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Molecular Approaches for Identification of Lactobacilli from Traditional Dairy Products

  • Dhiraj Kumar Nanda
  • Reeti Chaudhary
  • Dinesh Kumar
Chapter

Abstract

Traditional dairy food products harbour groups of several bacterial genera especially lactic acid bacteria (LAB) which play a role essentially in fermentation of these products and provide a unique flavour and identity to the product. Historically, many species of LAB have been considered as ‘generally regarded as safe’ (GRAS) bacteria and are associated with human foods. The GRAS status forms a base for increasing use of LAB in traditional foods and in expanding unique foods and food products that are formulated to have specific nutritional or additional health-enhancing benefits. Lactobacillus is considered as one of the most important genera among LAB. The genera have more than 180 species. Classical microbiological methods have been found insufficient to classify this huge diverse genus. Hence, a better approach is in demand to characterize new strains of lactobacilli. By using modern molecular methods, it has been possible to characterize the lactobacillus associated with traditional dairy products.

References

  1. Acinas SG, Marcelino LA, Klepac-Ceraj V, Polz MF (2004) Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons. J Bacteriol 186:2629–2635CrossRefPubMedPubMedCentralGoogle Scholar
  2. Almeida CC, Lorena SLS, Pavan CR, Akasaka HMI, Mesquita MA (2012) Beneficial effects of long-term consumption of a probiotic combination of Lactobacillus casei Shirota and Bifidobacterium breve Yakult may persist after suspension of therapy in lactose-intolerant patients. Nutr Clin Pract 27:247–251CrossRefPubMedGoogle Scholar
  3. Axelsson L, Ahrné S (2000) Lactic acid bacteria. Appl microbial systematics: Springer, The Netherlands, pp 367–388Google Scholar
  4. Babalola OO (2004) Molecular techniques: an overview of methods for the detection of bacteria. Afri J Biotech 2:710–713Google Scholar
  5. Baldauf SL, Palmer JD, Doolittle WF (1996) The root of the universal tree and the origin of eukaryotes based on elongation factor phylogeny. Proc Natl Acad Sci 93:7749–7754CrossRefPubMedGoogle Scholar
  6. Beresford TP, Fitzsimons NA, Brennan NL, Cogan TM (2001) Recent advances in cheese microbiology. Int Dairy J 11:259–274CrossRefGoogle Scholar
  7. Bianchi-Salvadori B, Cocconcelli PS, Fernandes I, Gomezr J, Gomez R et al (1997) Characterization of the lactic acid bacteria in artisanal dairy products. J Dairy Res 64:409–421CrossRefGoogle Scholar
  8. Björkroth J, Ridell J, Korkeala H (1996) Characterization of Lactobacillus sake strains associating with production of ropy slime by randomly amplified polymorphic DNA (RAPD) and pulsed-field gel electrophoresis (PFGE) patterns. Int J Food Microbiol 31:59–68CrossRefPubMedGoogle Scholar
  9. Blears MJ, De Grandis SA, Lee H, Trevors JT (1998) Amplified fragment length polymorphism (AFLP): a review of the procedure and its applications. J Industria Microbiol Biotechn 21:99–114CrossRefGoogle Scholar
  10. Brisse S, Verhoef J (2001) Phylogenetic diversity of Klebsiella pneumoniae and Klebsiella oxytoca clinical isolates revealed by randomly amplified polymorphic DNA, gyrA and parC genes sequencing and automated ribotyping. Int J Syst Evol Microbiol 51:915–924CrossRefPubMedGoogle Scholar
