Population Genetics of Lactobacillus sakei Reveals Three Lineages with Distinct Evolutionary Histories

PLoS ONE

Volumn 8, Issue 9, 2013, Pages

  Chaillou, Stéphane ^a   Lucquin, Isabelle ^a   Najjari, Afef ^b   Zagorec, Monique ^a,c   Champomier Vergès, Marie Christine ^a  

^a UMR1319 MICALIS   (France)

^b Campus Universitaire   (Tunisia)

^c Ecole Nationale d'Ingenieurs des Techniques des Industries Agricoles et Alimentaires ENITIAA   (France)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDE;

ALLELE; ARTICLE; BACTERIAL GENETICS; BACTERIAL STRAIN; BACTERIUM ISOLATE; CLONAL VARIATION; GENE LOCUS; GENEALOGY; GENETIC POLYMORPHISM; GENETIC VARIABILITY; HOMOLOGOUS RECOMBINATION; LACTOBACILLUS SAKEI; MOLECULAR EVOLUTION; MULTILOCUS SEQUENCE TYPING; NONHUMAN; NUCLEOTIDE SEQUENCE; POPULATION DYNAMICS; POPULATION GENETICS; UNINDEXED SEQUENCE;

EVOLUTION, MOLECULAR; GENETICS, POPULATION; LACTOBACILLUS; MOLECULAR SEQUENCE DATA; PHYLOGENY;

EID: 84884381841     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0073253     Document Type: Article

References (54)

