Complete genome sequence of Streptococcus hyointestinalis B19, a strain producing bacteriocin, isolated from chicken feces

In recent years, there have been increasing studies to find alternatives to antibiotics, such as antibodies, probiotics, bacteriophages, and bacteriocins because of the increase in antibiotic resistance [1,2]. In our previous study, we reported that S. hyointestinalis B19 has potential to be used in similar applications [3]. S. hyointestinalis B19 strain was found to produce antimicrobial protein molecules, which possess characteristics similar to those of bacteriocin (heat stability). The selected strains of Clostridium perfringens and Listeria monocytogenes were strongly inhibited by the strain B19. To confirm whether the antimicrobial substance is bacteriocin and to better understand the characteristics of the molecule, we carried out whole genome sequencing of the strain B19.

S. hyointestinalis B19 was isolated from chicken fecal samples collected from local farm in Anseong, Korea. The genomic DNA was extracted from the strain B19 cultured to stationary phase in M17 medium supplemented with 0.5% (w/v) glucose using QIAamp PowerFecal DNA Kit (Qiagen) according to the manufacturer’s instructions. The whole genome of strain B19 was sequenced using Pacific Biosciences (PacBio) RS II Single Molecule Real Time (SMRT) platform with a 20 kb SMRTbell^TM template library at ChunLab. The reads were assembled on PacBio SMAR Analysis 2.3.0. Genome analysis and annotation were performed by CLgenomics^TM v. 1.55 software. Transfer RNAs (tRNAs) were identified using tRNAscan-SE v. 1.3.1. Ribosomal RNAs (rRNAs) and non-coding RNAs (ncRNAs) were identified using INFERNAL v. 1.0.2 with Rfam 12.0 database. For CRISPR, PilerCR v. 1.06 and CRT v. 1.2 were used. Protein-coding sequences (CDSs) were identified by using PRODIGAL v. 2.6.2 [4] and compared to protein databases (SwissProt, KEGG, SEED, EggNOG) using USEARCH v. 8.1 [5] for functional annotation. The draft genome of S. hyointestinalis B19 consisted of a 2,217,061 bp chromosome with a G + C content of 42.95% (Table 1). The genome contained 2,266 coding sequences (CDSs), 18 rRNAs, and 61 tRNA genes (Fig. 1).

Fig. 1. Circular genome map of Streptococcus hyointestinalis B19. From the outermost circle to the center, each circle indicates information about tRNA/rRNA, forward and reverse coding sequences (CDSs), GC ratio, and GC skew.

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The mining of the bacteriocinogenic gene clusters was performed by using the BAGEL4 platform [6]. The genome possessed thmA-, thmB-like genes, and bovicin 255-like genes. The former genes encode peptides ThmA and ThmB, respectively, that form Thermophilin 13, the bacteriocin first isolated from S. thermophilus [7]. Strain 19 also contains the genes associated with ABC-transporter and bacteriocin immunity for bacteriocin export and self-immunity to bacteriocin, respectively. These two genes are common members of the lantibiotic gene clusters [8].