  11. Chandan RC (2011) Dairy ingredients for food processing: an overview. Wiley Online LibraryCrossRefGoogle Scholar
  12. Charteris WP, Kelly PM, Morelli L, Collins JK (1998) Development and application of an in vitro methodology to determine the transit tolerance of potentially probiotic Lactobacillus and Bifidobacterium species in the upper human gastrointestinal tract. J Appl Microbiol 84:759–768CrossRefPubMedGoogle Scholar
  13. Clayton RA, Sutton G, Hinkle PS, Bult C, Fields C (1995) Intraspecific variation in small-subunit rRNA sequences in GenBank: why single sequences may not adequately represent prokaryotic taxa. Int J Syst Bacteriol 45:595–599CrossRefPubMedGoogle Scholar
  14. Coeuret V, Dubernet S, Bernardeau M, Gueguen M, Vernoux JP (2003) Isolation, characterisation and identification of Lactobacilli focusing mainly on cheeses and other dairy products. Lait 83:269–306CrossRefGoogle Scholar
  15. Corroler D, Mangin I, Desmasures N, Gueguen M (1998) An ecological study of lactococci isolated from raw milk in the Camembert cheese registered designation of origin area. Appl Environ Microbiol 64:4729–4735PubMedPubMedCentralGoogle Scholar
  16. Daud Khaled AK, Neilan BA, Henriksson A, Conway PL (1997) Identification and phylogenetic analysis of Lactobacillus using multiplex RAPD-PCR. FEMS Microbiol Lett 153:191–197CrossRefPubMedGoogle Scholar
  17. De Gheldre Y, Vandamme P, Goossens H, Struelens MJ (1999) Identification of clinically relevant viridans streptococci by analysis of transfer DNA intergenic spacer length polymorphism. Int J Syst Evol Microbiol 49:1591–1598Google Scholar
  18. Dellaglio F, Torriani S, Felis GE (2004) Reclassification of Lactobacillus cellobiosus Rogosa et al. 1953 as a later synonym of Lactobacillus fermentum Beijerinck 1901. Int J Syst Evol Microbiol 54:809–812CrossRefPubMedGoogle Scholar
  19. Dong YP, Cui SH, Yu HX, Li FQ (2011) Development of pulsed field gel electrophoresis and application for characterization and identification of Lactobacillus and Streptococcus thermophilus. Chi J Prev Med 45:1086Google Scholar
  20. Drancourt M, Raoult D (2005) Sequence-based identification of new bacteria: a proposition for creation of an orphan bacterium repository. J Clin Microbiol 43:4311–4315CrossRefPubMedPubMedCentralGoogle Scholar
  21. Du Plessis EM, Dicks LMT (1995) Evaluation of random amplified polymorphic DNA (RAPD)-PCR as a method to differentiate Lactobacillus acidophilus, Lactobacillus crispatus, Lactobacillus amylovorus, Lactobacillus gallinarum, Lactobacillus gasseri, and Lactobacillus johnsonii. Curr Microbiol 31:114–118CrossRefPubMedGoogle Scholar
  22. Duhan JS, Nehra K, Gahlawat SK, Saharan P, Surekha (2013) Bacteriocins from lactic acid bacteria. In: Salar RK, Gahlawat SK, Siwach P, Duhan JS (eds) Biotechnology: prospects and applications. Springer, New Delhi, pp 127–142. ISBN 978-81-322-1682-7 ISBN 978-81-322-1683-4 (eBook).  https://doi.org/10.1007/978-81-322-1683-4CrossRefGoogle Scholar
  23. Enright MC, Spratt BG (1999) Multilocus sequence typing. Trends Microbiol 7:482–487CrossRefPubMedGoogle Scholar
  24. Euzéby JP (1997) List of bacterial names with standing in nomenclature: a folder available on the Internet. Int J Syst Bacteriol 47:590–592CrossRefPubMedGoogle Scholar
  25. Felis GE, Dellaglio F, Mizzi L, Torriani S (2001) Comparative sequence analysis of a recA gene fragment brings new evidence for a change in the taxonomy of the Lactobacillus casei group. Int J Syst Evol Microbiol 51:2113–2117CrossRefPubMedGoogle Scholar
