Abstract
Streptococcus infantarius subsp. infantarius, a member of the Streptococcus bovis/Streptococcus equinus complex, is highly prevalent in artisanal dairy fermentations in Africa. Here the complete genome sequence of the dairy-adapted S. infantarius subsp. infantarius CJ18 strain—a strain predominant in traditionally fermented camel milk (suusac) from Kenya—is presented.
GENOME ANNOUNCEMENT
Streptococcus infantarius subsp. infantarius and other members of the Streptococcus bovis/Streptococcus equinus complex (SBSEC) are increasingly isolated from traditionally fermented dairy and plant products in Europe, Mexico, and Africa (1, 3, 6, 10, 12). Particularly in Africa, S. infantarius subsp. infantarius seems to play a pivotal role in spontaneous dairy fermentations, being present at up to 108 CFU per ml in the end product (6). Members of the SBSEC are associated with various human and animal infections (4, 9). Therefore, ingestion of large quantities of live cells of S. infantarius subsp. infantarius may hold a potential health risk. S. infantarius subsp. infantarius strain CJ18 was isolated from spontaneously fermented Kenyan camel milk (suusac) (6). Interestingly, CJ18 and other African strains possess a gal-lac operon, otherwise absent in the SBSEC, and have growth characteristics on lactose that are similar to those of Streptococcus thermophilus, suggesting an adaptation to a dairy environment (5).
Genome sequencing was performed using Roche GS-FLX Titanium technology at GATC Biotech (Konstanz, Germany). DNA was prepared with a lysozyme/mutanolysine-based cell lysis and subsequent purification using the Wizard genomic DNA purification kit (Promega, Madison, WI) (5). Genomes of S. infantarius subsp. infantarius ATCC BAA-102T (GenBank accession numbers ABJK02000000 to ABJK02000022) and Streptococcus gallolyticus subsp. gallolyticus UCN34 (GenBank accession number FN597254) (8) were used as references for the alignment of contigs in Projector 2 (11). Sanger sequencing for subsequent gap closing was performed at Microsynth (Balgach, Switzerland). Primer walking was performed to localize unassigned contigs (7), which were assembled with Lasergene SeqMan Pro 8.0.2 (DNASTAR, Madison, WI) and CLC Genomics Workbench 4.0.2 (CLC bio, Aarhus, Denmark). The genome was annotated on the rapid annotations using subsystems technology (RAST) server (2) and manually curated.
The genome of S. infantarius subsp. infantarius CJ18 consists of a 1,988,420-bp circular molecule which is 49.8 kb larger than that of ATCC BAA-102T but 362.5 kb smaller than that of UCN34. Potential plasmid DNA of 19,829 bp with high sequence identity to Lactococcus lactis sequences was also detected in CJ18. The G+C content of the genome is 37.6%, which is within the 37.4 to 37.6% range of other members of the SBSEC. GC skew switches correspond with protein-coding sequence (CDS) density, the assigned origin upstream of the dnaA gene, and the terminus, which is slightly shifted toward the 5 o'clock position. CJ18 harbors 68 tRNA genes and 17 rRNA genes. A total of 1,964 CDS were predicted in the genome, excluding the plasmid. A high percentage of 4.6% of the genome CDS contained a deletion, insertion, or single nucleotide polymorphism, leading to premature stop codons and pseudogenes. In combination with the gal-lac operon, this suggests an evolutionary adaptation to the dairy niche, paralleling that of S. thermophilus, albeit in a less advanced state. The genome of CJ18 will allow investigation of these adaptations and the presence of virulence factors and sheds light on the strains predominance in fermented African milk products and putative health risks.
Nucleotide sequence accession numbers.
The genome and plasmid of S. infantarius subsp. infantarius CJ18 have been deposited at GenBank under accession numbers CP003295 and CP003296, respectively.
ACKNOWLEDGMENTS
This study was funded by the UBS Optimus Foundation, Switzerland, and the North South Centre at ETH Zurich, Switzerland.
We thank M. J. Loessner and J. Klumpp, Laboratory of Food Microbiology, ETH Zurich, Switzerland, for assistance with genome assembly.
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