Identification of dairy lactic acid bacteria by tRNAAla-23S rDNA-RFLP

Journal of Microbiological Methods

Volumn 91, Issue 3, 2012, Pages 380-390

  Mancini, Andrea ^a   Lazzi, Camilla ^a   Bernini, Valentina ^a   Neviani, Erasmo ^a   Gatti, Monica ^a  

^a UNIVERSITY OF PARMA   (Italy)

Author keywords

(GTG)5 rep PCR; Banding pattern based method; Dairy isolates; Fingerprinting; Methods comparison; P1 RAPD

Indexed keywords

BACTERIA (MICROORGANISMS);

ALANINE TRANSFER RNA; BACTERIAL DNA; LACTIC ACID; RIBOSOME DNA; RNA 23S;

ARTICLE; BACTERIUM; BACTERIUM IDENTIFICATION; CHEESE; CLASSIFICATION; EVALUATION; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; METHODOLOGY; MICROBIOLOGY; PHYLOGENY; RESTRICTION FRAGMENT LENGTH POLYMORPHISM;

BACTERIA; BACTERIAL TYPING TECHNIQUES; CHEESE; DNA, BACTERIAL; DNA, RIBOSOMAL; LACTIC ACID; PHYLOGENY; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; RNA, RIBOSOMAL, 23S; RNA, TRANSFER, ALA;

EID: 84868220096     PISSN: 01677012     EISSN: 18728359     Source Type: Journal    
DOI: 10.1016/j.mimet.2012.10.003     Document Type: Article

References (71)

