 150/425 
                 242/425 
               
               
                   
                 hemolysins and related proteins of  Anabaena variabilis   
                 (35%) 
                 (56%) 
               
               
                   
                 Nucleotide seq. SEQ ID No. 29 
               
               
                   
                 Amino acid seq. SEQ ID No. 30 
               
               
                 NAV-H46 
                 Lipase 
                 116/299 
                 188/299 
               
               
                   
                 Lysophospholipase 
                 (38%) 
                 (62%) 
               
               
                   
                 Nucleotide seq. SEQ ID No. 15 
               
               
                   
                 Amino acid seq. SEQ ID No. 16 
               
               
                 NAV-H66 
                 Toxin 
                 42/85 
                 60/85 
               
               
                   
                 toxin (YoeB) of  Escherichia coli   
                 (58%) 
                 (76%) 
               
               
                   
                 Nucleotide seq. SEQ ID No. 21 
               
               
                   
                 Amino acid seq. SEQ ID No. 22 
               
               
                 NAV-H68 
                 Hemolysin 
                 121/415 
                 204/415 
               
               
                   
                 hemolysin-related protein of  Dehalococcoides  sp. 
                 (29%) 
                 (49%) 
               
               
                   
                 Nucleotide seq. SEQ ID No. 31 
               
               
                   
                 Amino acid seq. SEQ ID No. 32 
               
               
                 NAV-H72 
                 Toxin 
                  51/141 
                  6/141 
               
               
                   
                 lytic murein transglycosylate (possibly outer membrane-bound) 
                 (36%) 
                 (53%) 
               
               
                   
                 Nucleotide seq. SEQ ID No. 23 
               
               
                   
                 Amino acid seq. SEQ ID No. 24 
               
               
                 NAV- 
                 Toxin 
                 44/86 
                 64/86 
               
               
                 H177 
                 toxin (YoeB) of  Actinobacillus pleuropneumoniae   
                 (51%) 
                 (74%) 
               
               
                   
                 Nucleotide seq. SEQ ID No. 17 
               
               
                   
                 Amino acid seq. SEQ ID No. 18 
               
               
                 NAV- 
                 Protease 
                 227/388 
                 291/388 
               
               
                 H179 
                 ATP-dependent ClpX protease 
                 (58%) 
                 (75%) 
               
               
                   
                 Nucleotide seq. SEQ ID No. 1 
               
               
                   
                 Amino acid seq. SEQ ID No. 2 
               
               
                 NAV- 
                 Peptidase 
                 148/445 
                 241/445 
               
               
                 H184 
                 Nucleotide seq. SEQ ID No. 9 
                 (33%) 
                 (54%) 
               
               
                   
                 Amino acid seq. SEQ ID No. 10 
               
               
                 NAV- 
                 Protease 
                 199/455 
                 289/455 
               
               
                 H185 
                 membrane associated zinc metalloprotease 
                 (43%) 
                 (63%) 
               
               
                   
                 Nucleotide seq. SEQ ID No. 3 
               
               
                   
                 Amino acid seq. SEQ ID No. 4 
               
               
                 NAV- 
                 Peptidase 
                 132/406 
                 234/406 
               
               
                 H186 
                 Zn-dependent peptidase 
                 (32%) 
                 (57%) 
               
               
                   
                 Nucleotide seq. SEQ ID No. 11 
               
               
                   
                 Amino acid seq. SEQ ID No. 12 
               
               
                 NAV- 
                 Protease 
                 147/509 
                 269/509 
               
               
                 H188 
                 adenylate cyclase 
                 (28%) 
                 (52%) 
               
               
                   
                 Nucleotide seq. SEQ ID No. 5 
               
               
                   
                 Amino acid seq. SEQ ID No. 6 
               
               
                 NAV- 
                 Lipase 
                  70/223 
                 117/223 
               
               
                 H191 
                 Nucleotide seq. SEQ ID No. 13 
                 (31%) 
                 (52%) 
               
               
                   
                 Amino acid seq. SEQ ID No. 14 
               
               
                 NAV- 
                 Protease 
                 184/445 
                 267/445 
               
               
                 H197 
                 trypsin-like serine protease 
                 (41%) 
                 (60%) 
               
               
                   
                 Nucleotide seq. SEQ ID No. 7 
               
               
                   
                 Amino acid seq. SEQ ID No. 8 
               
               
                   
               
            
           
         
       
     
     Example 6 
     Gene Distribution 
     The overall gene distribution of each ORF is summarized in Table 3. A total of 23  B. hyodysenteriae  strains are analysed. The distribution is determined from the cumulative result of PCR using up to two different primer sets. All of the ORFs are present in 87-100% of the  B. hyodysenteriae  strains tested. 
     
       
         
           
               
             
               
                 TABLE 3 
               
             
            
               
                   
               
               
                 GENE DISTRIBUTION OF THE  B. Hyodysenteriae  VACCINE 
               
               
                 CANDIDATES ANALYSED BY PCR USING A PANEL OF 23 
               
               
                 DIFFERENT STRAINS 
               
            
           
           
               
               
               
            
               
                   
                 Gene 
                 Distribution (%) 
               
               
                   
                   
               
            
           
           
               
               
               
            
               
                   
                 NAV-H32 
                 91 
               
               
                   
                 NAV-H33 
                 91 
               
               
                   
                 NAV-H40 
                 100 
               
               
                   
                 NAV-H43 
                 91 
               
               
                   
                 NAV-H46 
                 100 
               
               
                   
                 NAV-H66 
                 100 
               
               
                   
                 NAV-H68 
                 91 
               
               
                   
                 NAV-H72 
                 87 
               
               
                   
                 NAV-H177 
                 91 
               
               
                   
                 NAV-H179 
                 100 
               
               
                   
                 NAV-H184 
                 100 
               
               
                   
