Genome-scale diversity and niche adaptation analysis of Lactococcus lactis by comparative genome hybridization using multi-strain arrays

Microbial Biotechnology

Volumn 4, Issue 3, 2011, Pages 383-402

  Siezen, Roland J ^a,b,c,d   Bayjanov, Jumamurat R ^b,d   Felis, Giovanna E ^a,e   van der Sijde, Marijke R ^b,c   Starrenburg, Marjo ^a   Molenaar, Douwe ^a,c,f   Wels, Michiel ^a,b,c   van Hijum, Sacha A F T ^a,b,c,d   van Hylckama Vlieg, Johan E T ^a,c,g  

^a KLUYVER CENTRE FOR GENOMICS OF INDUSTRIAL FERMENTATION   (Netherlands)

^b RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

^c TOP INSTITUTE FOOD AND NUTRITION   (Netherlands)

^d NETHERLANDS BIOINFORMATICS CENTRE   (Netherlands)

^e UNIVERSITY OF VERONA   (Italy)

^f VU UNIVERSITY AMSTERDAM   (Netherlands)

^g Gut and Microbiology Platform   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARABINOSE; CITRIC ACID; EXOPOLYSACCHARIDE; GALACTOSIDE; GALACTURONIC ACID; LACTIC ACID; LACTOSE; XYLAN;

ARTICLE; BACTERIAL CHROMOSOME; BACTERIAL GENETICS; BACTERIAL STRAIN; BACTERIUM ISOLATE; CARBOHYDRATE SYNTHESIS; COMPARATIVE GENOMIC HYBRIDIZATION; DAIRY PRODUCT; FERMENTATION; GENE CLUSTER; GENE SEQUENCE; GENETIC CODE; GENETIC VARIABILITY; LACTOCOCCUS LACTIS; MICROARRAY ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PLASMID; PROTEIN DEGRADATION; SEQUENCE ANALYSIS; STRAIN DIFFERENCE;

ANIMALS; CATTLE; COMPARATIVE GENOMIC HYBRIDIZATION; FOOD MICROBIOLOGY; GENETIC VARIATION; GENOME, BACTERIAL; INSECTS; LACTOCOCCUS LACTIS; MOLECULAR SEQUENCE DATA; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHYLOGENY; SOIL MICROBIOLOGY;

BACTERIA (MICROORGANISMS); LACTOCOCCUS LACTIS;

EID: 79955456594     PISSN: 17517907     EISSN: 17517915     Source Type: Journal    
DOI: 10.1111/j.1751-7915.2011.00247.x     Document Type: Article

References (63)