1. Alves P.I., Martins M.P., Semedo T., Figueiredo Marques J.J., Tenreiro R., Barreto Crespo M.T. Comparison of phenotypic and genotypic taxonomic methods for the identification of dairy enterococci. Antonie Leeuwenhoek 2004, 85(3):237-252.
2. Andrighetto C., Marcazzan G., Lombardi A. Use of RAPD-PCR and TTGE for the evaluation of biodiversity of whey cultures for Grana Padano cheese. Lett. Appl. Microbiol. 2004, 38(5):400-405.
3. Antonio M.A., Hillier S.L. DNA fingerprinting of Lactobacillus crispatus strain CTV-05 by repetitive element sequence-based PCR analysis in a pilot study of vaginal colonization. J. Clin. Microbiol. 2003, 41(5):1881-1887.
4. Aquilanti L., Silvestri G., Zannini E., Osimani A., Santarelli S., Clementi F. Phenotypic, genotypic and technological characterization of predominant lactic acid bacteria in Pecorino cheese from central Italy. J. Appl. Microbiol. 2007, 103(4):948-960.
5. Ben Amor K., Vaughan E.E., de Vos W.M. Advanced molecular tools for the identification of lactic acid bacteria. J. Nutr. 2007, 137(3 Suppl. 2):741S-747S.
6. Ben Belgacem Z., Dousset X., Prevost H., Manai M. Polyphasic taxonomic studies of lactic acid bacteria associated with Tunisian fermented meat based on the heterogeneity of the 16S-23S rRNA gene intergenic spacer region. Arch. Microbiol. 2009, 191(9):711-720.
7. Beresford T.P., Fitzsimons N.A., Brennan N.L., Cogan T. Recent advances in cheese microbiology. Int. Dairy J. 2001, 11:16.
8. Berthier F., Ehrlich S.D. Rapid species identification within two groups of closely related lactobacilli using PCR primers that target the 16S/23S rRNA spacer region. FEMS Microbiol. Lett. 1998, 161(1):97-106.
9. Bouton Y., Guyot P., Beuvier E., Tailliez P., Grappin R. Use of PCR-based methods and PFGE for typing and monitoring homofermentative lactobacilli during Comte cheese ripening. Int. J. Food Microbiol. 2002, 76(1-2):27-38.
10. Bove C.G., De Dea Lindner J., Lazzi C., Gatti M., Neviani E. Evaluation of genetic polymorphism among Lactobacillus rhamnosus non-starter Parmigiano Reggiano cheese strains. Int. J. Food Microbiol. 2011, 144(3):569-572.
11. Cocconcelli P.S., Parisi M.G., Senini L., Bottazzi V. Use of RAPD and 16S rDNA sequencing for the study of Lactobacillus population dynamics in natural whey culture. Lett. Appl. Microbiol. 1997, 25(1):8-12.
12. Collins M.D., Rodriguets U., Ash C., Aguirre C., Farrow J.A.E., Martinez-Murcia A., Phillips B.A., Williams A.M., Wallbanks S. Phylogenetic analysis of the genus Lactobacillus and related lactic acid bacteria as determined by reverse transcriptase sequencing of 16S rRNA. FEMS Microbiol. Lett. 1991, 77(1):7.
13. Colombo F., Borgo F., Fortina M.G. Genotypic characterization of non starter lactic acid bacteria involved in the ripening of artisanal Bitto PDO cheese. J. Basic Microbiol. 2009, 49(6):521-530.
14. Coudeyras S., Marchandin H., Fajon C., Forestier C. Taxonomic and strain-specific identification of the probiotic strain Lactobacillus rhamnosus 35 within the Lactobacillus casei group. Appl. Environ. Microbiol. 2008, 74(9):2679-2689.
15. Dasen A., Berthier F., Grappin R., Williams A.G., Banks J. Genotypic and phenotypic characterization of the dynamics of the lactic acid bacterial population of adjunct-containing Cheddar cheese manufactured from raw and microfiltered pasteurised milk. J. Appl. Microbiol. 2003, 94(4):595-607.
16. De Angelis M., Corsetti A., Tosti N., Rossi J., Corbo M.R., Gobbetti M. Characterization of non-starter lactic acid bacteria from Italian ewe cheeses based on phenotypic, genotypic, and cell wall protein analyses. Appl. Environ. Microbiol. 2001, 67(5):2011-2020.
17. de Los Reyes-Gavilan C.G., Limsowtin G.K., Tailliez P., Sechaud L., Accolas J.P. A Lactobacillus helveticus-specific DNA probe detects restriction fragment length polymorphisms in this species. Appl. Environ. Microbiol. 1992, 58(10):3429-3432.