1. Hammes WP, Bantleon A, Min S, (1990) Lactic acid bacteria in meat fermentation. FEMS Microbiology Reviews 87: 165-174.
2. Hammes WP, Hertel C, (1998) New developments in meat starter cultures. Meat Science 49: S125-S138.
3. Champomier-Vergès MC, Chaillou S, Cornet M, Zagorec M, (2002) Erratum to "Lactobacillus sakei: recent developments and future prospects". Res Microbiol 153: 115-123.
4. Bredholt S, Nesbakken T, Holck A, (2001) Industrial application of an antilisterial strain of Lactobacillus sakei as a protective culture and its effect on the sensory acceptability of cooked, sliced, vacuum-packaged meats. Int J Food Microbiol 66: 191-196.
5. Vermeiren L, Devlieghere F, Debevere J, (2004) Evaluation of meat born lactic acid bacteria as protective cultures for the biopreservation of cooked meat products. Int J Food Microbiol 96: 149-164.
6. Jones RJ, Zagorec M, Brightwell G, Tagg JR, (2009) Inhibition by Lactobacillus sakei of other species in the flora of vacuum packaged raw meats during prolonged storage. Food Microbiol 26: 876-881.
7. Chaillou S, Champomier-Vergès MC, Cornet M, Crutz-Le Coq AM, Dudez AM, et al. (2005) The complete genome sequence of the meat-borne lactic acid bacterium Lactobacillus sakei 23K. Nat Biotechnol 23: 1527-1533.
8. Torriani S, Van Reenen GA, Klein G, Reuter G, Dellaglio F, et al. (1996) Lactobacillus curvatus subsp. curvatus subsp. nov. and Lactobacillus curvatus subsp. melibiosus subsp. nov. and Lactobacillus sake subsp. sake subsp. nov. and Lactobacillus sake subsp. carnosus subsp. nov., new subspecies of Lactobacillus curvatus Abo-Elnaga and Kandler 1965 and Lactobacillus sake Katagiri, Kitahara, and Fukami 1934 (Kleinet al. 1996, emended descriptions), respectively. Int J Syst Bacteriol 46: 1158-1163.
9. Klein G, Dicks LMT, Pack A, Hack B, Zimmermann K, et al. (1996) Emended descriptions of Lactobacillus sake (Katagiri, Kitahara, and Fukami) and Lactobacillus curvatus (Abo-Elnaga and Kandler): numerical classification revealed by protein fingerprinting and identification based on biochemical patterns and DNA-DNA hybridizations. Int J Syst Bacteriol 46: 367-376.
10. Berthier F, Ehrlich SD, (1999) Genetic diversity within Lactobacillus sakei and Lactobacillus curvatus and design of PCR primers for its detection using randomly amplified polymorphic DNA. Int J Syst Bacteriol 49: 997-1007.
11. Chaillou S, Daty M, Baraige F, Dudez AM, Anglade P, et al. (2009) Intraspecies genomic diversity and natural population structure of the meat-borne lactic acid bacterium Lactobacillus sakei. Appl Environ Microbiol 75: 970-980.
12. Maiden MC, (2006) Multilocus sequence typing of bacteria. Annu Rev Microbiol 60: 561-588.
13. de Las Rivas B, Marcobal A, Munoz R, (2006) Development of a multilocus sequence typing method for analysis of Lactobacillus plantarum strains. Microbiology 152: 85-93.
14. Tanigawa K, Watanabe K, (2011) Multilocus sequence typing reveals a novel subspeciation of Lactobacillus delbrueckii. Microbiology 157: 727-738.
15. 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.
16. Diancourt L, Passet V, Chervaux C, Garault P, Smokvina T, et al. (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. Picozzi C, Bonacina G, Vigentini I, Foschino R, (2010) Genetic diversity in Italian Lactobacillus sanfranciscensis strains assessed by multilocus sequence typing and pulsed-field gel electrophoresis analyses. Microbiology 156: 2035-2045.
18. Raftis EJ, Salvetti E, Torriani S, Felis GE, O'Toole PW, (2011) Genomic diversity of Lactobacillus salivarius. Appl Environ Microbiol 77: 954-965.
19. Oh PL, Benson AK, Peterson DA, Patil PB, Noriyama EN, et al. (2010) Diversification of the gut symbiot Lactobacillus reuteri as a result of host-driven evolution. ISME J 4: 377-387.
20. Bilhere E, Lucas PM, Claisse O, Lonvaud-Funel A, (2009) Multilocus sequence typing of Oenococcus oeni: detection of two subpopulations shaped by intergenic recombination. Appl Environ Microbiol 75: 1291-1300.
21. Passerini D, Beltramo C, Coddeville M, Quentin Y, Ritzenthaler P, et al. (2010) Genes but not genomes reveal bacterial domestication of Lactococcus lactis. PLoS One 5: e15306.
22. Delorme C, Bartholini C, Bolotine A, Ehrlich SD, Renault P, (2009) Emergence of a cell wall protease in the Streptococcus thermophilus population. Appl Environ Microbiol 76: 451-460.
23. Tajima F, (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
24. Pritchard JK, Stephens M, Donnelly P, (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
25. Falush D, Stephens M, Pritchard JK, (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164: 1567-1587.