                 NAV-H185 
                 100 
               
               
                   
                 NAV-H186 
                 100 
               
               
                   
                 NAV-H188 
                 100 
               
               
                   
                 NAV-H191 
                 100 
               
               
                   
                 NAV-H197 
                 100 
               
               
                   
                   
               
            
           
         
       
     
     Example 7 
     Plasmid Extraction 
       Escherichia coli  JM109 clones harbouring the pET-19b plasmid (Novagen) are streaked out from glycerol stock storage onto Luria-Bertani (LB) agar plates supplemented with 100 mg/l ampicillin and incubated at 37° C. for 16 h. A single colony is used to inoculate 10 ml of LB broth supplemented with 100 mg/l ampicillin and the broth culture was incubated at 37° C. for 12 h with shaking. The entire overnight culture is centrifuged at 5,000×g for 10 min and the plasmid contained in the cells extracted using the QIAprep Spin Miniprep Kit (Qiagen) according to the manufacturer&#39;s instructions. The purified plasmid is quantified using a fluorometer and the DNA concentration adjusted to 100 μg/ml by dilution with TE (10 mM Tris-HCl, 1 mM EDTA, pH 8.0) buffer. The purified pET-19b plasmid is stored at −20° C. 
     Example 8 
     Vector Preparation 
     Two μg of the purified pET-19b plasmid is digested at 37° C. for 1-4 h in a total volume of 50 μl containing 50 mM Tris-HCl (pH 7.5), 100 mM NaCl, 10 mM MgCl2, 0.1 mg/ml bovine serum albumin (BSA) and 5 U of NdeI and BamHI (Fermentas). The linearised vectors are verified by electrophoresing 1 μl of the digestion reaction through a 1% (w/v) agarose gel in 1×TAE buffer at 90V for 1 h. The electrophoresed DNA is stained with 1 μg/ml ethidium bromide and viewed over UV light. 
     Linearised pET-19b vectors are purified using the UltraClean PCR Clean-up Kit (Mo Bio Laboratories) according to the manufacturer&#39;s instructions. The purified linear vectors are quantified using the Nanoprop ND1000 spectrophotemeter and the DNA concentration adjusted to 50 μg/ml by dilution with TE buffer. The linearised vectors are stored at −20° C. 
     Example 9 
     Insert Preparation 
     Primer Design 
     Primer pairs are designed to amplify as much of the coding region of the target gene as possible. All primers sequences include terminal restriction enzyme recognition sites to enable cohesive-end ligation of the resultant amplicon into the linearised pET-19b vector. The primer sequences used for cloning are shown in Table 4. The primers are tested using Amplify 3.0 (University of Wisconsin) and the theoretical amplicon sequence is inserted into the appropriate position in the pET-19b vector sequence. Deduced translation of the chimeric pET-19b expression cassette is performed using Vector NTI Advance version 10 (Invitrogen) to confirm that the gene inserts would be in the correct reading frame. 
     
       
         
           
               
             
               
                 TABLE 4 
               
             
            
               
                   
               
               
                 OLIGONUCLEOTIDE PRIMERS USED IN THE CLONING OF THE  B. Hyodysenteriae   
               
               
                 GENES INTO THE pET-19b VECTOR. THE APPARENT MOLECULAR WEIGHT IS 
               
               
                 DETERMINED FROM SDS-PAGE 
               
            
           
           
               
               
               
               
               
            
               
                   
                   
                   
                 Predicted MW 
                 Apparent MW 
               
               
                   
                   
                   
                 of native 
                 of recombinant 
               
               
                 Gene 
                 Primer name 
                 Primer Sequence (5′-3′) 
                 protein (Da) 
                 protein (Da) 
               
               
                   
               
               
                 NAV-H34 
                 H32-F-NdeI 
                 TATGCATATGTCTGGTGATTCTCCTTTAG 
                 25.326 
                 20.5 
               
               
                   
                   
                 (SEQ ID No. 65) 
                   
                   
               
               
                   
               
               
                   
                 H32-R-BamHI 
                 TGCGGATCCTTTTTTGATAAATAAG 
                   
                   
               
               
                   
                   
                 (SEQ ID No. 66) 
                   
                   
               
               
                   
               
               
                 NAV-H33 
                 H33-F-NdeI 
                 GGAAGATAACATATGTTTAATACTC 
                 18.465 
                 13.9 
               
               
                   
                   
                 (SEQ ID No. 67) 
                   
                   
               
               
                   
               
               
                   
                 H33-R-BamHI 
                 TCCTAGGATCCTATCTAAAGGAGAATCACCAG 
                   
                   
               
               
                   
                   
                 (SEQ ID No. 68) 
                   
                   
               
               
                   
               
               
                 NAV-H40 
                 H40-F-NdeI 
                 AAATATGCATATGTTATAGGATGCACTTTTGCCTC 
                 69.479 
                 61.4 
               
               
                   
                   
                 (SEQ ID No. 69) 
                   
                   
               
               
                   
               
               
                   
                 H40-R-BamHI 
                 CTTTTAGGATCCAGTTTAACAGGATCTATTGATC 
                   
                   
               
               
                   
                   
                 (SEQ ID No. 70) 
                   
                   
               
               
                   
               
               
                 NAV-H43 
                 H43-F-NdeI 
                 AATCCATATGGATATAATTATAATAATAGTGTTAATAC 
                 51.176 
                 48.4 
               
               
                   
                   
                 (SEQ ID No. 71) 
                   
                   
               
               
                   
               
               
                   
                 H43-R-BamHI 
                 ATCTGGATCCTATTCAGTGTCTGAATCATTCTTTTCATCAG 
                   
                   
               
               
                   
                   
                 (SEQ ID No. 72) 
                   
                   
               
               
                   
               
               
                 NAV-H46 
                 H46-F-NdeI 
                 CTTCATATGGAAATGCTTAATAGAGTTTTAATATCAG 
                 38.153 
                 32.2 
               
