• Journal of Microbiology and Biotechnology
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• v.32 no.3
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• pp.333-340
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• 2022

Leuconostoc has been used as a principal starter in natural kimchi fermentation, but limited research has been conducted on its phages. In this study, prophage distribution and characterization in kimchi-derived Leuconostoc strains were investigated, and phage induction was performed. Except for one strain, 16 Leuconostoc strains had at least one prophage region with questionable and incomplete regions, which comprised 0.5-6.0% of the bacterial genome. Based on major capsid protein analysis, ten intact prophages and an induced incomplete prophage of Leu. lactis CBA3626 belonged to the Siphoviridae family and were similar to Lc-Nu-like, sha1-like, phiMH1-like, and TPA_asm groups. Bacterial immunology genes, such as superinfection exclusion proteins and methylase, were found on several prophages. One prophage of Leu. lactis CBA3626 was induced using mitomycin C and was confirmed as belonging to the Siphoviridae family. Homology of the induced prophage with 21 reported prophages was not high (< 4%), and 47% identity was confirmed only with TPA_asm from Siphoviridae sp. isolate ct3pk4. Therefore, it is suggested that Leuconostoc from kimchi had diverse prophages with less than 6% genome proportion and some immunological genes. Interestingly, the induced prophage was very different from the reported prophages of other Leuconostoc species.

• Microbiology and Biotechnology Letters
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• v.18 no.3
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• pp.215-220
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• 1990

Prophage cured strain derivatives from Luctobacillirs araei YIT 9018 were isolated from thermoinducible mutant of the parent lysogenic strain. Two thermoinducible mutants were isolated from L. casei YIT 9018 strain treated with N-methyl-N'-nitro-N-nitrosoguanidine. Prophage cured strains were selected after heat induction of thermoinducible strains at $42^{\circ}C$ for 30 min in MRT medium containing anti- 4 FSV serum. The prophage cured strains, L. casei HYM 1213 and L. casei HYM 4024, could be used an indicator strain for temperate phage $\phi$ FSW. The growth, lactic acid producing ability and carbohydrates fermentation of L. casei HYM 1213 were similar to the parent L. cmei YIT 9018 strain, but A. casei HYM 4024 was not. One of the prophage cured strain, L. cmei HYM 1213, could be used industrially .to produce lactic acid beverages because this strah could not induce the virulent phage$\phi$FSV. The physiological characterization of L. casei HYM 1213 strain was similar to the parent L. casei YIT 9018 strain.

• Microbiology and Biotechnology Letters
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• v.48 no.3
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• pp.322-327
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• 2020

Abortive infection systems (Abi) are phage resistance systems that can be prophage-encoded. Here, two genes encoding an Abi system were identified on a prophage sequence contained by the chromosome of the Levilactobacillus brevis strain UCCLBBS124. This Abi system is similar to the two-component AbiL system encoded by Lactococcus lactis biovar. diacetylactis LD10-1. The UCCLBBS124 prophage-derived Abi system (designated here as AbiL₁₂₄) was shown to exhibit specific activity against phages infecting L. brevis and L. lactis strains. Expression of the AbiL₁₂₄ system was shown to cause reduction in the efficiency of plaquing and cell lysis delay for phages of both species.

• Microbiology and Biotechnology Letters
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• v.22 no.5
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• pp.467-476
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• 1994

Lactobacillus casei HY 2782, prophage cured strain was characterized to be stable as much as L casei YIT 9018, parent strain. By southern hybridization, it was confirmed that the temperate phage was incorporated in chromosomal DNA of L. casei YIT 9018 as a prophage. It was also proved that the prophage was cured from chromosomal DNA of L casei HY 2782. The growth rate, lactic acid producing ability, carbohydrates fermentation, and enzymatic activity of L. casei HY 2782 were found to be similar to those of L. casei YIT 9018. When L casei HY 2782 was used as a host, the multiplicity of infection (M.O.I.) of the temperate phage for L. casei HY 2782 was 1.0~5.0. Restriction enzyme analysis of pLC90 plasmid from L. casei HY 2782 was shown that the size was an approximately 68.22 kb. The plasmid profiles, genomic DNA patterns, and cellular fatty acids composition of L. casei HY 2782 were similar to those of L casei YIT 9018. And the major fatty acids composition of these strains were C$_{14;0}$,C$_{16;1}$, C$_{16;0}$, C$_{18;1}$ and C$_{19;cyclo-}$ 10 sets of arbitrary primer in the PCR were screened to find differentiation against two strains of L. casei. Among them, b$_{5}-1/17-1 primer was produced an approximately 1.3 kb DNA band of only L casei YIT 9018. And b$_{5}-2/17-2 primer was produced an approximately 1.0 kb DNA band of only L casei HY 2782.