1. Bachmann, H. (2009) Regulatory and Adaptive Responses of Lactococcus lactis in Situ. Wageningen, the Netherlands: Wageningen University.
2. Bayjanov, J.R., Wels, M., Starrenburg, M., van Hylckama Vlieg, J.E., Siezen, R.J., and Molenaar, D. (2009) PanCGH: a genotype-calling algorithm for pangenome CGH data. Bioinformatics 25: 309-314.
3. Bayjanov, J.R., Siezen, R.J., and van Hijum, S.A. (2010) PanCGHweb: a web tool for genotype calling in pangenome CGH data. Bioinformatics 26: 1256-1257.
4. Bolotin, A., Wincker, P., Mauger, S., Jaillon, O., Malarme, K., Weissenbach, J., etal. (2001) The complete genome sequence of the lactic acid bacterium Lactococcus lactis ssp. lactis IL1403. Genome Res 11: 731-753.
5. Bolotin, A., Quinquis, B., Sorokin, A., and Ehrlich, D.S. (2004) Recent genetic transfer between Lactococcus lactis and enterobacteria. J Bacteriol 186: 6671-6677.
6. Brouwer, R.W., van Hijum, S.A., and Kuipers, O.P. (2009) MINOMICS: visualizing prokaryote transcriptomics and proteomics data in a genomic context. Bioinformatics 25: 139-140.
7. Budin-Verneuil, A., Maguin, E., Auffray, Y., Ehrlich, D.S., and Pichereau, V. (2006) Genetic structure and transcriptional analysis of the arginine deiminase (ADI) cluster in Lactococcus lactis MG1363. Can J Microbiol 52: 617-622.
8. Campo, N., Dias, M.J., Daveran-Mingot, M.L., Ritzenthaler, P., and Le Bourgeois, P. (2002) Genome plasticity in Lactococcus lactis. Antonie Van Leeuwenhoek 82: 123-132.
9. Danhorn, T., and Fuqua, C. (2007) Biofilm formation by plant-associated bacteria. Annu Rev Microbiol 61: 401-422.
10. Davidson, B.E., Kordias, N., Dobos, M., and Hillier, A.J. (1996) Genomic organization of lactic acid bacteria. Antonie Van Leeuwenhoek 70: 161-183.
11. Delorme, C., Godon, J.J., Ehrlich, S.D., and Renault, P. (1993) Gene inactivation in Lactococcus lactis: histidine biosynthesis. J Bacteriol 175: 4391-4399.
12. Earl, A.M., Losick, R., and Kolter, R. (2007) Bacillus subtilis genome diversity. J Bacteriol 189: 1163-1170.
13. Finking, R., and Marahiel, M.A. (2004) Biosynthesis of nonribosomal peptides. Annu Rev Microbiol 58: 453-488.
14. Garcia-Quintans, N., Repizo, G., Martin, M., Magni, C., and Lopez, P. (2008) Activation of the diacetyl/acetoin pathway in Lactococcus lactis subsp. lactis bv. diacetylactis CRL264 by acidic growth. Appl Environ Microbiol 74: 1988-1996.
15. Godon, J.J., Delorme, C., Bardowski, J., Chopin, M.C., Ehrlich, S.D., and Renault, P. (1993) Gene inactivation in Lactococcus lactis: branched-chain amino acid biosynthesis. J Bacteriol 175: 4383-4390.
16. Groot, M.N., Klaassens, E., de Vos, W.M., Delcour, J., Hols, P., and Kleerebezem, M. (2005) Genome-based in silico detection of putative manganese transport systems in Lactobacillus plantarum and their genetic analysis. Microbiology 151: 1229-1238.
17. Han, Y.H., Liu, W.Z., Shi, Y.Z., Lu, L.Q., Xiao, S., Zhang, Q.H., and Zhao, G.P. (2007) Comparative genomics profiling of clinical isolates of Helicobacter pylori in Chinese populations using DNA microarray. J Microbiol 45: 21-28.
18. van Hylckama Vlieg, J.E., Rademaker, J.L., Bachmann, H., Molenaar, D., Kelly, W.J., and Siezen, R.J. (2006) Natural diversity and adaptive responses of Lactococcus lactis. Curr Opin Biotechnol 17: 183-190.
19. Inaoka, T., Matsumura, Y., and Tsuchido, T. (1999) SodA and manganese are essential for resistance to oxidative stress in growing and sporulating cells of Bacillus subtilis. J Bacteriol 181: 1939-1943.
20. Kelly, W., and Ward, L. (2002) Genotypic vs. phenotypic biodiversity in Lactococcus lactis. Microbiology 148: 3332-3333.
21. Kelly, W.J., Davey, G.P., and Ward, L.J. (2000) Novel sucrose transposons from plant strains of Lactococcus lactis. FEMS Microbiol Lett 190: 237-240.
22. Kelly, W.J., Ward, L.J., and Leahy, S.C. (2010) Chromosomal diversity in Lactococcus lactis and the origin of dairy starter cultures. Genome Biol Evol 2: 729-744.
