Intraspecies genomic diversity and natural population structure of the meat-borne lactic acid bacterium Lactobacillus sakei

Applied and Environmental Microbiology

Volumn 75, Issue 4, 2009, Pages 970-980

  Chaillou, Stéphane ^a   Daty, Marie ^a   Baraige, Fabienne ^a   Dudez, Anne Marie ^a,d   Anglade, Patricia ^a   Jones, Rhys ^a,b   Alpert, Carl Alfred ^a,c   Champomier Vergès, Marie Christine ^a   Zagorec, Monique ^a  

^a CEMAGREF   (France)

^b RUAKURA RESEARCH CENTRE   (New Zealand)

^c GERMAN INSTITUTE OF HUMAN NUTRITION   (Germany)

^d CNRS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ECOLOGICAL HABITATS; FISH PRODUCTS; GENE POOLS; GENOME SIZES; GENOMIC DIVERSITIES; ISOFORMS; LACTIC ACID BACTERIUM; LACTOBACILLUS SAKEI; MEAT PRODUCTS; MICROBIAL ECO SYSTEMS; MIGRATION PATTERNS; NATURAL POPULATIONS; PROTEOMIC ANALYSIS; PULSED-FIELD GEL ELECTROPHORESIS;

ELECTROPHORESIS; FOOD PRODUCTS; GELATION; LACTIC ACID; MEATS; ORGANIC ACIDS;

ECOLOGY;

BACTERIUM; CHROMOSOME; ELECTROKINESIS; GEL; GENE EXPRESSION; GENOME; IDENTIFICATION METHOD; INTRASPECIFIC VARIATION; MEAT; MICROBIAL COMMUNITY; MOLECULAR ANALYSIS; ORGANIC ACID; POLYMERASE CHAIN REACTION; POPULATION STRUCTURE; PROTEOMICS; SUBSPECIES;

BACTERIAL PROTEINS; CLUSTER ANALYSIS; DNA FINGERPRINTING; DNA, BACTERIAL; ELECTROPHORESIS, GEL, PULSED-FIELD; FISH PRODUCTS; GENOTYPE; LACTOBACILLUS; MEAT PRODUCTS; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMERASE CHAIN REACTION; POLYMORPHISM, GENETIC; PROTEOME; SEQUENCE ANALYSIS, DNA;

BACTERIA (MICROORGANISMS); LACTOBACILLUS SAKEI;

EID: 59949102232     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.01721-08     Document Type: Article

References (42)