• Journal of Veterinary Science
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• v.19 no.6
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• pp.771-781
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• 2018

Staphylococcus aureus is one of the major pathogens causing bovine mastitis and foodborne diseases associated with dairy products. To determine the genetic relationships between human and bovine or bovine isolates of S. aureus, various molecular methods have been used. Previously we developed an rpoB sequence typing (RSTing) method for molecular differentiation of S. aureus isolates and identification of RpoB-related antibiotic resistance. In this study, we performed spa typing and RSTing with 84 isolates from mastitic cows (22 farms, 72 cows, and 84 udders) and developed a molecular prophage typing (mPPTing) method for molecular epidemiological analysis of bovine mastitis. To compare the results, human isolates from patients (n = 14) and GenBank (n = 166) were used for real and in silico RSTing and mPPTing, respectively. Based on the results, RST10-2 and RST4-1 were the most common rpoB sequence types (RSTs) in cows and humans, respectively, and most isolates from cows and humans clearly differed. Antibiotic resistance-related RSTs were not detected in the cow isolates. A single dominant prophage type and gradual evolution through prophage acquisition were apparent in most of the tested farms. Thus, RSTing and mPPTing are informative, simple, and economic methods for molecular epidemiological analysis of S. aureus infections.

• Microbiology and Biotechnology Letters
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• v.50 no.4
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• pp.563-573
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• 2022

Xanthomonas arboricola pv. juglandis (Xaj) is a globally important bacterial pathogen of walnut trees that causes substantial economic losses in commercial walnut production. Although prophages are common in bacterial plant pathogens and play important roles in bacterial diversity and pathogenicity, there has been limited investigation into the distribution and function of prophages in Xaj. In this study, we identified and characterized 13 predicted prophages from the genomes of 12 Xaj isolates from around the globe. These prophages ranged in length from 11.8 kb to 51.9 kb, with between 11-75 genes and 57.82-64.15% GC content. The closest relatives of these prophages belong to the Myoviridae and Siphoviridae families of the Caudovirales order. The phylogenetic analysis allowed the classification of the prophages into five groups. The gene constitution of these predicted prophages was revealed via Roary analysis. Amongst 126 total protein groups, the most prevalent group was only present in nine prophages, and 22 protein groups were present in only one prophage (singletons). Also, bioinformatic analysis of the 13 identified prophages revealed the presence of 431 genes with an average length of 389.7 bp. Prokka annotation of these prophages identified 466 hypothetical proteins, 24 proteins with known function, and six tRNA genes. The proteins with known function mainly comprised prophage integrase IntA, replicative DNA helicase, tyrosine recombinase XerC, and IS3 family transposase. There was no detectable insertion site specificity for these prophages in the Xaj genomes. The identified Xaj prophage genes, particularly those of unknown function, merit future investigation.

• Korean Journal of Microbiology
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• v.55 no.1
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• pp.77-79
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• 2019

Here we report the genome sequence of Veillonella atypica strain KHUD-V1 isolated from subgingival dental plaque of Korean chronic periodontitis patients. Unlike other V. atypica strains, KHUD-V1 carries two prophage regions and prophage remnants, as well as several genes homologous to prophage-associated virulence factors, such as virulence-associated protein E, a Clp protease, and a toxin-antitoxin system. The isolate and its genome sequence obtained here will aid to understand the diversity of the genome architecture of Veillonella within an evolutionary framework and the role of prophages that contribute to the genetic diversity as well as the virulence of V. atypica.

• Microbiology and Biotechnology Letters
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• v.19 no.2
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• pp.147-152
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• 1991

In order to study effect of the phage ${\phi}$ FSV on the growth of lactic acid bacteria, Lactobacillus casei YIT 9018(wild type strain with prophage) or L. casei HYM 1213 (prophage cured strain) was infected with various concentrations of phage ${\phi}$ FSV (called Lac S21) or wild type virulent phage (called Lac J-1). When L. casei YIT 9018 was infected with Lac S21 under the concentration of $6.0{\times}10^6$ pfu/ml, the growth and lactic acid production of the strain were normal and the number of phages decreased. But L. casei HYM 1213 was susceptible to Lac S21. Regardless of the concentration of the phage infection, the number of phages increased rapidly into $10^9$ to $10^{10}$ pfu/ml at 2 day cultures and was maintained $10^7$ to $10^9$pfu/ml phage until 6 day cultures. The lactic acid production of L. casei HYM 1213 infected with Lac S21 was abnormal. Therefore, phage ${\phi}$ FSV had an evil effect on growth of L. casei HYM 1213, but not L. casei YIT 9018. On the other hand Lac J-1 caused abnormal fermentation to either L. casei YIT 9018 or L. casei HYM 1213.

• Korean Journal of Microbiology
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• v.53 no.1
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• pp.58-60
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• 2017

Halioglobus sp. RR3-57 was isolated from a biofilter of a seawater recirculating aquaculture system and its complete genome sequence was obtained using the PacBio RS II platform. Two circular contigs were assembled and considered as a chromosome and a plasmid (size of 4,847,776 bp and 155,799 bp, and G+C content of 57.5% and 53.2%, respectively). Genomic analysis showed RR3-57 had 18 denitrification-related genes and an incomplete prophage.

• Journal of Microbiology and Biotechnology
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• v.30 no.3
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• pp.341-351
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• 2020

To shed light on the genetic differences among food-originated coagulase-negative Staphylococcus (CNS), we performed pan-genome analysis of five species: Staphylococcus carnosus (two strains), Staphylococcus equorum (two strains), Staphylococcus succinus (three strains), Staphylococcus xylosus (two strains), and Staphylococcus saprophyticus (one strain). The pan-genome size increases with each new strain and currently holds about 4,500 genes from 10 genomes. Specific genes were shown to be strain dependent but not species dependent. Most specific genes were of unknown function or encoded restriction-modification enzymes, transposases, or prophages. Our results indicate that unique genes have been acquired or lost by convergent evolution within individual strains.