Genotypic and phenotypic diversity of Pediococcus pentosaceus strains isolated from food matrices and characterisation of the penocin operon

Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology

Volumn 103, Issue 5, 2013, Pages 1149-1163

  Martino, Maria Elena ^a   Maifreni, Michela ^b   Marino, Marilena ^b   Bartolomeoli, Ingrid ^b   Carraro, Lisa ^a   Fasolato, Luca ^a   Cardazzo, Barbara ^a  

^a UNIVERSITY OF PADOVA   (Italy)

^b UNIVERSITY OF UDINE   (Italy)

Author keywords

Lactic acid bacteria; Multilocus sequence typing; PCR; Pediococcus pentosaceus; Pediococcus phylogenetics; Penocin

Indexed keywords

BACTERIOCIN; GENOMIC DNA; PENOCIN; RNA 16S; UNCLASSIFIED DRUG;

ACIDIFICATION; ALLELE; ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; BACTERIAL GROWTH; BACTERIAL STRAIN; BACTERIUM ISOLATE; BIOSYNTHESIS; CHEMOTAXONOMY; CONTROLLED STUDY; DALR GENE; DNA BASE COMPOSITION; FERMENTATION TECHNIQUE; FERMENTED PRODUCT; FOOD PROCESSING; FOOD QUALITY; GENETIC VARIABILITY; GENOTYPE PHENOTYPE CORRELATION; GLNA GENE; GYRB GENE; INCUBATION TEMPERATURE; LACTIC ACID BACTERIUM; LEUS GENE; MICROBIAL MORPHOLOGY; MULTILOCUS SEQUENCE TYPING; NONHUMAN; NUCLEOTIDE SEQUENCE; OPERON; PEDIOCOCCUS PENTOSACEUS; PGI GENE; PGM GENE; PRIORITY JOURNAL; PYC GENE; RNA GENE; RNA SEQUENCE; SEQUENCE HOMOLOGY; STRAIN DIFFERENCE; STRAIN IDENTIFICATION; STRUCTURAL GENOMICS;

BACTERIAL TYPING TECHNIQUES; BACTERIOCINS; BIOSYNTHETIC PATHWAYS; CLUSTER ANALYSIS; FOOD MICROBIOLOGY; GENOTYPE; MOLECULAR SEQUENCE DATA; MULTILOCUS SEQUENCE TYPING; OPERON; PEDIOCOCCUS; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

PEDIOCOCCUS; PEDIOCOCCUS PENTOSACEUS;

EID: 84876668589     PISSN: 00036072     EISSN: 15729699     Source Type: Journal    
DOI: 10.1007/s10482-013-9897-1     Document Type: Article

References (47)