18. Delgado S., Mayo B. Phenotypic and genetic diversity of Lactococcus lactis and Enterococcus spp. strains isolated from Northern Spain starter-free farmhouse cheeses. Int. J. Food Microbiol. 2004, 90(3):309-319.
19. Devirgiliis C., Caravelli A., Coppola D., Barile S., Perozzi G. Antibiotic resistance and microbial composition along the manufacturing process of Mozzarella di Bufala Campana. Int. J. Food Microbiol. 2008, 128(2):378-384.
20. Di Cagno R., Minervini G., Sgarbi E., Lazzi C., Bernini V., Neviani E., Gobbetti M. Comparison of phenotypic (Biolog System) and genotypic (random amplified polymorphic DNA-polymerase chain reaction, RAPD-PCR, and amplified fragment length polymorphism, AFLP) methods for typing Lactobacillus plantarum isolates from raw vegetables and fruits. Int. J. Food Microbiol. 2010, 143(3):246-253.
21. Ferchichi M., Valcheva R., Oheix N., Kabadjova P., Prévost H., Onno B., Dousset X. Rapid investigation of French sourdough microbiota by restriction fragment length polymorphism of the 16S-23S rRNA gene intergenic spacer region. World J. Microbiol. Biotechnol. 2008, 24:10.
22. Gatti M., Lazzi C., Rossetti L., Mucchetti G., Neviani E. Biodiversity in Lactobacillus helveticus strains present in natural whey starter used for Parmigiano Reggiano cheese. J. Appl. Microbiol. 2003, 95(3):463-470.
23. Gatti M., Trivisano C., Fabrizi E., Neviani E., Gardini F. Biodiversity among Lactobacillus helveticus strains isolated from different natural whey starter cultures as revealed by classification trees. Appl. Environ. Microbiol. 2004, 70(1):182-190.
24. Gatti M., Gardini F., Trivisano C., Fabrizi E., Neviani E. Classification techniques in order to study DNA fingerprinting of lactis acid bacteria of dairy origin. Trends in DNA fingerprinting research 2005, 20. Nova Science Publishers, Inc., New York. M.M. Read (Ed.).
25. Gevers D., Huys G., Swings J. Applicability of rep-PCR fingerprinting for identification of Lactobacillus species. FEMS Microbiol. Lett. 2001, 205(1):31-36.
26. Giraffa G., Rossetti L. Monitoring of the bacterial composition of dairy starter cultures by RAPD-PCR. FEMS Microbiol. Lett. 2004, 237(1):133-138.
27. Giraffa G., Lazzi C., Gatti M., Rossetti L., Mora D., Neviani E. Molecular typing of Lactobacillus delbrueckii of dairy origin by PCR-RFLP of protein-coding genes. Int. J. Food Microbiol. 2003, 82(2):163-172.
28. Grundmann H., Hori S., Tanner G. Determining confidence intervals when measuring genetic diversity and the discriminatory abilities of typing methods for microorganisms. J. Clin. Microbiol. 2001, 39(11):4190-4192.
29. Holzapfel W.H., Haberer P., Geisen R., Bjorkroth J., Schillinger U. Taxonomy and important features of probiotic microorganisms in food and nutrition. Am. J. Clin. Nutr. 2001, 73(Suppl. 2):365S-373S.
30. Hoppe-Seyler T.S., Jaeger B., Bockelmann W., Geis A., Heller K.J. Molecular identification and differentiation of Brevibacterium species and strains. Syst. Appl. Microbiol. 2007, 30(1):50-57.
31. Hunter P.R. Reproducibility and indices of discriminatory power of microbial typing methods. J. Clin. Microbiol. 1990, 28(9):1903-1905.
32. Huys G., Vancanneyt M., D'Haene K., Vankerckhoven V., Goossens H., Swings J. Accuracy of species identity of commercial bacterial cultures intended for probiotic or nutritional use. Res. Microbiol. 2006, 157(9):803-810.
33. Jany J.L., Barbier G. Culture-independent methods for identifying microbial communities in cheese. Food Microbiol. 2008, 25(7):839-848.
34. Jensen M.P., Ardo Y., Vogensen F.K. Isolation of cultivable thermophilic lactic acid bacteria from cheeses made with mesophilic starter and molecular comparison with dairy-related Lactobacillus helveticus strains. Lett. Appl. Microbiol. 2009, 49(3):396-402.