  26. Fisher MM, Triplett EW (1999) Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities. Appl Environ Microbiol 65:4630–4636PubMedPubMedCentralGoogle Scholar
  27. Food, Agriculture Organization of the United Nations (1990) The technology of traditional milk products in developing countries. Food and Agriculture Organization of the United Nations, RomeGoogle Scholar
  28. Fukushima M, Kakinuma K, Kawaguchi R (2002) Phylogenetic analysis of Salmonella, Shigella, and Escherichia coli strains on the basis of the gyrB gene sequence. J Clin Microbiol 40:2779–2785CrossRefPubMedPubMedCentralGoogle Scholar
  29. Garcia-Martinez J, Acinas SG, Anton AI, Rodriguez-Valera F (1999) Use of the 16S-23S ribosomal genes spacer region in studies of prokaryotic diversity. J Microbiologica Method 36:55–64CrossRefGoogle Scholar
  30. Gasser F (1970) Electrophoretic characterization of lactic dehydrogenases in the genus Lactobacillus. J Gen Microbiol 62:223–239CrossRefPubMedGoogle Scholar
  31. Gevers D, Huys G, Swings J (2001) Applicability of rep-PCR fingerprinting for identification of Lactobacillus species. FEMS Microbiol Lett 205:31–36CrossRefPubMedGoogle Scholar
  32. Giraffa G, Neviani E (2000) Molecular identification and characterization of food-associated Lactobacilli. Italian J food Sci 12:403–423Google Scholar
  33. Golic N, Strahinic I, Terzic-Vidojevic A, Begovic J, Nikolic M et al (2012) Molecular diversity among natural populations of Lactobacillus paracasei and Lactobacillus plantarum/paraplantarum strains isolated from autochthonous dairy products. Eur Food Res Technol 234:627–638CrossRefGoogle Scholar
  34. Gürtler V (1999) The role of recombination and mutation in 16S-23S rDNA spacer rearrangements. Gene 238:241–252CrossRefPubMedGoogle Scholar
  35. Gürtler V, Stanisich VA (1996) New approaches to typing and identification of bacteria using the 16S-23S rDNA spacer region. Microbiologica 142:3–16Google Scholar
  36. Gutell RR (1993) Collection of small subunit (16S-and 16S-like) ribosomal RNA structures. Nucleic Acids Res 21:3051CrossRefPubMedPubMedCentralGoogle Scholar
  37. Holzapfel WH, Haberer P, Geisen R, Bjorkroth J, Schillinger U (2001) Taxonomy and important features of probiotic microorganisms in food and nutrition. Am J Clin Nutr 73:365s–373sCrossRefPubMedGoogle Scholar
  38. Johansson ML, Quednau M, Molin G, Ahrn S (1995) Randomly amplified polymorphic DNA (RAPD) for rapid typing of Lactobacillus plantarum strains. Lett Appl Microbiol 21:155–159CrossRefPubMedGoogle Scholar
  39. Kandler O, Weiss N (1986) Genus lactobacillus. In: Bergey’s manual of systematic bacteriology, vol 2. Springer, Berlin, pp 1209–1234Google Scholar
  40. Kimura K, McCartney AL, McConnell MA, Tannock GW (1997) Analysis of fecal populations of bifidobacteria and lactobacilli and investigation of the immunological responses of their human hosts to the predominant strains. Appl Environ Microbiol 63:3394–3398PubMedPubMedCentralGoogle Scholar
  41. Klein G, Pack A, Bonaparte C, Reuter G (1998) Taxonomy and physiology of probiotic lactic acid bacteria. Int J Food Microbiol 41:103–125CrossRefPubMedGoogle Scholar
  42. König H, Fröhlich J (2009) Lactic acid bacteria. Biology of microorganisms on grapes, in must and in wine. Springer, Heidelberg, pp 3–29Google Scholar
