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Phenotypic and genomic diversity of Lactobacillus plantarum strains isolated from various environmental niches

Authors

  • Roland J. Siezen,

    Corresponding author
    1. TI Food and Nutrition, PO Box 557, 6700 AN Wageningen, The Netherlands.
    2. NIZO food research, Kernhemseweg 2, PO Box 20, 6710 BA Ede, The Netherlands.
    3. Center for Molecular and Biomolecular Informatics, Radboud University Nijmegen Medical Centre, PO Box 9101, 6500HB Nijmegen, The Netherlands.
      *E-mail roland.siezen@nizo.nl; Tel. (+31) 318659511; Fax (+31) 318650400.
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    • These authors contributed equally to the manuscript.

  • Vesela A. Tzeneva,

    1. TI Food and Nutrition, PO Box 557, 6700 AN Wageningen, The Netherlands.
    2. NIZO food research, Kernhemseweg 2, PO Box 20, 6710 BA Ede, The Netherlands.
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    • These authors contributed equally to the manuscript.

  • Anna Castioni,

    1. TI Food and Nutrition, PO Box 557, 6700 AN Wageningen, The Netherlands.
    2. Dipartimento Scientifico e Tecnologico, Università degli Studi di Verona, Strada le Grazie, 15, I-37134 Verona, Italy.
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  • Michiel Wels,

    1. TI Food and Nutrition, PO Box 557, 6700 AN Wageningen, The Netherlands.
    2. NIZO food research, Kernhemseweg 2, PO Box 20, 6710 BA Ede, The Netherlands.
    3. Center for Molecular and Biomolecular Informatics, Radboud University Nijmegen Medical Centre, PO Box 9101, 6500HB Nijmegen, The Netherlands.
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  • Hoa T. K. Phan,

    1. Food Industry Research Institute, Km 8 Nguyen Trai, Thanh Xuan, Hanoi, Vietnam.
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  • Jan L. W. Rademaker,

    1. NIZO food research, Kernhemseweg 2, PO Box 20, 6710 BA Ede, The Netherlands.
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  • Marjo J. C. Starrenburg,

    1. NIZO food research, Kernhemseweg 2, PO Box 20, 6710 BA Ede, The Netherlands.
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  • Michiel Kleerebezem,

    1. TI Food and Nutrition, PO Box 557, 6700 AN Wageningen, The Netherlands.
    2. NIZO food research, Kernhemseweg 2, PO Box 20, 6710 BA Ede, The Netherlands.
    3. Laboratory of Microbiology, Wageningen University, Dreijenplein 10. 6703 HB Wageningen, The Netherlands.
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  • Douwe Molenaar,

    1. TI Food and Nutrition, PO Box 557, 6700 AN Wageningen, The Netherlands.
    2. NIZO food research, Kernhemseweg 2, PO Box 20, 6710 BA Ede, The Netherlands.
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  • Johan E. T. Van Hylckama Vlieg

    1. TI Food and Nutrition, PO Box 557, 6700 AN Wageningen, The Netherlands.
    2. NIZO food research, Kernhemseweg 2, PO Box 20, 6710 BA Ede, The Netherlands.
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*E-mail roland.siezen@nizo.nl; Tel. (+31) 318659511; Fax (+31) 318650400.

Summary

Lactobacillus plantarum is a ubiquitous microorganism that is able to colonize several ecological niches, including vegetables, meat, dairy substrates and the gastro-intestinal tract. An extensive phenotypic and genomic diversity analysis was conducted to elucidate the molecular basis of the high flexibility and versatility of this species. First, 185 isolates from diverse environments were phenotypically characterized by evaluating their fermentation and growth characteristics. Strains clustered largely together within their particular food niche, but human fecal isolates were scattered throughout the food clusters, suggesting that they originate from the food eaten by the individuals. Based on distinct phenotypic profiles, 24 strains were selected and, together with a further 18 strains from an earlier low-resolution study, their genomic diversity was evaluated by comparative genome hybridization against the reference genome of L. plantarum WCFS1. Over 2000 genes were identified that constitute the core genome of the L. plantarum species, including 121 unique L. plantarum-marker genes that have not been found in other lactic acid bacteria. Over 50 genes unique for the reference strain WCFS1 were identified that were absent in the other L. plantarum strains. Strains of the L. plantarum subspecies argentoratensis were found to lack a common set of 24 genes, organized in seven gene clusters/operons, supporting their classification as a separate subspecies. The results provide a detailed view on phenotypic and genomic diversity of L. plantarum and lead to a better comprehension of niche adaptation and functionality of the organism.

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