               
                   
                   
                 (SEQ ID No. 73) 
                   
                   
               
               
                   
               
               
                   
                 H46-R-BamHI 
                 AATAGGATCCTATATGAGCATTAAGCCAAGCAATTATC 
                   
                   
               
               
                   
                   
                 (SEQ ID No. 74) 
                   
                   
               
               
                   
               
               
                 NAV-H66 
                 H66-F-NdeI 
                 ATTTCATATGATAAAGCTTGGGAAGATTATC 
                 12.678 
                 10.9 
               
               
                   
                   
                 (SEQ ID No. 75) 
                   
                   
               
               
                   
               
               
                   
                 H66-R-BamHI 
                 AATTGGATCCATAATGTGTTTTACATCCAAC 
                   
                   
               
               
                   
                   
                 (SEQ ID No. 76) 
                   
                   
               
               
                   
               
               
                 NAV-H68 
                 H68-F-NdeI 
                 ATTACATATGGAAATACTACTAGTTTATTTATTTG 
                 55.123 
                 50.4 
               
               
                   
                   
                 (SEQ ID No. 77) 
                   
                   
               
               
                   
               
               
                   
                 H68-R-BamHI 
                 CATTGGATCCTGAATCAGATGTCTCTTGTATAT 
                   
                   
               
               
                   
                   
                 (SEQ ID No. 78) 
                   
                   
               
               
                   
               
               
                 NAV-H72 
                 H72-F-NdeI 
                 GATACATATGATACAAAGAATACATGCCAGAATAG 
                 28.201 
                 24.6 
               
               
                   
                   
                 (SEQ ID No. 79) 
                   
                   
               
               
                   
               
               
                   
                 H72-R-BamHI 
                 ATGTGGATCCCATAGTTTTGAGTTTCCTC 
                   
                   
               
               
                   
                   
                 (SEQ ID No. 80) 
                   
                   
               
               
                   
               
               
                 NAV-H177 
                 H177-F-NdeI 
                 GTTTCATATGAAAGAGCTTGGCAG 
                 12.997 
                 10.8 
               
               
                   
                   
                 (SEQ ID No. 81) 
                   
                   
               
               
                   
               
               
                   
                 H177-R-BamHI 
                 ATATGGATCCCTTATCATAATGGTATTTACAAGATG 
                   
                   
               
               
                   
                   
                 (SEQ ID No. 82) 
                   
                   
               
               
                   
               
               
                 NAV-H179 
                 H179-F-NdeI 
                 TTAACATATGGTTCTCTTTGCGGAAGAG 
                 48.109 
                 54.6 
               
               
                   
                   
                 (SEQ ID No. 83) 
                   
                   
               
               
                   
               
               
                   
                 H179-R-BamHI 
                 TTAGGATCCCATCAATACCTAATTTTTCATTAAC 
                   
                   
               
               
                   
                   
                 (SEQ ID No. 84) 
                   
                   
               
               
                   
               
               
                 NAV-H184 
                 H184-F-NdeI 
                 TTAACATATGTCAGAGAATAGTTTTAAAAATAGAATAAAAG 
                 53.101 
                 57.2 
               
               
                   
                   
                 (SEQ ID No. 85) 
                   
                   
               
               
                   
               
               
                   
                 H184-R-BamHI 
                 TTAAGGATCCGAAGCAAATGAAAGTTCTTTAATC 
                   
                   
               
               
                   
                   
                 (SEQ ID No. 86) 
                   
                   
               
               
                   
               
               
                 NAV-H185 
                 H185-F-NdeI 
                 TTTTCATATGGCACAAACTAATGAATCAGCTATATT 
                 58.175 
                 67.8 
               
               
                   
                   
                 (SEQ ID No. 87) 
                   
                   
               
               
                   
               
               
                   
                 H185-R-BamHI 
                 TTAAGGATCCGTTAAGCAGCACCAGAGAATTATAATC 
                   
                   
               
               
                   
                   
                 (SEQ ID No. 88) 
                   
                   
               
               
                   
               
               
                 NAV-H186 
                 H186-F-NdeI 
                 CTTACATATGGGAACAAGAGTTGTTTTAGAAAAGATG 
                 59.786 
                 56.1 
               
               
                   
                   
                 (SEQ ID No. 89) 
                   
                   
               
               
                   
               
               
                   
                 H186-R-BamHI 
                 ACTGGGATCCGACTTGCTTATATCCTTAGTACCG 
                   
                   
               
               
                   
                   
                 (SEQ ID No. 90) 
                   
                   
               
               
                   
               
               
                 NAV-H188 
                 H188-F-NdeI 
                 TAATCATATGATGTACAGTCAGGTTATGATAG 
                 64.413 
                 68.8 
               
               
                   
                   
                 (SEQ ID No. 91) 
                   
                   
               
               
                   
               
               
                   
                 H188-R-BamHI 
                 ACTGGGATCCTGTACCGACATTCTCTTCAC 
                   
                   
               
               
                   
                   
                 (SEQ ID No. 92) 
                   
                   
               
               
                   
               
               
                 NAV-H191 
                 H191-F-NdeI 
                 AAAGCATATGGAAGAAAAAAAATTGGAAAG 
                 36.953 
                 37.8 
               
               
                   
                   
                 (SEQ ID No. 93) 
                   
                   
               
               
                   
               
               
                   
                 H191-R-BamHI 
                 ATACGGATCCAATATATGTTCACTGTCCATAGCCTC 
                   
                   
               
               
                   
                   
                 (SEQ ID No. 94) 
                   
                   
               
               
                   
               
               
                 NAV-H197 
                 H197-F-NdeI 
                 CTTTCATATGCTTGGGCTTACATTTACTTTGGTTGG 
                 56.670 
                 66.6 
               