35. Jeyaram K., Mohendro Singh W., Premarani T., Devi A.R., Chanu K.S., Talukdar N.C., Singh M.R. Molecular identification of dominant microflora associated with 'Hawaijar' - a traditional fermented soybean (Glycine max (L.)) food of Manipur, India. Int. J. Food Microbiol. 2008, 122(3):259-268.
36. Jeyaram K., Romi W., Singh T.A., Devi A.R., Devi S.S. Bacterial species associated with traditional starter cultures used for fermented bamboo shoot production in Manipur state of India. Int. J. Food Microbiol. 2010, 143(1-2):1-8.
37. Kabadjova P., Dousset X., Le Cam V., Prevost H. Differentiation of closely related Carnobacterium food isolates based on 16S-23S ribosomal DNA intergenic spacer region polymorphism. Appl. Environ. Microbiol. 2002, 68(11):5358-5366.
38. Lazzi C., Bove C.G., Sgarbi E., Gatti M., La Gioia F., Torriani S., Neviani E. Application of AFLP fingerprint analysis for studying the biodiversity of Streptococcus thermophilus. J. Microbiol. Methods 2009, 79(1):48-54.
39. Le Jeune C., Lonvaud-Funel A. Sequence of DNA 16S/23S spacer region of Leuconostoc oenos (Oenococcus oeni): application to strain differentiation. Res. Microbiol. 1997, 148(1):79-86.
40. Li W., Raoult D., Fournier P.E. Bacterial strain typing in the genomic era. FEMS Microbiol. Rev. 2009, 33(5):892-916.
41. Markiewicz L.H., Biedrzycka E., Wasilewska E., Bielecka M. Rapid molecular identification and characteristics of Lactobacillus strains. Folia Microbiol. (Praha) 2010, 55(5):481-488.
42. Michel C., Pelletier C., Boussaha M., Douet D.G., Lautraite A., Tailliez P. Diversity of lactic acid bacteria associated with fish and the fish farm environment, established by amplified rRNA gene restriction analysis. Appl. Environ. Microbiol. 2007, 73(9):2947-2955.
43. Mohania D., Nagpal R., Kumar M., Bhardwaj A., Yadav M., Jain S., Marotta F., Singh V., Parkash O., Yadav H. Molecular approaches for identification and characterization of lactic acid bacteria. J. Dig. Dis. 2008, 9(4):190-198.
44. Monfredini L., Settanni L., Poznanski E., Cavazza A., Franciosi E. The spatial distribution of bacteria in Grana-cheese during ripening. Syst. Appl. Microbiol. 2012, 35(1):54-63.
45. Morea M., Matarante A., Di Cagno R., Baruzzi F., Minervini F. Contribution of autochthonous non-starter lactobacilli to proteolysis in Caciocavallo Pugliese cheese. Int. Dairy J. 2007, 17(5):10.
46. Moreira J.L., Mota R.M., Horta M.F., Teixeira S.M., Neumann E., Nicoli J.R., Nunes A.C. Identification to the species level of Lactobacillus isolated in probiotic prospecting studies of human, animal or food origin by 16S-23S rRNA restriction profiling. BMC Microbiol. 2005, 5:15.
47. Ndoye B., Rasolofo E.A., LaPointe G., Roy D. A review of the molecular approaches to investigate the diversity and activity of cheese microbiota. Dairy Sci. Technol. 2011, 91(5):30.
48. Nour M. 16S-23S and 23S-5S intergenic spacer regions of lactobacilli: nucleotide sequence, secondary structure and comparative analysis. Res. Microbiol. 1998, 149(6):433-448.
49. O'Sullivan L., Ross R.P., Hill C. Potential of bacteriocin-producing lactic acid bacteria for improvements in food safety and quality. Biochimie 2002, 84(5-6):593-604.
50. Ouoba L.I., Diawara B., Amoa-Awua W., Traore A.S., Moller P.L. Genotyping of starter cultures of Bacillus subtilis and Bacillus pumilus for fermentation of African locust bean (Parkia biglobosa) to produce Soumbala. Int. J. Food Microbiol. 2004, 90(2):197-205.
51. Parente E., Ciocia F., Ricciardi A., Zotta T., Felis G.E., Torriani S. Diversity of stress tolerance in Lactobacillus plantarum, Lactobacillus pentosus and Lactobacillus paraplantarum: a multivariate screening study. Int. J. Food Microbiol. 2010, 144(2):270-279.
52. Pogačić T., Samaržija D., Corich V., D'Andrea M., Kagkli D.-M., Giacomini A., Čanžek Majhenič A., Rogelj I. Microbiota of Karakačanski skakutanac, an artisanal fresh sheep cheese studied by culture-independent PCR-ARDRA and PCR-DGGE. Dairy Sci. Technol. 2010, 90(4):8.