1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403-410
2. Bisharat N, Cohen DI, Maiden MC, Crook DW, Peto T, Harding RM (2007) The evolution of genetic structure in the marine pathogen, Vibrio vulnificus. Infect Genet Evol 7:685-693
3. Bolotin A, Wincker P, Mauger S, Jaillon O, Malarme K, Weissenbach J, Ehrlich SD, Sorokin A (2001) The complete genome sequence of the lactic acid bacterium Lactococcus lactis spp. Lactis IL1403. Genome Res 11:731-753
4. Bruen TC, Philippe H, Bryant D (2006) A simple and robust statistical test for detecting the presence of recombination. Genetics 172:2665-2681
5. Cai H, Rodriguez BT, Zhang W, Broadbent JR, Steele JL (2007) Genotypic and phenotypic characterization of Lactobacillus casei strains isolated from different ecological niches suggests frequent recombination and niche specificity. Microbiology 153:2655-2665
6. Calmin G, Lefort F, Belbahri L (2008) Multi-loci sequence typing (MLST) for two lacto-acid bacteria (LAB) species: Pediococcus parvulus and P. damnosus. Mol Biotechnol 40:170-179. doi: 10.1007/s12033-008-9073-4
7. Campelo AB, Gaspar P, Roces C, Rodríguez A, Kok J, Kuipers OP, Neves AR, Martínez B (2011) The Lcn972 bacteriocin-encoding plasmid pBL1 impairs cellobiose metabolism in Lactococcus lactis. Appl Environ Microbiol 77:7576-7585. doi: 10.1128/AEM.06107-11
8. Carraro L, Maifreni M, Bartolomeoli I, Martino ME, Novelli E, Frigo F, Marino M, Cardazzo B (2011) Comparison of culture-dependent and -independent methods for bacterial community monitoring during Montasio cheese manufacturing. Res Microbiol 162:231-239. doi: 10.1016/j.resmic.2011.01.002
9. Christensen GD, Simpson WA, Younger JJ, Baddour LM, Barrett FF, Melton DM, Beachey EH (1985) Adherence of coagulase-negative staphylococci to plastic tissue culture plates: a quantitative model for the adherence of staphylococci to medical devices. J Clin Microbiol 22:996-1006
10. Coton E, Rollan G, Bertrand A, Lonvaud-Funel A (1998) Histamine producing lactic acid bacteria in wines: early detection, frequency and distribution. Am J Enol Vitic 49:199-204
11. DalmIş Ü, Soyer A (2008) Effect of processing methods and starter culture (Staphylococcus xylosus and Pediococcus pentosaceus) on proteolytic changes in Turkish sausages (sucuk) during ripening and storage. Meat Sci 80:345-354. doi: 10.1016/j.meatsci.2007.12.022
12. De Brabandere AG, De Baerdemaeker JG (1999) Effects of process conditions on the pH development during yogurt fermentation. J Food Eng 41:221-227
13. De las Rivas B, Marcobal A, Muñoz R (2004) Allelic diversity and population structure in Oenococcus oeni as determined from sequence analysis of housekeeping genes. Appl Environ Microbiol 70:7210-7219
14. De las Rivas B, Marcobal A, Muñoz R (2006) Development of a multilocus sequence typing method for analysis of Lactobacillus plantarum strains. Microbiology 152:85-93
15. Delétoile A, Passet V, Aires J, Chambaud I, Butel MJ, Smokvina T, Brisse S (2010) Species delineation and clonal diversity in four Bifidobacterium species as revealed by multilocus sequencing. Res Microbiol 161:82-90. doi: 10.1016/j.resmic.2009.12.006
16. Diancourt L, Passet V, Chervaux C, Garault P, Smokvina T, Brisse S (2007) Multilocus sequence typing of Lactobacillus casei reveals a clonal population structure with low levels of homologous recombination. Appl Environ Microbiol 73:6601-6611
17. Didelot X, Falush D (2007) Inference of bacterial microevolution using multilocus sequence data. Genetics 175:1251-1266
18. Diep DB, Godager L, Brede D, Nes IF (2006) Data mining and characterization of a novel pediocin-like bacteriocin system from the genome of Pediococcus pentosaceus ATCC 25745. Microbiology 152:1649-1659
19. Dobson CM, Deneer H, Lee S, Hemmingsen S, Glaze S, Ziola B (2002) Phylogenetic analysis of the genus Pediococcus, including Pediococcus claussenii sp. nov., a novel lactic acid bacterium isolated from beer. Int J Syst Evol Microbiol 52:2003-2010
20. Francisco AP, Bugalho M, Ramirez M, Carrico JA (2009) Global optimal eBURST analysis of multilocus typing data using a graphic matroid approach. BMC Bioinformatics 10:152
21. Huson DH, Bryant D (2006) Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 23:254-267
22. Jolley KA, Maiden MC (2010) BIGSdb: scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics 11:595. doi: 10.1186/1471-2105-11-595
23. Kjos M, Nes IF, Diep DB (2009) Class II one-peptide bacteriocins target a phylogenetically defined subgroup of mannose phosphotransferase systems on sensitive cells. Microbiology 155:2949-2961. doi: 10.1099/mic.0.030015-0
24. Lazzi C, Bove CG, Sgarbi E, Gatti M, La Gioia F, Torriani S, Neviani E (2009) Application of AFLP fingerprint analysis for studying the biodiversity of Streptococcus thermophilus. J Microbiol Meth 79:48-54. doi: 10.1016/j.mimet.2009.07.021