  43. Lortal S, Valence F, Bizet C, Maubois JL (1997) Electrophoretic pattern of peptidoglycan hydrolases, a new tool for bacterial species identification: application to 10 Lactobacillus species. Res Microbiol 148:461–474CrossRefPubMedGoogle Scholar
  44. Ludwig W, Neumaier J, Klugbauer N, Brockmann E, Roller C et al (1993) Phylogenetic relationships of bacteria based on comparative sequence analysis of elongation factor Tu and ATP-synthase Î2-subunit genes. Anton Leeuw 64:285–305CrossRefGoogle Scholar
  45. Maassen C, Boersma WJA, van Holten-Neelen C, Claassen E, Laman JD (2003) Growth phase of orally administered Lactobacillus strains differentially affects IgG1/IgG2a ratio for soluble antigens: implications for vaccine development. Vaccine 21:2751–2757CrossRefPubMedGoogle Scholar
  46. Makarova K, Slesarev A, Wolf Y, Sorokin A, Mirkin B et al (2006) Comparative genomics of the lactic acid bacteria. Proc Natl Acad Sci 103:15611–15616CrossRefPubMedGoogle Scholar
  47. Mardis ER (2008) The impact of next-generation sequencing technology on genetics. Trend Geneti 24:133–141CrossRefGoogle Scholar
  48. Mardis ER (2013) Next-generation sequencing platforms. Ann Rev Anal Chem 6:287–303CrossRefGoogle Scholar
  49. Marilley L, Casey MG (2004) Flavours of cheese products: metabolic pathways, analytical tools and identification of producing strains. Int J Food Microbiol 90:139–159CrossRefPubMedGoogle Scholar
  50. Marshall E, Mejia D (2011) Traditional fermented food and beverages for improved livelihoods. FAOGoogle Scholar
  51. McCartney AL (2002) Application of molecular biological methods for studying probiotics and the gut flora. British J Nutri 88:S29–S37CrossRefGoogle Scholar
  52. McCartney AL, Wenzhi W, Tannock GW (1996) Molecular analysis of the composition of the bifidobacterial and Lactobacillus microflora of humans. Appl Environ Microbiol 62:4608–4613PubMedPubMedCentralGoogle Scholar
  53. Mollet C, Drancourt M, Raoult D (1997) rpoB sequence analysis as a novel basis for bacterial identification. Mol Microbiol 26:1005–1011CrossRefPubMedGoogle Scholar
  54. Mueller UG, Wolfenbarger LL (1999) AFLP genotyping and fingerprinting. Trends Ecol Evol 14:389–394CrossRefPubMedGoogle Scholar
  55. Nguyen DTL, Cnockaert M, Van Hoorde K, De Brandt E, Snauwaert I et al (2013a) Lactobacillus porcinae sp. nov., isolated from traditional Vietnamese nem chua. Int J Syst Evol Microbiol 63:1754–1759CrossRefPubMedGoogle Scholar
  56. Nguyen HKT, Ha DL, Doan TTV, Quach TT, Nguyen HK (2013b) Study of Lactobacillus acidophilus by Restriction Fragment Length Polymorphism (RFLP) analysis. Springer, Berlin, pp 195–197Google Scholar
  57. O’Sullivan TF, Fitzgerald GF (1998) Comparison of Streptococcus thermophilus strains by pulse field gel electrophoresis of genomic DNA. FEMS Microbiol Lett 168:213–219CrossRefPubMedGoogle Scholar
  58. O’sullivan L, Ross RP, Hill C (2002) Potential of bacteriocin-producing lactic acid bacteria for improvements in food safety and quality. Biochimie 84:593–604CrossRefPubMedGoogle Scholar
  59. Olive DM, Bean P (1999) Principles and applications of methods for DNA-based typing of microbial organisms. J Clin Microbiol 37:1661–1669PubMedPubMedCentralGoogle Scholar
  60. Olsen GJ, Woese CR (1993) Ribosomal RNA: a key to phylogeny. FASEB J 7:113–123CrossRefPubMedGoogle Scholar