               
                   
                   
                 (SEQ ID No. 95) 
                   
                   
               
               
                   
               
               
                   
                 H197-R-BamHI 
                 ATAAGGATCCCATAAGTCATTCTTGCTCGTTTTATAG 
                   
                   
               
               
                   
                   
                 (SEQ ID No. 96) 
                   
                   
               
               
                   
               
            
           
         
       
     
     Example 10 
     Amplification of the Gene Inserts 
     All target gene inserts are amplified by PCR in a 100 μl total volume using Taq DNA polymerase and Pfu DNA polymerase. Briefly, the amplification mixture consists of 1×PCR buffer (containing 1.5 mM of MgCl2), 2 U of Taq DNA polymerase, 0.01 U Pfu DNA polymerase, 0.2 mM of each dNTP, 0.5 μM of the appropriate primer pair and 1 μl of purified chromosomal DNA. The chromosomal DNA is prepared from the same  B. hyodysenteriae  strain used for genome sequencing. Cycling conditions involve an initial template denaturation step of 5 min at 94° C., followed by 30 cycles of denaturation at 94° C. for 30 s, annealing at 50° C. for 15 s, and primer extension at 72° C. for 1 min. The PCR products are subjected to electrophoresis in 1% (w/v) agarose gels in 1×TAE buffer, stained with a 1 μg/ml ethidium bromide solution and viewed over UV light. After verifying the presence of the correct size PCR product, the PCR reaction is purified using the UltraClean PCR Clean-up Kit (Mo Bio Laboratories). 
     Example 11 
     Restriction Enzyme Digestion of the Gene Inserts 
     Thirty μl of the purified PCR product is digested in a 50 μl total volume with 1 U of NdeI and 1 U of BamHI. The digested insert DNA are purified using the UltraClean PCR Clean-up Kit (Mo Bio Laboratories). Purified digested insert DNA are quantified using the NanoDrop ND1000 spectrophotemeter and the DNA concentration adjusted to 10 μg/ml by dilution with TE buffer. The purified restricted insert DNA are used immediately for vector ligation. 
     Example 12 
     Ligation of the Gene Inserts into the pET-19B Vector 
     Ligation reactions are all performed in a total volume of 20 μl. Twenty five ng of linearised pTrcHis is incubated with an equi-molar amount of restricted insert at 16° C. for 16 h in 30 mM Tris-HCl (pH 7.8), 10 mM MgCl2, 10 mM DTT and 1 mM ATP containing 1 U of T4 DNA ligase (Fermentas). An identical ligation reaction containing no insert DNA is also included as a vector re-circularisation negative control. 
     Example 13 
     Transformation of pET-19B Ligations into  E. coli  JM109 Cells 
     Competent  E. coli  JM109 cells are thawed from −80° C. storage on ice and then 50 μl of the cells are transferred into ice-cold 1.5 ml microfuge tubes containing 5 μl of the overnight ligation reactions. The tubes are mixed by gently tapping the bottom of each tube on the bench and left on ice for 30 min. The cells are then heat-shocked by placing the tubes into a 42° C. waterbath for 45 s before returning the tube to ice for 2 min. The transformed cells are recovered in 1 ml LB broth for 1 h at 37° C. with gentle mixing. The recovered cells are harvested at 2,500×g for 5 min and the cells resuspended in 50 μl of fresh LB broth. The entire 50 μl of resuspended cells are spread evenly onto a LB agar plate containing 100 mg/l ampicillin using a sterile glass rod. Plates are incubated at 37° C. for 16 h. 
     Example 14 
     Detection of Recombinant pET-19b Constructs in  E. coli  by PCR 
     Twelve single transformant colonies for each construct are streaked onto fresh LB agar plates containing 100 mg/l ampicillin and incubated at 37° C. for 16 h. A single colony from each transformation event is resuspended in 50 μl of TE buffer and boiled for 1 min. Two μl of boiled cells are used as template for PCR. The amplification mixture consists of 1×PCR buffer (containing 1.5 mM of MgCl2), 1 U of Taq DNA polymerase, 0.2 mM of each dNTP, 0.5 μM of the pET-19b-F primer (5′-GGAATTGTGAGCGGATAAC-3′) and 0.5 μM of the pET-19b-R primer (5′-GCAAAAAACCCCTCAAGAC-3′). Cycling conditions involve an initial template denaturation step of 5 min at 94° C., followed by 30 cycles of denaturation at 94° C. for 30 s, annealing at 60° C. for 15 s, and a primer extension at 72° C. for 1 min. The PCR products are subjected to electrophoresis in 1% (w/v) agarose gels in 1×TAE buffer, stained with a 1 μg/ml ethidium bromide solution and viewed over UV light. 
     Example 15 
     Purification of Recombinant pET-19b Plasmids 
     An  E. coli  JM109 clone harbouring the successfully ligated pET-19b plasmids are inoculated into 5 ml of LB broth supplemented with 100 mg/l ampicillin and the broth culture is incubated at 37° C. for 12 h with shaking. The entire overnight culture is centrifuged at 5,000×g for 10 min and the plasmid contained in the cells extracted using the QIAprep Spin Miniprep Kit (Qiagen) according to the manufacturer&#39;s instructions. The purified recombinant pET-19b plasmid is stored at −20° C. 
     Example 16 
     Transformation of Recombinant pET-19b Plasmids into  E. coli  BL21 (DE3) Cells 
     Competent  E. coli  BL21 (DE3) cells are thawed from −80° C. storage on ice and then 20 μl of the cells are transferred into ice-cold 1.5 ml microfuge tubes containing 1 μl of the recombinant purified pET-19b plasmid. The tubes are mixed by gently tapping the bottom of each tube on the bench and left on ice for 30 min. The cells are then heat-shocked by placing the tubes into a 42° C. waterbath for 45 s before returning the tube to ice for 2 min. The transformed cells are recovered in 1 ml LB broth for 1 h at 37° C. with gentle mixing. Fifty μl of the recovered cells are spread evenly onto a LB agar plate containing 100 mg/l ampicillin using a sterile glass rod. Plates are incubated at 37° C. for 16 h. 
     Example 17 
     Expression of Recombinant His-Tagged Proteins 
     Four isolated colonies of recombinant pET-19b plasmid in  E. coli  BL21 (DE3) is inoculated into 3 ml LB broth in a 10 ml centrifuge tube containing 100 mg/l ampicillin and 1 mM IPTG and incubated at 37° C. for 16 h with shaking. The cells are harvested by centrifugation at 5,000×g for 10 min at 4° C. The supernatant is discarded and each pellet is resuspended with 300 μl of 1×SDS-PAGE loading buffer (250 mM Tris-HCl pH 6.0, 8% w/v SDS, 200 mM DTT, 40% v/v glycerol and 0.04% w/v bromophenol blue). After boiling the tube for 5 min, the cellular debris is pelleted by centrifugation at 10,000×g for 10 min at 4° C. The supernatant is transferred to a new tube and stored at −20° C. until analysis. 
     Example 18 
     SDS-PAGE 
