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

R.J. Siezen, J.R. Bayjanov, G.E. Felis, M.R. van der Sijde, M. Starrenburg, D. Molenaar, M. Wels, S.A. Hijum, J.E.T. van Hylckama Vlieg

Research output: Contribution to JournalArticleAcademicpeer-review

Abstract

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. © 2011 The Authors. Journal compilation © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.
Original languageEnglish
Pages (from-to)383-402
JournalMicrobial Biotechnology
Volume4
DOIs
Publication statusPublished - 2011

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Lactococcus lactis
Comparative Genomic Hybridization
Genes
Genome
Multigene Family
Biosynthesis
Dairies
Plasmids
Cultured Milk Products
Nisin
Xylans
Galactosides
Arabinose
Lactose
Microbiology
Dairy products
Proteolysis
Citric Acid
Fermentation
Lactic Acid

Cite this

Siezen, R.J. ; Bayjanov, J.R. ; Felis, G.E. ; van der Sijde, M.R. ; Starrenburg, M. ; Molenaar, D. ; Wels, M. ; Hijum, S.A. ; van Hylckama Vlieg, J.E.T. / Genome-scale diversity and niche adaptation analysis of Lactococcus lactis by comparative genome hybridization using multi-strain arrays. In: Microbial Biotechnology. 2011 ; Vol. 4. pp. 383-402.
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abstract = "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. {\circledC} 2011 The Authors. Journal compilation {\circledC} 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.",
author = "R.J. Siezen and J.R. Bayjanov and G.E. Felis and {van der Sijde}, M.R. and M. Starrenburg and D. Molenaar and M. Wels and S.A. Hijum and {van Hylckama Vlieg}, J.E.T.",
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Siezen, RJ, Bayjanov, JR, Felis, GE, van der Sijde, MR, Starrenburg, M, Molenaar, D, Wels, M, Hijum, SA & van Hylckama Vlieg, JET 2011, 'Genome-scale diversity and niche adaptation analysis of Lactococcus lactis by comparative genome hybridization using multi-strain arrays.' Microbial Biotechnology, vol. 4, pp. 383-402. https://doi.org/10.1111/j.1751-7915.2011.00247.x

Genome-scale diversity and niche adaptation analysis of Lactococcus lactis by comparative genome hybridization using multi-strain arrays. / Siezen, R.J.; Bayjanov, J.R.; Felis, G.E.; van der Sijde, M.R.; Starrenburg, M.; Molenaar, D.; Wels, M.; Hijum, S.A.; van Hylckama Vlieg, J.E.T.

In: Microbial Biotechnology, Vol. 4, 2011, p. 383-402.

Research output: Contribution to JournalArticleAcademicpeer-review

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T1 - Genome-scale diversity and niche adaptation analysis of Lactococcus lactis by comparative genome hybridization using multi-strain arrays.

AU - Siezen, R.J.

AU - Bayjanov, J.R.

AU - Felis, G.E.

AU - van der Sijde, M.R.

AU - Starrenburg, M.

AU - Molenaar, D.

AU - Wels, M.

AU - Hijum, S.A.

AU - van Hylckama Vlieg, J.E.T.

PY - 2011

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N2 - 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. © 2011 The Authors. Journal compilation © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

AB - 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. © 2011 The Authors. Journal compilation © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

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DO - 10.1111/j.1751-7915.2011.00247.x

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JF - Microbial Biotechnology

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