53. Porcellato D., Gronnevik H., Rudi K., Narvhus J., Skeie S.B. Rapid lactic acid bacteria identification in dairy products by high-resolution melt analysis of DGGE bands. Lett. Appl. Microbiol. 2012, 54(4):344-351.
54. Power E.G. RAPD typing in microbiology-a technical review. J. Hosp. Infect. 1996, 34(4):247-265.
55. Psoni L., Kotzamanidis C., Yiangou M., Tzanetakis N., Litopoulou-Tzanetaki E. Genotypic and phenotypic diversity of Lactococcus lactis isolates from Batzos, a Greek PDO raw goat milk cheese. Int. J. Food Microbiol. 2007, 114(2):211-220.
56. Quigley L., O'Sullivan O., Beresford T.P., Ross R.P., Fitzgerald G.F., Cotter P.D. Molecular approaches to analysing the microbial composition of raw milk and raw milk cheese. Int. J. Food Microbiol. 2011, 150(2-3):81-94.
57. Rachman C.N., Kabadjova P., Prevost H., Dousset X. Identification of Lactobacillus alimentarius and Lactobacillus farciminis with 16S-23S rDNA intergenic spacer region polymorphism and PCR amplification using species-specific oligonucleotide. J. Appl. Microbiol. 2003, 95(6):1207-1216.
58. Rachman C., Kabadjova P., Valcheva R., Prevost H., Dousset X. Identification of Carnobacterium species by restriction fragment length polymorphism of the 16S-23S rRNA gene intergenic spacer region and species-specific PCR. Appl. Environ. Microbiol. 2004, 70(8):4468-4477.
59. Rademaker J.L., Herbet H., Starrenburg M.J., Naser S.M., Gevers D., Kelly W.J., Hugenholtz J., Swings J., van Hylckama Vlieg J.E. Diversity analysis of dairy and nondairy Lactococcus lactis isolates, using a novel multilocus sequence analysis scheme and (GTG)5-PCR fingerprinting. Appl. Environ. Microbiol. 2007, 73(22):7128-7137.
60. Randazzo C.L., Caggia C., Neviani E. Application of molecular approaches to study lactic acid bacteria in artisanal cheeses. J. Microbiol. Methods 2009, 78(1):1-9.
61. Rossetti L., Giraffa G. Rapid identification of dairy lactic acid bacteria by M13-generated, RAPD-PCR fingerprint databases. J. Microbiol. Methods 2005, 63(2):135-144.
62. Rossetti L., Fornasari M.E., Gatti M., Lazzi C., Neviani E., Giraffa G. Grana Padano cheese whey starters: microbial composition and strain distribution. Int. J. Food Microbiol. 2008, 127(1-2):168-171.
63. Simpson E.H. Measurement of diversity. Nature 1949, 163(4148):688.
64. Singh S.G.P., Singhb R., Hellerc K.J. Application of molecular identification tools for Lactobacillus, with a focus on discrimination between closely related species: a review. LWT- Food Sci. Technol. 2009, 42(2):10.
65. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 2011, 28(10):2731-2739.
66. Terzic-Vidojevic A., Vukasinovic M., Veljovic K., Ostojic M., Topisirovic L. Characterization of microflora in homemade semi-hard white Zlatar cheese. Int. J. Food Microbiol. 2007, 114(1):36-42.
67. Tyler K.D., Wang G., Tyler S.D., Johnson W.M. Factors affecting reliability and reproducibility of amplification-based DNA fingerprinting of representative bacterial pathogens. J. Clin. Microbiol. 1997, 35(2):339-346.
68. Tynkkynen S., Satokari R., Saarela M., Mattila-Sandholm T., Saxelin M. 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. 1999, 65(9):3908-3914.
69. Versalovic J., Schneider M., de Bruijn F.J., Lupski J.R. Genomic fingerprinting of bacteria using repetitive sequence based PCR (rep-PCR). Using repetitive sequence based PCR (rep-PCR). Meth. Cell. Mol. Biol. 1994, 5:16.
70. Woods C.R., Versalovic J., Koeuth T., Lupski J.R. Whole-cell repetitive element sequence-based polymerase chain reaction allows rapid assessment of clonal relationships of bacterial isolates. J. Clin. Microbiol. 1993, 31(7):1927-1931.
71. Zavaleta A.I., Martinez-Murcia A.J., Rodriguez-Valera F. 16S-23S rDNA intergenic sequences indicate that Leuconostoc oenos is phylogenetically homogeneous. Microbiology 1996, 142(Pt 8):2105-2114.