  61. Ouoba LII, Nyanga-Koumou CAG, Parkouda C, Sawadogo H, Kobawila SC et al (2009) Genotypic diversity of lactic acid bacteria isolated from African traditional alkaline-fermented foods. J Appl Microbiol 108:2019–2029PubMedGoogle Scholar
  62. Palys T, Berger E, Mitrica I, Nakamura LK, Cohan FM (2000) Protein-coding genes as molecular markers for ecologically distinct populations: the case of two Bacillus species. Int J Syst Evol Microbiol 50:1021–1028CrossRefPubMedGoogle Scholar
  63. Prajapati JB (2011) Traditional dairy products in developing countries. Invited paper presented at World Dairy Summit organized by International Dairy Federation. p 16–19Google Scholar
  64. Prasad J, Gill H, Smart J, Gopal PK (1998) Selection and characterisation of Lactobacillus and Bifidobacterium strains for use as probiotics. Int Dairy J 18:993–1002CrossRefGoogle Scholar
  65. Rainey FA, Ward-Rainey NL, Janssen PH, Hippe H, Stackebrandt E (1996) Clostridium paradoxum DSM 7308T contains multiple 16S rRNA genes with heterogeneous intervening sequences. Microbiologica 142:2087–2095Google Scholar
  66. Ramachandran P, Lacher DW, Pfeiler EA, Elkins CA (2013) Development of a tiered multilocus sequence typing scheme for members of the Lactobacillus acidophilus complex. Appl Environ Microbiol 79:7220–7228CrossRefPubMedPubMedCentralGoogle Scholar
  67. Singh S, Goswami P, Singh R, Heller KJ (2009) Application of molecular identification tools for Lactobacillus, with a focus on discrimination between closely related species: a review. LWT-Food Sci Tech 42:448–457CrossRefGoogle Scholar
  68. Song Y (2005) PCR-based diagnostics for anaerobic infections. Anaerobe 11:79–91CrossRefPubMedGoogle Scholar
  69. Stackebrandt E (2003) The richness of prokaryotic diversity: there must be a species somewhere. Food Technol Biotechnol 41:17–22Google Scholar
  70. Stackebrandt E, Goebel BM (1994) Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44:846–849CrossRefGoogle Scholar
  71. Švec P, Sedláček I, Žáčková L, Nováková D, Kukletová M (2009) Lactobacillus spp. associated with early childhood caries. Folia Microbiol 54:53–58CrossRefGoogle Scholar
  72. Tannock GW (1999) Identification of lactobacilli and bifidobacteria. Curr Issues Mol Biol 1:53–64PubMedGoogle Scholar
  73. Teuber M (1993) Lactic acid bacteria. In: Biotechnology set, 2nd edn. Weinheim: Wiley p 325–366Google Scholar
  74. Thomson CH, Hassan I, Dunn K (2012) Yakult: a role in combating multi-drug resistant Pseudomonas aeruginosa? J Wound Care 21:566–569CrossRefPubMedGoogle Scholar
  75. Tynkkynen S, Satokari R, Saarela M, Mattila-Sandholm T, Saxelin M (1999) Comparison of ribotyping, randomly amplified polymorphic DNA analysis, and pulsed-field gel electrophoresis in typing of Lactobacillus rhamnosus and L. casei strains. Appl Environ Microbiol 65:3908–3914PubMedPubMedCentralGoogle Scholar
  76. van den Berg DJC, Smits A, Pot B, Ledeboer AM, Kersters K et al (1993) Isolation, screening and identification of lactic acid bacteria from traditional food fermentation processes and culture collections. Food Biotechnol 7:189–205CrossRefGoogle Scholar
  77. Van Hoorde K, Verstraete T, Vandamme P, Huys G (2008) Diversity of lactic acid bacteria in two Flemish artisan raw milk Gouda-type cheeses. Food Microbiol 25:929–935CrossRefPubMedGoogle Scholar
  78. Vandamme P, Pot B, Gillis M, De Vos P, Kersters K et al (1996) Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev 60:407–438PubMedPubMedCentralGoogle Scholar
