Present addresses: Systems Bioinformatics IBIVU, Free University of Amsterdam, 1081HV Amsterdam, the Netherlands;
Genome-scale diversity and niche adaptation analysis of Lactococcus lactis by comparative genome hybridization using multi-strain arrays
Article first published online: 21 FEB 2011
© 2011 The Authors. Journal compilation © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd
Special Issue: Lactic Acid Bacteria. Editors: Michiel Kleerebezem and Willem M. de Vos.
Volume 4, Issue 3, pages 383–402, May 2011
How to Cite
Siezen, R. J., Bayjanov, J. R., Felis, G. E., van der Sijde, M. R., Starrenburg, M., Molenaar, D., Wels, M., van Hijum, S. A. F. T. and van Hylckama Vlieg, J. E. T. (2011), Genome-scale diversity and niche adaptation analysis of Lactococcus lactis by comparative genome hybridization using multi-strain arrays. Microbial Biotechnology, 4: 383–402. doi: 10.1111/j.1751-7915.2011.00247.x
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.
- Issue published online: 25 APR 2011
- Article first published online: 21 FEB 2011
- Received 15 October, 2010; accepted 28 December, 2010.
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.