25. Leroy F, De Vuyst L (2004) Lactic acid bacteria as functional starter cultures for the food fermentation industry. Trends Food Sci Tech 15:67-78. doi: 10.1016/j.tifs.2003.09.004
26. Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451-1452. doi: 10.1093/bioinformatics/btp187
27. Maiden MC, Bygraves JA, Feil E, Morelli G, Russell JE, Urwin R, Zhang Q, Zhou J, Zurth K, Caugant DA, Feavers IM, Achtman M, Spratt BG (1998) Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci USA 95:3140-3145
28. Maifredi M, Marino M, Conte L (2004) Lactic acid fermentation of Brassica rapa: chemical and microbial evaluation of a typical Italian product (brovada). Eur Food Res Technol 218:469-473
29. Makarova K, Slesarev A, Wolf Y, Sorokin A, Mirkin B, Koonin E, Pavlov A, Pavlova N, Karamychev V, Polouchine N, Shakhova V, Grigoriev I, Lou Y, Rohksar D, Lucas S, Huang K, Goodstein DM, Hawkins T, Plengvidhya V, Welker D, Hughes J, Goh Y, Benson A, Baldwin K, Lee JH, Díaz-Muñiz I, Dosti B, Smeianov V, Wechter W, Barabote R, Lorca G, Altermann E, Barrangou R, Ganesan B, Xie Y, Rawsthorne H, Tamir D, Parker C, Breidt F, Broadbent J, Hutkins R, O'Sullivan D, Steele J, Unlu G, Saier M, Klaenhammer T, Richardson P, Kozyavkin S, Weimer B, Mills D (2006) Comparative genomics of the lactic acid bacteria. Proc Natl Acad Sci USA 103:15611-15616
30. Manca de Nadra MC, Strasser de Saad AM (1995) Polysaccharide production by Pediococcus pentosaceus from wine. Int J Food Microbiol 27:101-106
31. Martin DP, Williamson C, Posada D (2005) RDP2: recombination detection and analysis from sequence alignments. Bioinformatics 21:260-262
32. Mora D, Fortina MG, Parini C, Ricci G, Gatti M, Giraffa G, Manachini PL (2002) Genetic diversity and technological properties of Streptococcus thermophilus strains isolated from dairy products. J Appl Microbiol 93:278-287
33. Nadkarni MA, Martin FE, Jacques NA, Hunter N (2002) Determination of bacterial load by real-time PCR using a broad-range (universal) probe and primer set. Microbiology 148:257-266
34. Ortu S, Felis GE, Marzotto M, Deriu A, Molicotti P, Sechi LA, Dellaglio F, Zanetti S (2007) Identification and functional characterization of Lactobacillus strains isolated from milk and Gioddu, a traditional Sardinian fermented milk. Int Dairy J 17:1312-1320
35. Osborne JP, Mira de Orduna R, Pilone G, Liu SQ (2000) Acetaldehyde metabolism by wine lactic acid bacteria. FEMS Microbiol Lett 191:51-55
36. Pereira CS, Santos AJ, Bejerano-Sagie M, Correia PB, Marques JC, Xavier KB (2012) Phosphoenolpyruvate phosphotransferase system regulates detection and processing of the quorum sensing signal autoinducer-2. Mol Microbiol 84:93-104. doi: 10.1111/j.1365-2958.2012.08010.x
37. Pfannebecker J, Fröhlich J (2008) Use of a species-specific multiplex PCR for the identification of pediococchi. Int J Food Microbiol 128:288-296. doi: 10.1016/j.ijfoodmicro.2008.08.019
38. Rasmussen TB, Danielsen M, Valina O, Garrigues C, Johansen E, Pedersen MB (2008) Streptococcus thermophilus core genome: comparative genome hybridization study of 47 strains. Appl Environ Microbiol 74:4703-4710. doi: 10.1128/AEM.00132-08
39. Santos EM, Jaime I, Rovira J, Lyhs U, Korkeala H, Björkroth J (2005) Characterization and identification of lactic acid bacteria in "morcilla de Burgos". Int J Food Microbiol 97:285-296
40. Schillinger U, Lücke F (1989) Antibacterial activity of Lactobacillus sake isolated from meat. Appl Environ Microbiol 55:1901-1906
41. Sharpe ME (1979) Identification of the lactic acid bacteria. In: Skinner FA, Lovelock DW (eds) Identification methods for microbiologists. Academic Press, London, pp 233-259
42. Simpson PJ, Stanton C, Fitzgerald GF, Ross RP (2002) Genomic diversity within the genus Pediococcus as revealed by randomly amplified polymorphic DNA PCR and pulsed-field gel electrophoresis. Appl Environ Microbiol 68:765-771
43. Stiles ME (1996) Biopreservation by lactic acid bacteria. Antonie Van Leeuwenhoek 70:331-345
44. Tanganurat W, Quinquis B, Leelawatcharamas V, Bolotin A (2009) Genotypic and phenotypic characterization of Lactobacillus plantarum strains isolated from Thai fermented fruits and vegetables. J Basic Microbiol 49:377-385. doi: 10.1002/jobm.200800185
45. Thomas TD, McKay LL, Morris HA (1985) Lactate metabolism by pediococci isolated from cheese. Appl Environ Microbiol 49:908-913
46. Titgemeyer F, Hillen W (2002) Global control of sugar metabolism: a gram-positive solution. Antonie Van Leeuwenhoek 82:9-71
47. Vos M, Didelot X (2009) A comparison of homologous recombination rates in 805 bacteria and archaea. ISME J 3:199-208. doi: 10.1038/ismej.2008.93