     SDS-PAGE analysis of protein involved electrophoretic separation using a discontinuous Tris-glycine buffer system. Ten μl of the prepared cell lysate is loaded into the wells of a polyacrylamide gel. The gel is comprised of a stacking gel (125 mM Tris-HCl ph 6.8, 4% w/v acylamide, 0.15% w/v bis-acrylamide and 0.1% w/v SDS) and a separating gel (375 mM Tris-HCl ph 8.8, 12% w/v acylamide, 0.31% w/v bis-acrylamide and 0.1% w/v SDS). These gels are polymerised by the addition of 0.1% (v/v) TEMED and 0.05% (w/v) freshly prepared ammonium sulphate solution and cast into the mini-Protean dual slab cell (Bio-Rad). Samples are run at 150 V at room temperature (RT) until the bromophenol blue dye-front reached the bottom of the gel. Pre-stained molecular weight standards are electrophoresed in parallel with the samples in order to allow molecular weight estimations. After electrophoresis, the gel is immediately stained using Coomassie Brilliant Blue G250 or subjected to electro-transfer onto nitrocellulose membrane for Western blotting. 
     Example 19 
     Western Blot Analysis 
     Electrophoretic transfer of separated proteins from the SDS-PAGE gel to nitrocellulose membrane is performed using the Towbin transfer buffer system. After electrophoresis, the gel is equilibrated in transfer buffer (25 mM Tris, 192 mM glycine, 20% v/v methanol, pH 8.3) for 15 min. The proteins in the gel are transferred to nitrocellulose membrane using the mini-Protean transblot apparatus (Bio-Rad). After assembly of the gel holder according to the manufacturer&#39;s instructions, electrophoretic transfer is performed at 30 V overnight at 4° C. The freshly transferred nitrocellulose membrane containing the separated proteins is blocked with 10 ml of tris-buffered saline (TBS; 20 mM Tris-HCl, 500 mM NaCl, pH 7.5) containing 5% (w/v) skim milk powder for 1 h at RT. The membrane is washed with TBS containing 0.1% (v/v) Tween 20 (TBST) and then incubated with 10 ml mouse anti-his antibody (diluted 5,000-fold with TBST) for 1 h at RT. After washing three times for 5 min with TBST, the membrane is incubated with 10 mL goat anti-mouse IgG (whole molecule)-AP diluted 5,000-fold in TBST for 1 h at RT. The membrane is developed using the Alkaline Phosphatase Substrate Kit (Bio-Rad). The development reaction is stopped by washing the membrane with distilled water. The membrane is then dried and scanned for presentation. 
     Example 20 
     Expression and Purification of Recombinant His-Tagged Proteins 
     A single colony of the recombinant pET-19b plasmid in  E. coli  BL21 (DE3) is inoculated into 20 ml LB broth in a 50 ml centrifuge tube containing 100 mg/l ampicillin and incubated at 37 C for 16 h with shaking. A 2 l conical flask containing 500 ml of LB broth supplemented with 100 mg/l ampicillin is inoculated with 10 ml of the overnight culture and incubated at 37° C. until the optical density of the cells at 600 nm is 0.5 (approximately 3-4 h). The culture is then induced by adding IPTG to a final concentration of 1 mM and the cells returned to 37° C. with shaking. After 6 h of induction, the culture is transferred to two 250 ml centrifuge bottles and the bottles are centrifuged at 5,000×g for 10 min at 25° C. The supernatant is discarded and each pellet is resuspended with 4 ml of Ni-NTA native lysis buffer (50 mM NaH2PO4, 300 mM NaCl, 10 mM imidazole, pH 8.0). The resuspended cells are pooled and stored at −20° C. overnight. 
     The cell suspension is removed from −20° C. storage and thawed on ice. Five μl of DNAse I (10 mg/ml) is added to the thawed lysate and incubated on ice for 1 h. The lysate is centrifuged at 20,000×g for 15 min at 4° C. The supernatant is transferred to a 10 ml column containing a 1 ml bed volume of Ni-NTA agarose resin (Qiagen). The recombinant his-tagged protein is allowed to bind to the resin for 1 h at 4° C. with end-over-end mixing. The resin is then fished with 30 ml of Ni-NTA native ish buffer (50 mM NaH2PO4, 300 mM NaCl, 20 mM imidazole, pH 8.0) before elution with 9 ml of Ni-NTA native elution buffer (50 mM NaH2PO4, 300 mM NaCl, 250 mM imidazole, pH 8.0). Three 3 ml fractions of the eluate are collected and stored at 4° C. Thirty μl of each eluate is treated with 10 μl of 4× sample treatment buffer and boiled for 5 min. The samples are subjected to SDS-PAGE and stained with Coomassie Brilliant Blue G250. The stained gel is equilibrated in distilled water for 1 h and dried between two sheets of cellulose overnight at RT. 
     Example 21 
     Dialysis and Lyophilisation of the Purified Recombinant His-Tagged Protein 
     The eluted proteins are pooled and transferred into a hydrated dialysis tube with a molecular weight cut-off (MWCO) of 3,500 Da. A 200 μl aliquot of the pooled eluate is taken and quantified using a commercial Protein Assay (Bio-Rad). The proteins are dialysed against 2 l of distilled water at 4° C. with stirring. The dialysis buffer is changed 8 times at 12-hourly intervals. The dialysed proteins are transferred from the dialysis tube into a 50 ml centrifuge tubes (40 ml maximum volume) and the tubes are placed at −80° C. overnight. Tubes are placed into a freeze-drier and lyophilised to dryness. The lyophilised proteins are then re-hydrated with PBS to a calculated concentration of 2 mg/ml and stored at −20° C. 
     Example 22 
     Serology Using Recombinant Protein 
     Ten μg of purified recombinant protein is diluted in 10 ml of carbonate buffer and 100 μl is added to each well of a 96-well microtitre plate. The protein is allowed to coat overnight at 4° C. The plate is blocked with 150 μl of PBS-BSA (1% w/v) in each well for 1 hour at room temperature (RT) with mixing and then washed three times with 150 μl of PBST (0.05% v/v). Pig sera are diluted 1:800 in 100 μl of PBST-BSA (0.1% w/v) and incubated at RT for 2 hours with mixing. Plates are washed before adding 100 μl of goat anti-swine IgG (whole molecule)-HRP diluted 1:5,000 in PBST. After incubating for 1 hr at RT, the plates are washed and 100 μl of TMB substrate added. Colour development is allowed to occur for 10 minutes at RT before being stopped with the addition of 50 μl of 1 M sulphuric acid. The optical density of each well is read at 450 nm. Pooled serum from pigs of different sources and health status were used in this analysis. These included pigs from high health status herds (N1-N3), hyperimmunised pigs (M1-M3), experimentally challenged pigs (H1-H5) and recovered pigs from different herds (H6-H13). 
     As shown in Tables 5A and 5B, all proteins reacted strongly with serum from the pig hyperimmunised with  B. hyodysenteriae  bacteria (M1; 1.5077±0.1635) and reacted less strongly with serum from pigs hyperimmunised with  B. pilosicoli  (M2; 1.1646±0.1206) and  B. innocens  (M3; 1.2777±0.1626) indicating some level of cross-reactivity with pigs recognising other  Brachyspira  spp. The proteins reacted weakest with serum taken from high-health status pigs (N1-N3; 0.2087 to 0.4695), followed by experimentally challenged pigs showing acute severe symptoms of SD (H1-H5; 0.4586 to 0.7992), and strongest with pigs which had recovered from SD (H6-H13; 0.8043 to 1.0068). As a whole, these results indicate that all these toxin proteins are immunogenic in naturally and experimentally infected pigs. 
     
