• Open Access

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

Authors

  • Roland J. Siezen,

    Corresponding author
    1. Kluyver Centre for Genomics of Industrial Fermentation, NIZO food research, P.O. Box 20, 6710 BA Ede, the Netherlands
    2. Center for Molecular and Biomolecular Informatics, Radboud University Medical Centre, PO Box 9101, Nijmegen, the Netherlands
    3. TI Food and Nutrition, P.O. Box 557, 6700 AN Wageningen, the Netherlands
    4. Netherlands Bioinformatics Centre, 260 NBIC, P.O. Box 9101, 6500 HB Nijmegen, the Netherlands
      E-mail r.siezen@cmbi.ru.nl; Tel. +31 (0)24-36 19559; Fax +31 (0)24 36 19395.
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  • Jumamurat R. Bayjanov,

    1. Center for Molecular and Biomolecular Informatics, Radboud University Medical Centre, PO Box 9101, Nijmegen, the Netherlands
    2. Netherlands Bioinformatics Centre, 260 NBIC, P.O. Box 9101, 6500 HB Nijmegen, the Netherlands
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  • Giovanna E. Felis,

    1. Kluyver Centre for Genomics of Industrial Fermentation, NIZO food research, P.O. Box 20, 6710 BA Ede, the Netherlands
    2. Department of Biotechnology, University of Verona, Strada le Grazie 15 – Ca' Vignal 2, 37134 Verona, Italy
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  • Marijke R. van der Sijde,

    1. Center for Molecular and Biomolecular Informatics, Radboud University Medical Centre, PO Box 9101, Nijmegen, the Netherlands
    2. TI Food and Nutrition, P.O. Box 557, 6700 AN Wageningen, the Netherlands
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  • Marjo Starrenburg,

    1. Kluyver Centre for Genomics of Industrial Fermentation, NIZO food research, P.O. Box 20, 6710 BA Ede, the Netherlands
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  • Douwe Molenaar,

    1. Kluyver Centre for Genomics of Industrial Fermentation, NIZO food research, P.O. Box 20, 6710 BA Ede, the Netherlands
    2. TI Food and Nutrition, P.O. Box 557, 6700 AN Wageningen, the Netherlands
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    • Present addresses: Systems Bioinformatics IBIVU, Free University of Amsterdam, 1081HV Amsterdam, the Netherlands;

  • Michiel Wels,

    1. Kluyver Centre for Genomics of Industrial Fermentation, NIZO food research, P.O. Box 20, 6710 BA Ede, the Netherlands
    2. Center for Molecular and Biomolecular Informatics, Radboud University Medical Centre, PO Box 9101, Nijmegen, the Netherlands
    3. TI Food and Nutrition, P.O. Box 557, 6700 AN Wageningen, the Netherlands
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  • Sacha A. F. T. van Hijum,

    1. Kluyver Centre for Genomics of Industrial Fermentation, NIZO food research, P.O. Box 20, 6710 BA Ede, the Netherlands
    2. Center for Molecular and Biomolecular Informatics, Radboud University Medical Centre, PO Box 9101, Nijmegen, the Netherlands
    3. TI Food and Nutrition, P.O. Box 557, 6700 AN Wageningen, the Netherlands
    4. Netherlands Bioinformatics Centre, 260 NBIC, P.O. Box 9101, 6500 HB Nijmegen, the Netherlands
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  • Johan E. T. van Hylckama Vlieg

    1. Kluyver Centre for Genomics of Industrial Fermentation, NIZO food research, P.O. Box 20, 6710 BA Ede, the Netherlands
    2. TI Food and Nutrition, P.O. Box 557, 6700 AN Wageningen, the Netherlands
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    • Danone Research, Gut and Microbiology Platform, R.D. 128, 91767 Palaiseau Cedex, France.


  • Authors' contributions: G.F., D.M., R.S. and J.H.V. conceived the study. G.F. and M.S. performed the experimental work, while J.B., D.M., M.W., and M.v.d.S. performed the bioinformatics analyses. R.S., G.F. and J.H.V. wrote the article. S.v.H. supervised the bioinformatics analyses performed by M.v.d.S. and J.B. and corrected the article. All authors have read and approved the final manuscript.

E-mail r.siezen@cmbi.ru.nl; Tel. +31 (0)24-36 19559; Fax +31 (0)24 36 19395.

Summary

Lactococcus lactis produces lactic acid and is widely used in the manufacturing of various fermented dairy products. However, the species is also frequently isolated from non-dairy niches, such as fermented plant material. Recently, these non-dairy strains have gained increasing interest, as they have been described to possess flavour-forming activities that are rarely found in dairy isolates and have diverse metabolic properties. We performed an extensive whole-genome diversity analysis on 39 L. lactis strains, isolated from dairy and plant sources. Comparative genome hybridization analysis with multi-strain microarrays was used to assess presence or absence of genes and gene clusters in these strains, relative to all L. lactis sequences in public databases, whereby chromosomal and plasmid-encoded genes were computationally analysed separately. Nearly 3900 chromosomal orthologous groups (chrOGs) were defined on basis of four sequenced chromosomes of L. lactis strains (IL1403, KF147, SK11, MG1363). Of these, 1268 chrOGs are present in at least 35 strains and represent the presently known core genome of L. lactis, and 72 chrOGs appear to be unique for L. lactis. Nearly 600 and 400 chrOGs were found to be specific for either the subspecies lactis or subspecies cremoris respectively. Strain variability was found in presence or absence of gene clusters related to growth on plant substrates, such as genes involved in the consumption of arabinose, xylan, α-galactosides and galacturonate. Further niche-specific differences were found in gene clusters for exopolysaccharides biosynthesis, stress response (iron transport, osmotolerance) and bacterial defence mechanisms (nisin biosynthesis). Strain variability of functions encoded on known plasmids included proteolysis, lactose fermentation, citrate uptake, metal ion resistance and exopolysaccharides biosynthesis. The present study supports the view of L. lactis as a species with a very flexible genome.

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