Streptococcus thermophilus Core Genome: Comparative Genome Hybridization Study of 47 Strains

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 co...

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Bibliographic Details
Published in:Applied and Environmental Microbiology 2008-08, Vol.74 (15), p.4703-4710
Main Authors: Rasmussen, Thomas Bovbjerg, Danielsen, Morten, Valina, Ondrej, Garrigues, Christel, Johansen, Eric, Pedersen, Martin Bastian
Format: Article
Language:English
Subjects:
Bacteria
Bacteriology
Biological and medical sciences
Comparative analysis
Deoxyribonucleic acid
DNA
DNA microarrays
DNA, Bacterial - genetics
Fundamental and applied biological sciences. Psychology
Genome, Bacterial
Genomics
Hybridization
Meeting Presentations
Microbiology
Nucleic Acid Hybridization
Oligonucleotide Array Sequence Analysis
Phylogeny
RNA, Bacterial - genetics
RNA, Ribosomal, 16S - genetics
RNA, Ribosomal, 23S - genetics
Streptococcus thermophilus
Streptococcus thermophilus - classification
Streptococcus thermophilus - genetics
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Summary: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.
ISSN:0099-2240
1098-5336
1098-6596
DOI:10.1128/AEM.00132-08