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Applied and Environmental Microbiology, August 2008, p. 4703-4710, Vol. 74, No. 15
0099-2240/08/$08.00+0     doi:10.1128/AEM.00132-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Streptococcus thermophilus Core Genome: Comparative Genome Hybridization Study of 47 Strains{triangledown} ,{dagger}

Thomas Bovbjerg Rasmussen,1* Morten Danielsen,2 Ondrej Valina,3 Christel Garrigues,1 Eric Johansen,4 and Martin Bastian Pedersen1

Physiology, Cultures & Enzymes Division,1 Identification, Cultures & Enzymes Division,2 Discovery, Human Health & Nutrition Division,3 Innovation Management, Cultures & Enzymes Division, Chr. Hansen A/S, Hørsholm, Denmark4

Received 15 January 2008/ Accepted 16 April 2008

A DNA microarray platform based on 2,200 genes from publicly available sequences was designed for Streptococcus thermophilus. We determined how single-nucleotide polymorphisms in the 65- to 75-mer oligonucleotide probe sequences affect the hybridization signals. The microarrays were then used for comparative genome hybridization (CGH) of 47 dairy S. thermophilus strains. An analysis of the exopolysaccharide genes in each strain confirmed previous findings that this class of genes is indeed highly variable. A phylogenetic tree based on the CGH data showed similar distances for most strains, indicating frequent recombination or gene transfer within S. thermophilus. By comparing genome sizes estimated from the microarrays and pulsed-field gel electrophoresis, the amount of unknown DNA in each strain was estimated. A core genome comprised of 1,271 genes detected in all 47 strains was identified. Likewise, a set of noncore genes detected in only some strains was identified. The concept of an industrial core genome is proposed. This is comprised of the genes in the core genome plus genes that are necessary in an applied industrial context.

* Corresponding author. Mailing address: Department of Physiology, Cultures & Enzymes Division, Chr. Hansen A/S, Bøge Alle 10-12, DK-2970 Hørsholm, Denmark. Phone: 45 45 74 84 30. Fax: 45 45 74 88 16. E-mail: dktbo{at}chr-hansen.com

{triangledown} Published ahead of print on 6 June 2008.

{dagger} Supplemental material for this article may be found at http://aem.asm.org/.

Applied and Environmental Microbiology, August 2008, p. 4703-4710, Vol. 74, No. 15
0099-2240/08/$08.00+0     doi:10.1128/AEM.00132-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.



This article has been cited by other articles:

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  • Bayjanov, J. R., Wels, M., Starrenburg, M., van Hylckama Vlieg, J. E. T., Siezen, R. J., Molenaar, D. (2009). PanCGH: a genotype-calling algorithm for pangenome CGH data. Bioinformatics 25: 309-314 [Abstract] [Full Text]  


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