       
         
           
               
             
               
                 TABLE 5A 
               
             
            
               
                   
               
               
                 REACTIVITY OF TOXIN PROTEINS WITH HEALTHY PIG SERUM 
               
               
                 AND HYPERIMMUNISED PIG SERUM. 
               
            
           
           
               
               
            
               
                   
                 ELISA Reactivity (absorbance) 
               
            
           
           
               
               
               
               
               
               
               
            
               
                 Protein 
                 N1 
                 N2 
                 N3 
                 M1 
                 M2 
                 M3 
               
               
                   
               
               
                 H32 
                 0.2717 
                 0.3117 
                 0.2952 
                 1.5901 
                 1.3577 
                 1.3059 
               
               
                 H33 
                 0.4091 
                 0.2087 
                 0.4378 
                 1.4951 
                 1.1724 
                 1.1682 
               
               
                 H40 
                 0.2555 
                 0.4695 
                 0.3649 
                 1.4227 
                 1.0322 
                 1.2454 
               
               
                 H43 
                 0.3619 
                 0.4015 
                 0.2229 
                 1.5621 
                 1.1762 
                 1.2901 
               
               
                 H46 
                 0.4477 
                 0.4233 
                 0.4080 
                 1.4551 
                 1.0495 
                 1.3666 
               
               
                 H66 
                 0.3879 
                 0.3948 
                 0.3532 
                 1.5907 
                 1.1884 
                 1.2712 
               
               
                 H68 
                 0.4324 
                 0.3032 
                 0.4305 
                 1.4700 
                 1.3013 
                 1.2538 
               
               
                 H72 
                 0.4063 
                 0.3464 
                 0.3994 
                 1.4398 
                 1.1234 
                 1.3686 
               
               
                 H177 
                 0.3120 
                 0.2691 
                 0.2416 
                 1.4369 
                 1.0888 
                 1.1734 
               
               
                 H184 
                 0.3122 
                 0.4090 
                 0.3337 
                 1.5272 
                 1.1815 
                 1.3018 
               
               
                 H186 
                 0.4182 
                 0.2953 
                 0.3807 
                 1.5170 
                 1.0628 
                 1.3069 
               
               
                 H191 
                 0.2279 
                 0.4236 
                 0.3064 
                 1.5856 
                 1.2405 
                 1.2804 
               
               
                   
               
               
                 N1, N2, N3; pooled serum from high-health status pigs; 
               
               
                 M1; serum from pig hyperimmunised with  B. hyodysenteriae  bacterin; 
               
               
                 M2; serum from pig hyperimmunised with  B. pilosicoli  bacterin; 
               
               
                 M3; serum from pig hyperimmunised with  B. innocens  bacterin 
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 5B 
               
             
            
               
                   
               
               
                 REACTIVITY OF TOXIN PROTEINS WITH NATURALLY AND EXPERIMENTALLY INFECTED PIG SERUM. 
               