  79. Ventura M, Zink R (2002) Rapid identification, differentiation, and proposed new taxonomic classification of Bifidobacterium lactis. Appl Environ Microbiol 68:6429–6434CrossRefPubMedPubMedCentralGoogle Scholar
  80. Versalovic J, Koeuth T, Lupski R (1991) Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Res 19:6823–6831CrossRefPubMedPubMedCentralGoogle Scholar
  81. Versalovic J, Schneider M, De Bruijn FJ, Lupski JR (1994) Genomic fingerprinting of bacteria using repetitive sequence-based polymerase chain reaction. Methods Mole Cellular Biol 5:25–40Google Scholar
  82. Zabeau M, Vos P (1993) Selective restriction fragment amplification: a general method for DNA fingerprinting. CA Patent CA2,119,557Google Scholar
  83. Vos P, Hogers R, Bleeker M, Reijans M, van De Lee T et al (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414CrossRefPubMedPubMedCentralGoogle Scholar
  84. Wells JM, Mercenier A (2008) Mucosal delivery of therapeutic and prophylactic molecules using lactic acid bacteria. Nat Rev Microbiol 6:349–362CrossRefGoogle Scholar
  85. Wells JM, Robinson K, Chamberlain LM, Schofield KM, Page RWF (1996) Lactic acid bacteria as vaccine delivery vehicles. Anton Leeuw 70:317–330CrossRefGoogle Scholar
  86. Wertz JE, Goldstone C, Gordon DM, Riley MA (2003) A molecular phylogeny of enteric bacteria and implications for a bacterial species concept. J Evol Biol 16:1236–1248CrossRefPubMedGoogle Scholar
  87. Williams AG, Banks JM (1997) Proteolytic and other hydrolytic enzyme activities in non-starter lactic acid bacteria (NSLAB) isolated from cheddar cheese manufactured in the United Kingdom. Int Dairy J 7:763–774CrossRefGoogle Scholar
  88. Williams RAD, Sadler SA (1971) Electrophoresis of glucose-6-phosphate dehydrogenase, cell wall composition and the taxonomy of heterofermentative lactobacilli. J Gen Microbiol 65:351–358CrossRefPubMedGoogle Scholar
  89. Winslow CEA, Broadhurst J, Buchanan RE, Krumwiede C Jr, Rogers LA et al (1917) The families and genera of the bacteria preliminary report of the Committee of the Society of American bacteriologists on characterization and classification of bacterial types. J Bacteriol 2:505–566PubMedPubMedCentralGoogle Scholar
  90. Wong P, Houry WA (2004) Chaperone networks in bacteria: analysis of protein homeostasis in minimal cells. J Struct Biol 146:79–89CrossRefPubMedGoogle Scholar
  91. Wouters J, Ayad EHE, Hugenholtz J, Smit G (2002) Microbes from raw milk for fermented dairy products. Int Dairy J 12:91–109CrossRefGoogle Scholar
  92. Xu F-L, Guo Y-C, Wang H-X, Fu P, Zeng H-W et al (2012) PFGE genotyping and antibiotic resistance of Lactobacillus distributed strains in the fermented dairy products. Ann Microbiol 62:255–262CrossRefGoogle Scholar
  93. Zwieb C, Gorodkin J, Knudsen B, Burks J, Wower J (2003) tmRDB (tmRNA database). Nucleic Acids Res 31:446–447CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2018

Authors and Affiliations

  • Dhiraj Kumar Nanda
    • 1
    • 3
  • Reeti Chaudhary
    • 1
  • Dinesh Kumar
    • 2
  1. 1.Department of BiotechnologyD C R University of Science and TechnologyMurthalIndia
  2. 2.Centre for Agricultural BioinformaticsIndian Agricultural Statistics Research Institute, PUSANew DelhiIndia
  3. 3.Asian Institute of Public HealthBhubaneswarIndia

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