26. Jakobsen IB, Easteal S, (1996) A program for calculating and displaying compatibility matrices as an aid in determining reticulate evolution in molecular sequences. Comput Appl Biosci 12: 291-295.
27. 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.
28. Feil EJ, Li BC, Aanensen DM, Hanage WP, Spratt BG, (2004) eBURST: inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data. J Bacteriol 186: 1518-1530.
29. Didelot X, Falush D, (2007) Inference of bacterial microevolution using multilocus sequence data. Genetics 175: 1251-1266.
30. Huson DH, (1998) SplitsTree: analyzing and visualizing evolutionary data. Bioinformatics 14: 68-73.
31. Lucquin I, Zagorec M, Champomier-Vergès M, Chaillou S, (2012) Fingerprint of lactic acid bacteria population in beef carpaccio is influenced by storage process and seasonal changes. Food Microbiol 29: 187-196.
32. Vos M, Didelot X, (2009) A comparison of homologous recombination rates in bacteria and archaea. ISME J 3: 199-208.
33. Achtman M, Wagner M, (2008) Microbial diversity and the genetic nature of microbial species. Nat Rev Microbiol 6: 431-440.
34. Bridier J, Claisse O, Coton M, Coton E, Lonvaud-Funel A, (2010) Evidence of distinct populations and specific subpopulations within the species Oenococcus oeni. Appl Environ Microbiol 76: 7754-7764.
35. Labadie J, (1999) Consequences of packaging on bacterial growth. Meat is an ecological niche. Meat Sci 52: 299-305.
36. Tohno M, Kobayashi H, Nomura M, Uegaki R, Cai Y, (2012) Identification and characterization of lactic acid bacteria isolated from mixed pasture of timothy and orchardgrass, and its badly preserved silage. Anim Sci J 83: 318-330.
37. Champomier MC, Montel MC, Grimont F, Grimont PAD, (1987) Genomic identification of meat lactobacilli as Lactobacillus sake. Annales de l' Institut Pasteur/Microbiology 138: 751-758.
38. Chiaramonte F, Blugeon S, Chaillou S, Langella P, Zagorec M, (2009) Behavior of the meat-borne bacterium Lactobacillus sakei during its transit through the gastrointestinal tracts of axenic and conventional mice. Appl Environ Microbiol 75: 4498-4505.
39. Dal Bello F, Walter J, Hammes WP, Hertel C, (2003) Increased complexity of the species composition of lactic acid bacteria in human feces revealed by alternative incubation condition. Microb Ecol 45: 455-463.
40. Hugas M, Garriga M, Aymerich T, Monfort JM, (1993) Biochemical characterization of lactobacilli from dry fermented sausages. Int J Food Microbiol 18: 107-113.
41. Joffraud JJ, Cardinal M, Cornet J, Chasles JS, Leon S, et al. (2006) Effect of bacterial interactions on the spoilage of cold-smoked salmon. Int J Food Microbiol 112: 51-61.
42. Morishita Y, Shiromizu K, (1986) Characterization of lactobacilli isolated from meats and meat products. Int J Food Microbiol 3: 19-29.
43. Najjari A, Ouzari H, Boudabous A, Zagorec M, (2008) Method for reliable isolation of Lactobacillus sakei strains originating from Tunisian seafood and meat products. Int J Food Microbiol 121: 342-351.
44. Samelis J, Maurogenakis F, Metaxopoulos J, (1994) Characterisation of lactic acid bacteria isolated from naturally fermented Greek dry salami. Int J Food Microbiol 23: 179-196.
45. Scheirlinck I, Van der Meulen R, Van Schoor A, Vancanneyt M, De Vuyst L, et al. (2008) Taxonomic structure and stability of the bacterial community in belgian sourdough ecosystems as assessed by culture and population fingerprinting. Appl Environ Microbiol 74: 2414-2423.
46. Schillinger U, Lucke FK, (1989) Antibacterial activity of Lactobacillus sake isolated from meat. Appl Environ Microbiol 55: 1901-1906.
47. Shaw BG, Harding CD, (1984) A numerical taxonomy study of lactic acid bacteria from vacuum-packed beef, pork, lamb and bacon. J Appl Bacteriol 56: 25-40.
48. Vogel RF, Lohmann M, Weller AN, Hugas M, Hammes WP, (1991) Structural similarity and distribution of small cryptic plasmids of Lactobacillus curvatus and Lactobacillus sake. FEMS Microbiol Lett 84: 183-190.
49. Gordon D, Abajian C, Green P, (1998) Consed: a graphical tool for sequence finishing. Genome Res 8: 195-202.
50. McLeod A, Nyquist OL, Snipen L, Naterstad K, Axelsson L, (2008) Diversity of Lactobacillus sakei strains investigated by phenotypic and genotypic methods. Syst Appl Microbiol 31: 393-403.
51. Librado P, Rozas J, (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451-1452.
52. Tamura K, Dudley J, Nei M, Kumar S, (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24: 1596-1599.
53. Martin DP, Lemey P, Lott M, Moulton V, Posada D, et al. (2010) RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics 826: 2462-2463.
54. Watterson GA, (1978) The homogosity test of neutrality. Genetics 88: 405-417.