1. Abby, S., and V. Daubin. 2007. Comparative genomics and the evolution of prokaryotes. Trends Microbiol. 15:135-141.
2. Alpert, C.-A., A.-M. Crutz-Le Coq, C. Malleret, and M. Zagorec. 2003. Characterization of a theta-type plasmid from Lactobacillus sakei: a potential basis for low-copy-number vectors in lactobacilli. Appl. Environ. Microbiol. 69:5574-5584.
3. Anderson, D. G., and L. L. McKay. 1983. Simple and rapid method for isolating large plasmid DNA from lactic streptococci. Appl. Environ. Microbiol. 46:549-552.
4. Berthier, F., M. Zagorec, M. C. Champomier-Vergès, S. D. Ehrlich, and F. Morel-Deville. 1996. Efficient transformation of Lactobacillus sake by electroporation. Microbiology 142:1273-1279.
5. Berthier, F., and S. D. Ehrlich. 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.
6. Chaillou, S., M. C. Champomier-Vergès, A. M. Crutz Le Coq, M. Cornet, A. M. Dudez, V. Martin, S. Beaufils, E. Darbon-Rongère, V. Loux, R. Bossy, and M. Zagorec. 2005. The complete genome sequence of the meat-borne lactic acid bacterium Lactobacillus sakei 23K. Nat. Biotechnol. 23:1527-1533.
7. Champomier-Vergès, M. C., M. C. Montel, F. Grimont, and P. A. Grimont. 1987. Genomic identification of meat lactobacilli as Lactobacillus sake. Ann. Inst. Pasteur Microbiol. 138:751-758.
8. Champomier-Vergès, M. C., S. Chaillou, M. Cornet, and M. Zagorec. 2002. Lactobacillus sakei: recent developments and future prospects. Res. Microbiol. 152:115-123.
9. Coenye, T., D. Gevers, Y. Van de Peer, P. Vandamme, and J. Swings. 2005. Towards a prokaryotic genomic taxonomy. FEMS Microbiol. Rev. 29:147-167.
10. Cohan, F. M. 2002. What are bacterial species? Annu. Rev. Microbiol. 56:457-487.
11. De man, J. C., M. Rogosa, and M. E. Sharpe. 1960. A medium for the cultivation of lactobacilli. J. Appl. Bacteriol. 23:133-135.
12. Doolittle, W. F., and R. T. Papke. 2006. Genomics and the bacterial species problem. Genome Biol. 7:116.
13. Dudez, A. M., S. Chaillou, L. Hissler, R. Stentz, M. C. Champomier-Vergès C. A. Alpert, and M. Zagorec. 2002. Physical and genetic map of the Lactobacillus sakei 23K chromosome. Microbiology 148:421-431.
14. Eisen, J. A. 2000. Horizontal gene transfer among microbial genomes: new insights from complete genome analysis. Curr. Opin. Genet. Dev. 10:606-611.
15. Fontana, C., G. Vignolo, and P. S. Cocconcelli. 2005. PCR-DGGE analysis for the identification of microbial populations from Argentinean dry fermented sausages. J. Microbiol. Methods 63:254-263.
16. Guillot, A., C. Gitton, P. Anglade, and M. Y. Mistou. 2000. Proteomic analysis of Lactococcus lactis, a lactic acid bacterium. Proteomics 3:337-354.
17. Hugas, M., M. Garriga, T. Aymerich, and J. M. Monfort. 1993. Biochemical characterization of lactobacilli from dry fermented sausages. Int. J. Food Microbiol. 18:107-113.
18. Hugas, M., M. Garriga, T. Aymerich, and J. M. Monfort. 1995. Inhibition of Listeria in dry fermented sausages by the bacteriogenic Lactobacillus sake CTC494. J. Appl. Bacteriol. 79:322-330.
19. Jacquard, A. 1974. The genetic structure of populations. Springer-Verlag, Berlin, Germany.
20. Joffraud, J. J., M. Cardinal, J. Cornet, J. S. Chasles, S. Léon, F. Gigout, and F. Leroi. 2006. Effect of bacterial interactions on the spoilage of cold-smoked salmon. Int. J. Food Microbiol. 112:51-61.
21. Jofré, A., M. C. Champomier-Vergès, P. Anglade, F. Baraige, B. Martín, M. Garriga, M. Zagorec, and T. Aymerich. 2007. Protein synthesis in lactic acid and pathogenic bacteria during recovery from a high pressure treatment. Res. Microbiol. 158:512-520.
22. Katagiri, H., K. Kitahara, and K. Fukami. 1934. The characteristics of the lactic acid bacteria isolated from moto, yeast mashes for saké manufacture. IV. Classification of the lactic acid bacteria. Bull. Agr. Chem. Soc. Jpn. 10:156-157.
