Multi-loci sequence typing (MLST) for two lacto-acid bacteria (LAB) species: Pediococcus parvulus and P. damnosus

Molecular Biotechnology

Volumn 40, Issue 2, 2008, Pages 170-179

  Calmin, Gautier ^a   Lefort, Francois ^a   Belbahri, Lassaad ^a  

^a UNIVERSITY OF APPLIED SCIENCES WESTERN SWITZERLAND   (Switzerland)

Author keywords

Lacto acid bacteria; Multi loci sequence typing; PCR; Pediococcus damnosus; Pediococcus parvulus; Real time PCR

Indexed keywords

ACIDS; BACTERIOLOGY; BIOCHEMICAL ENGINEERING; COSMIC RAYS; DIFFERENTIATION (CALCULUS); FERMENTATION; GENES; LABORATORIES; LACTIC ACID; MAGNETIC LEAKAGE; MICROORGANISMS; NUCLEIC ACIDS; ORGANIC ACIDS; POPULATION STATISTICS;

LACTO-ACID BACTERIA; MULTI-LOCI SEQUENCE TYPING; PCR; PEDIOCOCCUS DAMNOSUS; PEDIOCOCCUS PARVULUS; REAL TIME PCR;

WINE;

DNA 16S;

ARTICLE; BACTERIAL GENE; BACTERIUM IDENTIFICATION; GENE LOCUS; HOUSEKEEPING GENE; LEUS GENE; MARKER GENE; MLE GENE; NONHUMAN; NUCLEOTIDE SEQUENCE; PEDIOCOCCUS; PEDIOCOCCUS DAMNOSUS; PEDIOCOCCUS PARVULUS; PHYLOGENETIC TREE; POLYMERASE CHAIN REACTION; REAL TIME POLYMERASE CHAIN REACTION; RECA GENE; RPLB GENE; STRAIN DIFFERENCE; WINE;

BASE SEQUENCE; GENETIC MARKERS; PEDIOCOCCUS; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA;

BACTERIA (MICROORGANISMS); PEDIOCOCCUS; PEDIOCOCCUS DAMNOSUS; PEDIOCOCCUS PARVULUS;

EID: 56749085839     PISSN: 10736085     EISSN: None     Source Type: Journal    
DOI: 10.1007/s12033-008-9073-4     Document Type: Article

References (31)

