Streptococcus thermophilus strains ST106 and ST109 produce broad-spectrum bacteriocins encoded within a bacteriocin-like peptide (blp) gene cluster. This study reports the complete genome sequences for both strains, with the ST109 chromosome containing 1,788,866 nucleotides (nt) and 1,572 predicted genes, and ST106 having 1,856,083 nt and 1,601 predicted genes.
ABSTRACT
Streptococcus thermophilus strains ST106 and ST109 produce broad-spectrum bacteriocins encoded within a bacteriocin-like peptide (blp) gene cluster. This study reports the complete genome sequences for both strains, with the ST109 chromosome containing 1,788,866 nucleotides (nt) and 1,572 predicted genes, and ST106 having 1,856,083 nt and 1,601 predicted genes.
ANNOUNCEMENT
Streptococcus thermophilus is routinely isolated from raw milk and has been designated a generally recognized as safe (GRAS) bacterium due to its extensive use in the production of cheese and yogurt. Some S. thermophilus strains have been investigated for food safety and probiotic applications due to their production of broad-spectrum bacteriocins (1). In several strains, bacteriocins are encoded at a chromosomal locus which resembles the bacteriocin-like peptide (blp) gene cluster in Streptococcus pneumoniae (2). The blp gene cluster has been characterized for S. thermophilus strains LMD-9 (3), ST106, and ST118 (4), where bacteriocin production was induced with a recombinant or synthetic quorum sensing peptide, BlpC-30, and for strain B59671 (5, 6), where production occurs naturally.
Here, we report the complete genome sequences for S. thermophilus strains ST106 and ST109, raw milk isolates from our in-house culture collection. The strains have previously been reported to produce the broad-spectrum bacteriocins thermophilin 106 and thermophilin 109, respectively (4, 7). S. thermophilus cultures were grown overnight in tryptone-yeast extract-lactose (TYL) medium, and genomic DNA was isolated from mutanolysin-pretreated cells using the DNeasy blood and tissue kit (Qiagen). Genomes were sequenced using a Pacific Biosciences RS II system (PacBio, Menlo Park, CA) by the Genomics Core Facility, Clinical and Translational Research Institute at Drexel College of Medicine (Philadelphia, PA). P6-C4 PacBio chemistry was performed using one single-molecule real-time (SMRT) cell per genome (8), producing 260,568 reads (mean subread length, 3,368 nucleotides [nt]; N50 value, 4,826 nt) and 284,854 reads (mean subread length, 3,549 nt; N50 value, 4,973 nt) for ST106 and ST109, respectively. De novo assembly was achieved using the HGAP assembler (version 2.3), estimating a genome size of 2 Mb, which yielded a single contig for strain ST109, with a mean coverage of 565-fold, and a single contig for ST106, with a mean coverage of 469-fold. Both chromosomes were circularized using Circlator (version 1.0.2) and resequenced with RS_Modification_and _Motif_Anlysis (version 2.3) using default settings (9). The genomes were analyzed with Taxator-tk (version 1.2) (10) using the nonredundant-microbial_20140513 database (http://research.bifo.helmholtz-hzi.de/software), the megan-lca algorithm, and custom Python scripts for postprocessing. The results confirmed the strain identities and showed that the fully assembled ST109 genome consisted of 1,788,866 nt with 39.2% G+C content, and ST106 contained 1,856,083 nt with 39.3% G+C content.
Genome annotation using the NCBI Prokaryotic Genome Annotation Pipeline version 4.6 (11, 12) showed a total of 1,572 and 1,601 protein-encoding genes in ST109 and ST106, respectively, with both strains possessing 67 tRNAs and 6 rRNAs (5S, 16S, and 23S rRNA). Similar to other S. thermophilus strains (6, 13), the ST109 genome contained 13.5% nonfunctional genes; however, ST106 possessed 323 pseudogenes, corresponding to 16.8% of the predicted coding sequences. Previous studies showed that thermophilin 109 was naturally produced and may be encoded within the blp gene cluster (4, 7). The Clone Manager software version 9 (Sci-Ed Software, NC) was used to compare the chromosomal locus flanked by blpA and blpX, which consisted of 13,350 nt in ST106 and 13,332 nt in ST109. Alignment of the two loci revealed 18 mismatched nucleotides. The completed ST106 and ST109 genomes are expected to provide additional information needed to understand the molecular mechanisms regulating the production of thermophilins 106 and 109.
Data availability.
The complete genome sequences for S. thermophilus ST106 and ST109 have been deposited in GenBank under the accession numbers CP031881 and CP031545 and in the NCBI SRA database under the accession numbers SRP162362 and SRP155251, respectively.
ACKNOWLEDGMENTS
We thank Garth Ehrlich and staff from Drexel College of Medicine for their assistance in sequencing and analysis of the genomes.
The mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture.
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Data Availability Statement
The complete genome sequences for S. thermophilus ST106 and ST109 have been deposited in GenBank under the accession numbers CP031881 and CP031545 and in the NCBI SRA database under the accession numbers SRP162362 and SRP155251, respectively.