            
           
           
               
               
            
               
                   
                 ELISA Reactivity (absorbance) 
               
            
           
           
               
               
               
               
               
               
               
               
               
               
               
               
               
               
            
               
                 Protein 
                 H1 
                 H2 
                 H3 
                 H4 
                 H5 
                 H6 
                 H7 
                 H8 
                 H9 
                 H10 
                 H11 
                 H12 
                 H13 
               
               
                   
               
               
                 H32 
                 0.4833 
                 0.6912 
                 0.5262 
                 0.6574 
                 0.7546 
                 0.9813 
                 0.9178 
                 0.9255 
                 0.9175 
                 0.9818 
                 0.8449 
                 0.9348 
                 0.9648 
               
               
                 H33 
                 0.5222 
                 0.5676 
                 0.6789 
                 0.7410 
                 0.6260 
                 0.8055 
                 0.9209 
                 0.9399 
                 1.0015 
                 0.9940 
                 0.9935 
                 0.8112 
                 0.9104 
               
               
                 H40 
                 0.5420 
                 0.5971 
                 0.7517 
                 0.6687 
                 0.7598 
                 0.9529 
                 0.8589 
                 0.9741 
                 0.9707 
                 0.9547 
                 0.9941 
                 0.8493 
                 0.9247 
               
               
                 H43 
                 0.7525 
                 0.7265 
                 0.6551 
                 0.7322 
                 0.6341 
                 0.9296 
                 0.8495 
                 0.9727 
                 0.8595 
                 0.8740 
                 0.8904 
                 0.8561 
                 0.9640 
               
               
                 H46 
                 0.5805 
                 0.6675 
                 0.7590 
                 0.4625 
                 0.7028 
                 1.0068 
                 0.8821 
                 0.8777 
                 1.0061 
                 0.8220 
                 0.8861 
                 0.9881 
                 0.9221 
               
               
                 H66 
                 0.7491 
                 0.4752 
                 0.5211 
                 0.7666 
                 0.6005 
                 0.9489 
                 0.9014 
                 0.9198 
                 0.9346 
                 0.8687 
                 0.9511 
                 0.8935 
                 0.9807 
               
               
                 H68 
                 0.5704 
                 0.4900 
                 0.6527 
                 0.7199 
                 0.6310 
                 0.9498 
                 0.8224 
                 0.8103 
                 0.9700 
                 0.8518 
                 0.9759 
                 0.8348 
                 0.9201 
               
               
                 H72 
                 0.7278 
                 0.5590 
                 0.7650 
                 0.6436 
                 0.7045 
                 0.8182 
                 0.8109 
                 0.9585 
                 0.8662 
                 0.9753 
                 0.9535 
                 0.8751 
                 0.8683 
               
               
                 H177 
                 0.6225 
                 0.7260 
                 0.6126 
                 0.4586 
                 0.6151 
                 0.8633 
                 0.9477 
                 0.9244 
                 0.8944 
                 0.9351 
                 0.9108 
                 0.9347 
                 0.9111 
               
               
                 H184 
                 0.7287 
                 0.7513 
                 0.6898 
                 0.7992 
                 0.7451 
                 0.8312 
                 0.9383 
                 0.8721 
                 0.8894 
                 0.8818 
                 0.9832 
                 0.8301 
                 0.9998 
               
               
                 H186 
                 0.5169 
                 0.5928 
                 0.5295 
                 0.7065 
                 0.7003 
                 0.8853 
                 0.9182 
                 0.9092 
                 0.9155 
                 0.9263 
                 0.8836 
                 0.8453 
                 0.8878 
               
               
                 H191 
                 0.6753 
                 0.5940 
                 0.6794 
                 0.7840 
                 0.7252 
                 0.8043 
                 0.9727 
                 0.8179 
                 0.8280 
                 0.9880 
                 0.9468 
                 0.9598 
                 0.8049 
               
               
                   
               
               
                 H1, H2, H3, H4, H5; pooled serum from experimentally infected pigs showing acute severe clinical signs of SD 
               
               
                 H6, H7, H8, H9, H10, H11, H12, H13; pooled serum from commercial pigs recovered from SD 
               
            
           
         
       
     
     Example 23 
     Construction of the Recombinant pET-19b Constructs 
     Cloning of the various inserts into the pET-19b expression vector produced recombinant constructs of various sizes. Nucleotide sequencing of the pET-19b constructs verified that the expression cassette is in the correct frame for all the constructs. The predicted translation of the pET-19b expression cassette indicated that all the recombinant his-tagged proteins and the deduced amino acid sequence of the native spirochaete proteins were identical. 
     Example 24 
     Expression and Purification of Recombinant Proteins 
     Expression of the selected recombinant  E. coli  clones is performed in medium-scale to generate sufficient recombinant protein for vaccination of mice. All genes cloned produce recombinant proteins possessing the hexa-histidine fusion with an apparent molecular weight similar to the predicted molecular weight of the native protein as shown in Table 4. All recombinant proteins were highly reactive in western blotting using the anti-his antibody. Purification of the his-tagged recombinant proteins is by affinity chromatography under denaturing conditions. SDS-PAGE and Coomassie Blue staining of all recombinant proteins show purification of the proteins. 
     Example 25 
     Vaccination of Pigs Using the Purified Recombinant His-Tagged Proteins 
     Four purified recombinant his-tagged proteins (0.5 mg of each) were pooled in a total volume of 1 ml. Four vaccines were made:
         a) Haemolysin recombinant consisting of: NAV-H32, NAV-H33, NAV-H43 and NAV-H68;   b) Toxin recombinant consisting of: NAV-H40, NAV-H66, NAV-H72 and NAV-H177;   c) Lipase/Peptidase recombinant consisting of NAV-H46, NAV-H184, NAV-H186 and NAV-H191;   d) Protease recombinant consisting of: NAV-H179, NAV-H185, NAV-H188 and NAV-H197.
 