1. Fleet, G. H. (1997). The microbiology of alcoholic beverages. In B. J. B. Wood (Ed.), Microbiology of fermented foods (Vol. 1, 2nd edn.). Blackie Academic & Professional, pp. 217-262.
2. I Lopez F Ruiz-Larrea L Cocolin E Orr T Phister M Marshall 2003 Design and evaluation of PCR primers for analysis of bacterial populations in wine by denaturing gradient gel electrophoresis Applied and Environmental Microbiology 69 6801 6807 10.1128/AEM.69.11.6801-6807.2003
3. A Lonvaud-Funel 1999 Lactic acid bacteria in the quality improvement and depreciation of wine Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology 76 317 331 10.1023/A:1002088931106
4. Ribereau-Gayon, P. (2000). Handbook of enology. Chichester, United Kingdom: Wiley.
5. CR Davis D Wibowo R Eschenbruch TH Lee GH Fleet 1985 Practical implications of malolactic fermentation: A review American Journal of Enology and Viticulture 36 290 301
6. M Manca de Nadra A Strasser de Saad 1995 Polysaccharide production by Pediococcus pentosaceus from wine International Journal of Food Microbiology 27 101 106 10.1016/0168-1605(94)00118-P
7. JP Osborne R Mira de Orduna GJ Pilone SQ Liu 2000 Acetaldehyde metabolism by wine lactic acid bacteria FEMS Microbiology Letters 191 51 55 10.1111/j.1574-6968.2000.tb09318.x
8. E Coton G Rollan A Bertrand A Lonvaud-Funel 1998 Histamine-producing lactic acid bacteria in wines: Early detection, frequency, and distribution American Journal of Enology and Viticulture 49 199 204
9. V Renouf O Claisse A Lonvaud-Funel 2006 rpoB gene: A target for identification of LAB cocci by PCR-DGGE and melting curves analyses in Real Time PCR Journal of Microbiological Methods 67 162 170 10.1016/j.mimet.2006.03.008
10. O Claisse V Renouf A Lonvaud-Funel 2007 Differentiation of wine lactic acid bacteria species based on RFLP analysis of a partial sequence of rpoB gene Journal of Microbiological Methods 69 387 390 10.1016/j.mimet.2007.01.004
11. V Renouf O Claisse A Lonvaud-Funel 2007 Inventory and monitoring of wine microbial consortia Applied Microbiology and Biotechnology 75 149 164 10.1007/s00253-006-0798-3
12. S Lafon-Lafourcade A Joyeux 1979 Techniques simplifiées pour le dénombrement et l'identification des micro-organismes vivants dans les moûts et les vins Conn. Vigne Vin 13 295 310
13. EM Santos I Jaime J Rovira U Lyhs H Korkeala J Bjorkroth 2005 Characterization and identification of lactic acid bacteria in "morcilla de Burgos" International Journal of Food Microbiology 97 285 296 10.1016/j.ijfoodmicro.2004.04.021
14. K Rantsiou G Comi L Cocolin 2004 The rpoB gene as a target for PCR-DGGE analysis to follow lactic acid bacterial population dynamics during food fermentations Food Microbiology 21 481 487 10.1016/j.fm.2003.10.002
15. Tamang, B., Tamang, J. P., Schillinger, U., Franz, C. M., Gores, M., & Holzapfel, W. H. (2007). Phenotypic and genotypic identification of lactic acid bacteria isolated from ethnic fermented bamboo tender shoots of North East India. International Journal of Food Microbiology, 121, 35-40.
16. V Plengvidhya F Breidt Jr Z Lu HP Fleming 2007 DNA fingerprinting of lactic Acid bacteria in sauerkraut fermentations 1 Applied and Environmental Microbiology 73 23 7697 7702 10.1128/AEM.01342-07
17. H Cai BT Rodriguez W Zhang JR Broadbent JL Steele 2007 Genotypic and phenotypic characterization of Lactobacillus casei strains isolated from different ecological niches suggests frequent recombination and niche specificity Microbiology-Sgm 153 2655 2665 10.1099/mic.0.2007/006452-0
18. B de las Rivas A Marcobal R Munoz 2004 Allelic diversity and population structure in Oenococcus oeni as determined from sequence analysis of housekeeping genes Applied and Environmental Microbiology 70 7210 7219 10.1128/AEM.70.12.7210-7219.2004
19. B de las Rivas A Marcobal R Muñoz 2006 Development of a multilocus sequence typing method for analysis of Lactobacillus plantarum strains Microbiology 152 85 93 10.1099/mic.0.28482-0
20. D Mora MG Fortina C Parini D Daffonchio PL Manachini 2000 Genomic subpopulations within the species Pediococcus acidilactici detected by multilocus typing analysis: Relationships between pediocin AcH/PA-1 producing and non-producing strains Microbiology-Sgm 146 2027 2038
21. AM Rodas S Ferrer I Pardo 2003 16S-ARDRA, a tool for identification of lactic acid bacteria isolated from grape must and wine Systematic and Applied Microbiology 26 412 442 10.1078/072320203322497446
22. E Chenoll MC Macian R Aznar 2003 Identification of Carnobacterium, Lactobacillus, Oenococcus and Pediococcus by rDNA-based techniques Systematic and Applied Microbiology 26 546 556 10.1078/072320203770865855
23. A Groisillier A Lonvaud-Funel 1999 Comparison of partial malolactic enzyme gene sequences for phylogenetic analysis of some lactic acid bacteria species and relationships with the malic enzyme International Journal of Systematic Bacteriology 49 1417 1428
24. MCJ Maiden JA Bygraves E Feil G Morelli JE Russell R Urwin 1998 Multilocus sequence typing: A portable approach to the identification of clones within populations of pathogenic microorganisms Proceedings of the National Academy of Sciences of the United States of America 95 3140 3145 10.1073/pnas.95.6.3140
25. WG Weisburg SM Barns DA Pelletier DJ Lane 1991 16S ribosomal DNA amplification for phylogenetic study Journal of Bacteriology 173 2 697 703
26. SR Santos H Ochman 2004 Identification and phylogenetic sorting of bacterial lineages with universally conserved genes and proteins Environmental Microbiology 6 7 754 759 10.1111/j.1462-2920.2004.00617.x
27. N Galtier M Gouy C Gautier 1996 SEAVIEW and PHYLO-WIN: Two graphic tools for sequence alignment and molecular phylogeny Computer Applications in the Biosciences 12 543 548
28. S Guindon O Gascuel 2003 A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood Systematic Biology 52 696 704 10.1080/10635150390235520
29. L Belbahri E Moralejo G Calmin T Oszako JA Garcia E Descals 2006 Phytophthora polonica, a new species isolated from declining Alnus glutinosa stands in Poland FEMS Microbiology Letters 261 165 174 10.1111/j.1574-6968.2006. 00349.x
30. SF Altschul TL Madden AA Schaffer JH Zhang Z Zhang W Miller 1997 Gapped BLAST and PSI-BLAST: A new generation of protein database search programs Nucleic Acids Research 25 3389 3402 10.1093/nar/25.17.3389
31. K Makarova A Slesarev Y Wolf A Sorokin B Mirkin E Koonin 2006 Comparative genomics of lactic acid bacteria Proceedings of the National Academy of Sciences of the United States of America 103 15611 15616 10.1073/pnas.0607117103