23. Kleerebezem, M., Boekhorst, J., van Kranenburg, R., Molenaar, D., Kuipers, O.P., Leer, R., etal. (2003) Complete genome sequence of Lactobacillus plantarum WCFS1. Proc Natl Acad Sci USA 100: 1990-1995.
24. La, M.V., Crapoulet, N., Barbry, P., Raoult, D., and Renesto, P. (2007) Comparative genomic analysis of Tropheryma whipplei strains reveals that diversity among clinical isolates is mainly related to the WiSP proteins. BMC Genomics 8: 349.
25. Lan, R., and Reeves, P.R. (2000) Intraspecies variation in bacterial genomes: the need for a species genome concept. Trends Microbiol 8: 396-401.
26. McBride, S.M., Fischetti, V.A., Leblanc, D.J., Moellering, R.C., Jr, and Gilmore, M.S. (2007) Genetic diversity among Enterococcus faecalis. PLoS ONE 2: e582.
27. Machielsen, R., Siezen, R.J., van Hijum, S.A., and van Hylckama Vlieg, J.E. (2010) Molecular description and industrial potential of Tn6098-mediated conjugative transfer of alpha-galactosides metabolism in Lactococcus lactis. Appl Environ Microbiol 77: 555-563.
28. McKay, L.L. (1983) Functional properties of plasmids in lactic streptococci. Antonie Van Leeuwenhoek 49: 259-274.
29. Makarova, K.S., and Koonin, E.V. (2007) Evolutionary genomics of lactic acid bacteria. J Bacteriol 189: 1199-1208.
30. Makarova, K., Slesarev, A., Wolf, Y., Sorokin, A., Mirkin, B., Koonin, E., etal. (2006) Comparative genomics of the lactic acid bacteria. Proc Natl Acad Sci USA 103: 15611-15616.
31. Medini, D., Donati, C., Tettelin, H., Masignani, V., and Rappuoli, R. (2005) The microbial pan-genome. Curr Opin Genet Dev 15: 589-594.
32. Molenaar, D., Bringel, F., Schuren, F.H., de Vos, W.M., Siezen, R.J., and Kleerebezem, M. (2005) Exploring Lactobacillus plantarum genome diversity by using microarrays. J Bacteriol 187: 6119-6127.
33. Nomura, M., Nakajima, I., Fujita, Y., Kobayashi, M., Kimoto, H., Suzuki, I., and Aso, H. (1999) Lactococcus lactis contains only one glutamate decarboxylase gene. Microbiology 145 (Part 6): 1375-1380.
34. Nomura, M., Kobayashi, M., Ohmomo, S., and Okamoto, T. (2000) Inactivation of the glutamate decarboxylase gene in Lactococcus lactis subsp. cremoris. Appl Environ Microbiol 66: 2235-2237.
35. Nomura, M., Kobayashi, M., and Okamoto, T. (2002) Rapid PCR-based method which can determine both phenotype and genotype of Lactococcus lactis subspecies. Appl Environ Microbiol 68: 2209-2213.
36. Obis, D., Guillot, A., and Mistou, M.Y. (2001) Tolerance to high osmolality of Lactococcus lactis subsp. lactis and cremoris is related to the activity of a betaine transport system. FEMS Microbiol Lett 202: 39-44.
37. Overbeek, R., Larsen, N., Walunas, T., D'Souza, M., Pusch, G., Selkov, E., Jr, etal. (2003) The ERGO genome analysis and discovery system. Nucleic Acids Res 31: 164-171.
38. Pace, N.R. (2009) Mapping the tree of life: progress and prospects. Microbiol Mol Biol Rev 73: 565-576.
39. Peng, J., Zhang, X., Yang, J., Wang, J., Yang, E., Bin, W., etal. (2006) The use of comparative genomic hybridization to characterize genome dynamics and diversity among the serotypes of Shigella. BMC Genomics 7: 218.
40. Quiberoni, A., Rezaiki, L., El Karoui, M., Biswas, I., Tailliez, P., and Gruss, A. (2001) Distinctive features of homologous recombination in an 'old' microorganism, Lactococcus lactis. Res Microbiol 152: 131-139.
41. R Development Core Team (2006) R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing [WWW document]. URL
42. Rademaker, J.L., Herbet, H., Starrenburg, M.J., Naser, S.M., Gevers, D., Kelly, W.J., etal. (2007) Diversity analysis of dairy and nondairy Lactococcus lactis isolates, using a novel multilocus sequence analysis scheme and (GTG)5-PCR fingerprinting. Appl Environ Microbiol 73: 7128-7137.
43. Rasmussen, T.B., Danielsen, M., Valina, O., Garrigues, C., Johansen, E., and Pedersen, M.B. (2008) Streptococcus thermophilus core genome: comparative genome hybridization study of 47 strains. Appl Environ Microbiol 74: 4703-4710.
44. Remm, M., Storm, C.E., and Sonnhammer, E.L. (2001) Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J Mol Biol 314: 1041-1052.
