The complete genome sequence of the yogurt isolate Streptococcus thermophilus ACA-DC 2

Alexandraki, Voula; Kazou, Maria; Blom, Jochen; Pot, Bruno; Tsakalidou, Effie; Papadimitriou, Konstantinos

doi:10.1186/s40793-017-0227-5

Title: The complete genome sequence of the yogurt isolate Streptococcus thermophilus ACA-DC 2

Journal Article · Tue Jan 31 00:00:00 EST 2017 · Standards in Genomic Sciences

DOI:https://doi.org/10.1186/s40793-017-0227-5· OSTI ID:1627071

Alexandraki, Voula ^[1]; Kazou, Maria ^[1]; Blom, Jochen ^[2]; Pot, Bruno ^[3]; Tsakalidou, Effie ^[1]; Papadimitriou, Konstantinos ^[1]

Agricultural Univ. of Athens (Greece). Dept. of Food Science and Human Nutrition. Lab. of Dairy Research
Justus-Liebig-Univ. Giessen, Hesse (Germany). Bioinformatics & Systems Biology
Vrije Univ., Amsterdam (Netherlands). Research Group of Industrial Microbiology and Food Biotechnology (IMDO)

Streptococcus thermophilus ACA-DC 2 is a newly sequenced strain isolated from traditional Greek yogurt. Among the 14 fully sequenced strains of S. thermophilus currently deposited in the NCBI database, the ACA-DC 2 strain has the smallest chromosome, containing 1,731,838 bp. The annotation of its genome revealed the presence of 1,850 genes, including 1,556 protein-coding genes, 70 RNA genes and 224 potential pseudogenes. A large number of pseudogenes were identified. This was also accompanied by the absence of pathogenic features suggesting evolution of strain ACA-DC 2 through genome decay processes, most probably due to adaptation to the milk ecosystem. Analysis revealed the existence of one complete lactose-galactose operon, several proteolytic enzymes, one exopolysaccharide cluster, stress response genes and four putative antimicrobial peptides. Interestingly, one CRISPR-cas system and one orphan CRISPR, both carrying only one spacer, were predicted indicating low activity or inactivation of the cas proteins. Nevertheless, four putative restriction-modification systems were determined that may compensate any deficiencies of the CRISPR-cas system. Furthermore, whole genome phylogeny indicated three distinct clades within S. thermophilus. Comparative analysis among selected strains representative for each clade, including strain ACA-DC 2, revealed a high degree of conservation at the genomic scale, but also strain specific regions. Unique genes and genomic islands of strain ACA-DC 2 contained a number of genes potentially acquired through horizontal gene transfer events, that could be related to important technological properties for dairy starters. Our study suggests genomic traits in strain ACA-DC 2 compatible to the production of dairy fermented foods.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1627071

Journal Information:: Standards in Genomic Sciences, Vol. 12, Issue 1; ISSN 1944-3277

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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