23. Klein, G., L. M. Dicks, A. Pack, B. Hack, K. Zimmerman, F. Dellaglio, and G. Reuter. 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.
24. Klein, G., and International Committee on Systematic Bacteriology. 2001. Subcommittee on the taxonomy of Bifidobacterium, Lactobacillus and related organisms. Int. J. Syst. Evol. Microbiol. 51:259-261.
25. Konstantinidis, K. T., A. Ramette, and J. M. Tiedje. 2006. The bacterial species definition in the genomic era. Philos. Trans. R. Soc. Lond. B 361: 1929-1940.
26. Koort, J., P. Vandamme, U. Schillinger, W. Holzapfel, and J. Bjorkroth. 2004. Lactobacillus curvatus subsp. melibiosus is a later synonym of Lactobacillus sakei subsp. carnosus. Int. J. Syst. Evol. Microbiol. 54:1621-1626.
27. Labadie, J. 1999. Consequences of packaging on bacterial growth. Meat is an ecological niche. Meat Sci. 52:299-305.
28. Lauret, R., F. Morel-Deville, F. Berthier, M. C. Champomier- Vergès, P. Postma, S. D. Ehrlich, and M. Zagorec. 1996. Carbohydrate utilization in Lactobacillus sake. Appl. Environ. Microbiol. 62:1922-1927.
29. Marceau, A., T. Méra, M. Zagorec, and M. C. Champomier-Vergès. 2001. Protein expression under uracil privation in Lactobacillus sakei. FEMS Microbiol. Lett. 200:49-52.
30. Marceau, A., M. Zagorec, S. Chaillou, T. Méra, and M. C. Champomier-Vergès. 2004. Evidence for involvement of at least six proteins in adaptation of Lactobacillus sakei to cold temperature and addition of NaCl. Appl. Eviron. Microbiol. 70:7260-7268.
31. Montel, M. C., R. Talon, J. Fournaud, and M. C. Champomier. 1991. A simplified key for identifying homofermentative Lactobacillus and Carnobacterium spp. from meat. J. Appl. Bacteriol. 70:469-472.
32. Morishita, Y., and K. Shiromizu. 1986. Characterization of lactobacilli from meats and meat products. Int. J. Food Microbiol. 3:19-29.
33. Noonpakdee, W., K. Phucharoen, P. Teerawattanamontri, T. Valyasevi, and S. Panyim. 1996. Molecular cloning, DNA sequencing and expression of catalase gene of Lactobacillus sake TISTR911 in Escherichia coli UM2. Asia Pac. J. Mol. Biol. Biotechnol. 4:229-235.
34. Ohnishi, M., K. Kurokawa, and T. Hayashi. 2001. Diversification of Escherichia coli genomes: are bacteriophages the major contributors? Trends Microbiol. 9:481-485.
35. Schillinger, U., and F. K. Lucke. 1987. Identification of lactobacilli from meat and meat products. Food Microbiol. 4:199-208.
36. Shaw, B., and C. Harding. 1984. A numerical taxonomic study of lactic acid bacteria from vacuum-packed beef, pork, lamb and bacon. J. Appl. Bacteriol. 56:25-40.
37. Tanasupawat, S., and W. Daengsubha. 1983. Pediococcus species and related bacteria found in fermented foods and related materials in Thailand. J. Gen. Appl. Microbiol. 29:487-506.
38. Torriani, S., C. A. Van Reenen, G. Klein, G. Reuter, F. Dellaglio, and L. M. T. Dicks. 1996. Lactobacillus curvatus subsp. curvatus nov. and Lactobacillus curvatus subsp. melibiosus 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 (Klein et al. 1996, emended descriptions), respectively. Int. J. Syst. Bacteriol. 46:1158-1163.
39. Vermeiren, L., F. Devlieghere, and J. Debevere. 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.
40. Vogel, R. F., M. Lohmann, A. N. Weller, M. Hugas, and W. P. Hammes. 1991. Structural similarity and distribution of small cryptic plasmids of Lactobacillus curvatus and L. sake. FEMS Microbiol. Lett. 84:183-190.
41. Vogel, R. F., M. Lohmann, M. Nguyen, A. N. Weller, and W. P. Hammes. 1993. Molecular characterization of Lactobacillus curvatus and L. sake isolated from sauerkraut and their application in sausage fermentations. J. Appl. Bacteriol. 74:295-300.
42. Walter, J., C. Hertel, G. W. Tannock, C. M. Lis, K. Munro, and W. P. Hammes. 2001. Detection of Lactobacillus, Pediococcus, Leuconostoc, and Weissella species in human feces by using group-specific PCR primers and denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 67:2578-2585.