Four groups of ten sero-negative pigs (5 weeks old) were injected intramuscularly with 2 ml of vaccine consisting of 2 mg of the pooled antigen emulsified with a water-in-oil adjuvant. The pigs were vaccinated twice intramuscularly into the back of the neck at 5 weeks of age and at 8 weeks of age. All pigs were bled immediately before the first vaccination, immediately before the second vaccination and two weeks after the second vaccination. Serum was collected from the blood and used to measure immune-responsiveness to the proteins contained in the vaccines. Since four proteins are combined in each vaccine, serum from each group of pigs is tested against all four proteins individually. The ELISA was performed the same way as outlined in Example 22.
 
As shown in Table 6, all pigs responded strongly to the vaccination regime given with antibody levels increasing significantly after the first (11.60-fold-17.69-fold increase; P&lt;0.001) and second (2.41-fold-2.78-fold increase; P&lt;0.001) intramuscular injections. These results clearly demonstrate the immunogenicity of these toxin proteins in pigs and the effectiveness of the vaccination regime in inducing high antibody levels in the pig.
       

     
       
         
           
               
             
               
                 TABLE 6 
               
             
            
               
                   
               
               
                 IMMUNOGENICITY OF TOXIN PROTEINS IN PIGS FOLLOWING INTRAMUSCULAR 
               
               
                 VACCINATION. ALL ELISA VALUES ARE EXPRESSED AS MEAN 
               
               
                 ABSORBANCE ± STANDARD DEVIATION 
               
            
           
           
               
               
               
               
            
               
                   
                 Pre-Vacc. 
                 Pre-Boost 
                 Post-vaccination (2 weeks) 
               
            
           
           
               
               
               
               
               
               
            
               
                 Protein 
                 ELISA value 
                 ELISA Value 
                 Fold increase 
                 ELISA value 
                 Fold increase 
               
               
                   
               
               
                 H32 
                 0.0721 ± 0.0261 
                 1.0371 ± 0.2187 
                 14.39 
                 2.6219 ± 0.2817 
                 2.53 
               
               
                 H33 
                 0.0598 ± 0.0283 
                 1.0015 ± 0.3433 
                 16.75 
                 2.5104 ± 0.3236 
                 2.51 
               
               
                 H40 
                 0.0851 ± 0.0222 
                 1.0007 ± 0.2019 
                 11.76 
                 2.5329 ± 0.3949 
                 2.53 
               
               
                 H43 
                 0.0727 ± 0.0276 
                 1.0419 ± 0.2801 
                 14.34 
                 2.6357 ± 0.2240 
                 2.53 
               
               
                 H46 
                 0.0642 ± 0.0216 
                 0.9950 ± 0.2223 
                 15.51 
                 2.7623 ± 0.2948 
                 2.78 
               
               
                 H66 
                 0.0926 ± 0.0240 
                 1.0750 ± 0.2101 
                 11.60 
                 2.6948 ± 0.2723 
                 2.51 
               
               
                 H68 
                 0.0768 ± 0.0237 
                 1.0454 ± 02731  
                 13.62 
                 2.6750 ± 0.2824 
                 2.56 
               
               
                 H72 
                 0.0708 ± 0.0268 
                 1.0108 ± 0.1963 
                 14.27 
                 2.6665 ± 0.3795 
                 2.64 
               
               
                 H177 
                 0.0724 ± 0.0216 
                 1.0251 ± 0.2169 
                 14.15 
                 2.6791 ± 0.2818 
                 2.61 
               
               
                 H184 
                 0.0569 ± 0.0212 
                 0.9983 ± 0.1978 
                 17.55 
                 2.5985 ± 0.2409 
                 2.60 
               
               
                 H186 
                 0.0676 ± 0.0225 
                 1.0783 ± 0.2352 
                 15.96 
                 2.6001 ± 0.3314 
                 2.41 
               
               
                 H191 
                 0.0598 ± 0.0210 
                 1.0585 ± 0.2455 
                 17.69 
                 2.6283 ± 0.3248 
                 2.48 
               
               
                   
               
            
           
         
       
     
     Example 26 
     Protection of Pigs by Vaccination with Purified Recombinant His-Tagged Proteins 
     Four purified recombinant his-tagged proteins (0.5 mg of each) are pooled in a total volume of 1 ml. Four vaccines are made:
         a) Hemolysin recombinant consisting of: NAV-H32, NAV-H33, NAV-H43 and NAV-H68;   b) Toxin recombinant consisting of: NAV-H40, NAV-H66, NAV-H72 and NAV-H177;   c) Lipase/Peptidase recombinant consisting of NAV-H46, NAV-H184, NAV-H186 and NAV-H191;   d) Protease recombinant consisting of: NAV-H179, NAV-H185, NAV-H188 and NAV-H197.
 
Four groups of ten sero-negative pigs (5 weeks old) are injected intramuscularly with 2 ml of vaccine consisting of 2 mg of the pooled antigen emulsified with a water-in-oil adjuvant. A fifth group of ten sero-negative pigs is used as negative controls and are sham vaccinated with PBS emulsified in the adjuvant. All the pigs are vaccinated twice intramuscularly into the back of the neck at 5 weeks of age and at 8 weeks of age. All pigs are challenged with 100 ml of an active  B. hyodysenteriae  culture (˜10 9  cells/ml) by gastric gavage at ten weeks of age, and the pigs are observed daily for clinical signs of swine dysentery during the experiment (up to six weeks post-challenge) and at post-mortem examination. Twice weekly, all pigs are rectally swabbed for selective bacteriological culture.