45. Romeo, Y., Bouvier, J., and Gutierrez, C. (2007) Osmotic regulation of transcription in Lactococcus lactis: ionic strength-dependent binding of the BusR repressor to the busA promoter. FEBS Lett 581: 3387-3390.
46. Salzberg, S.L., Delcher, A.L., Kasif, S., and White, O. (1998) Microbial gene identification using interpolated Markov models. Nucleic Acids Res 26: 544-548.
47. Sambrook, J., Fritsch, E.F., and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual. New York, USA: Cold Spring Harbor Laboratory Press.
48. Sanders, J.W., Leenhouts, K., Burghoorn, J., Brands, J.R., Venema, G., and Kok, J. (1998) A chloride-inducible acid resistance mechanism in Lactococcus lactis and its regulation. Mol Microbiol 27: 299-310.
49. Sandine, W.E. (1972) Ecology of lactic streptococci. A review. J Milk Food Technol 35: 179-206.
50. Siezen, R.J., and Khayatt, B. (2008) Natural products genomics. Microb Biotechnol 1: 275-282.
51. Siezen, R.J., Renckens, B., van Swam, I., Peters, S., van Kranenburg, R., Kleerebezem, M., and de Vos, W.M. (2005) Complete sequences of four plasmids of Lactococcus lactis subsp. cremoris SK11 reveal extensive adaptation to the dairy environment. Appl Environ Microbiol 71: 8371-8382.
52. Siezen, R.J., Starrenburg, M.J., Boekhorst, J., Renckens, B., Molenaar, D., and van Hylckama Vlieg, J.E. (2008) Genome-scale genotype-phenotype matching of two Lactococcus lactis isolates from plants identifies mechanisms of adaptation to the plant niche. Appl Environ Microbiol 74: 424-436.
53. Siezen, R.J., Bayjanov, J., Renckens, B., Wels, M., van Hijum, S.A., Molenaar, D., and van Hylckama Vlieg, J.E. (2010) Complete genome sequence of Lactococcus lactis subsp. lactis KF147, a plant-associated lactic acid bacterium. J Bacteriol 192: 2649-2650.
54. Smit, G., Smit, B.A., and Engels, W.J. (2005) Flavour formation by lactic acid bacteria and biochemical flavour profiling of cheese products. FEMS Microbiol Rev 29: 591-610.
55. Taibi, A., Dabour, N., Lamoureux, M., Roy, D., and Lapointe, G. (2010) Evaluation of the genetic polymorphism among Lactococcus lactis subsp. cremoris strains using comparative genomic hybridization and multilocus sequence analysis. Int J Food Microbiol 144: 20-28.
56. Tailliez, P., Tremblay, J., Ehrlich, S.D., and Chopin, A. (1998) Molecular diversity and relationship within Lactococcus lactis, as revealed by randomly amplified polymorphic DNA (RAPD). Syst Appl Microbiol 21: 530-538.
57. Teusink, B., van Enckevort, F.H.J., Francke, C., Wiersma, A., Wegkamp, A., Smid, E.J., and Siezen, R.J. (2005) In silico reconstruction of the metabolic pathways of Lactobacillus plantarum: comparing predictions of nutrient requirements with those from growth experiments. Appl Environ Microbiol 71: 7253-7262.
58. Turner, M.S., Tan, Y.P., and Giffard, P.M. (2007) Inactivation of an iron transporter in Lactococcus lactis results in resistance to tellurite and oxidative stress. Appl Environ Microbiol 73: 6144-6149.
59. de Vos, W.M., Vos, P., de Haard, H., and Boerrigter, I. (1989) Cloning and expression of the Lactococcus lactis subsp. cremoris SK11 gene encoding an extracellular serine proteinase. Gene 85: 169-176.
60. Wang, X., Han, Y., Li, Y., Guo, Z., Song, Y., Tan, Y., etal. (2007) Yersinia genome diversity disclosed by Yersinia pestis genome-wide DNA microarray. Can J Microbiol 53: 1211-1221.
61. Wegmann, U., O'Connell-Motherway, M., Zomer, A., Buist, G., Shearman, C., Canchaya, C., etal. (2007) Complete genome sequence of the prototype lactic acid bacterium Lactococcus lactis subsp. cremoris MG1363. J Bacteriol 189: 3256-3270.
62. Zdobnov, E.M., and Apweiler, R. (2001) InterProScan - an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17: 847-848.
63. Zhou, M., Theunissen, D., Wels, M., and Siezen, R.J. (2010) LAB-Secretome: a genome-scale comparative analysis of the predicted extracellular and surface-associated proteins of Lactic Acid Bacteria. BMC Genomics 11: 651.