• The Plant Pathology Journal
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• 제28권3호
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• pp.295-298
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• 2012

Genetic diversity among Pseudomonas syringae pv. morsprunorum isolates from Prunus mume in Korea and Japan was investigated by comparative sequence analysis of the 16S rRNA gene. The strains included 24 field isolates recovered from P. mume in Korea along with seven Japanese strains. Two strains isolated from P. salicina in Japan, one strain from P. avium in the United Kingdom, and the pathotype strain were also used for comparison with their 16S rRNA gene sequences. Nearly complete 16S rRNA gene sequences were sequenced in all 35 strains, and three sequence types, designated types I, II and III, were identified. Eleven strains consisting of five Korean isolates, five Japanese strains, and one strain from the United Kingdom belonged to type I, whereas the pathotype strain and another 19 Korean isolates belonged to type III. Another four Japanese strains belonged to type II. Type I showed 98.9% sequence homology with type III. Type I and II had only two heterogeneous bases. The 16S rRNA sequence types were correlated with the races of P. syringae pv. morsprunorum. Type I and II strains belonged to race 1, whereas type III isolates were included in race 2. Sequence analyses of the 16S rRNA gene from P. syringae pv. morsprunorum were useful in identifying the races and can further be used for epidemiological surveillance of this pathogen.

• Journal of Periodontal and Implant Science
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• 제28권4호
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• pp.691-703
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• 1998

The 16S rRNA analyzing method is a bacterial identification method that is useful in identifying bacteria which is difficult to do by other means. The following 7 types of bacteria which are Treponema, A. actinomycetemcomitans, P. gingivalis, Fusobacterium, B. forsythus, P. intermedia, P. micros were evaluated in order to study their distribution among patients with adult periodontitis. The 16S rRNA analyzing method was used to compare bacterial distribution among 3 groups. Subgingival plaque acquired from the affected sites(pocket depth ${\geq}6mm$) of 29 patients with adult periodontitis were grouped as the experimental group while plaque from the non-affected sites(pocket depth ${\leq}3mm$) were grouped as control 2 and finally plaque acquired from students with healthy periodontal tissues were grouped as control 1. The results are as follows ; 1. The distribution of Treponema was 12.5% for control 1, 21.4% for control 2 and 75.4% for the experimental group. For A. actinomycetemcomitans the distribution was 0.5%, 19.0%, 44.4% in respect to the order of groups mentioned above. P.gingivalis showed 10.5%, 43.1%, 94.0% distribution, Fusobacterium 33.0%, 48.3%, 81.0% distribution, B. forsythus 9.5%, 17.2%, 65.9% distribution, P. intermedia 1.0%, 12.1%, 26.3% distribution and finally P. micros 5.0%, 19.0%, 48.7% respectively. In all 7 types of bacteria, the experimental group showed higher bacterial distribution compared to the other two groups with statistically significant difference. 2. In the case of Treponema, A. actinomycetemcomitans, gingivalis,Fusobacterium, B. forsythus, P. intermedia, P. micros showed significant difference between control 1 and 2. These results suggest that the 16S rRNA analyzing method which was applied on Koreans for the first time could be utilized and useful in finding potential pathogens of periodontal disease.

• 대한의생명과학회지
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• 제9권3호
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• pp.139-144
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• 2003

Since water borne infection causes acute diseases and results in spread of diseases by secondary infection, the prevention is very important. Therefore, it is necessary to have a method that is rapid and effective to monitor pathogenic bacteria in drinking water. In this study, we employed a systematic method, Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) analysis, to develop an effective monitoring system for possible bacterial contaminants in drinking water. For this purpose, PCR primers were derived from 992 bp region of the 16s rRNA gene that is highly conserved through the different species of prokaryotes. To test whether the PCR primers designed are indeed useful for detecting all the possible microbial contaminants in the water, the primers were used to amplify 16s rRNA regions of different microbial water-borne pathogens such as E. coli, Salmonella, Yersinia, Listeria, and Staphylococcus. As expected, all of tested microorganisms amplified expected size of PCR products indicating designed PCR primers for 16s rRNA indeed can be useful to amplify all different microbial water-borne pathogens in the water. Furthermore, to test whether these 16s rRNA based PCR primers can detect bacterial populations present in the water, water samples taken from diverse sources, such as river, tap, and sewage, were used for amplification. PCR products were for then subjected for cloning into a T-vector to generate a library containing 16s rRNA sequences from various bacteria. With cloned PCR products, RFLP analysis was done using PCR products digested with restriction enzyme such as Hae III to obtain species-specific RFLP profiles. After PCR-RFLP, the bacterial clones which showed the same RFLP profiles were regarded as the same ones, and the clones which showed distinctive RFLP profiles were subsequently subjected for sequence analysis for species identification. By this PCR-RFLP analysis, we were able to reveal diverse populations of bacteria living in water. In brief, in unsterilized natural river water, over 60 different species of bacteria were found. On the other hand, no PCR products were detected in drinking tap-water. The results from this study clearly indicate that the PCR-RFLP-sequence analysis can be a useful method for monitoring diverse, perhaps pathogenic bacteria contaminated in water in a rapid fashion.

• Fisheries and Aquatic Sciences
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• 제22권7호
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• pp.14.1-14.8
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• 2019

Olive flounder (Paralichthys olivaceus) is the major species developed for aquaculture in South Korea. Over the long history of olive flounder aquaculture, complex and diverse diseases have been a major problem, negatively impacting industrial production. Vibriosis is a prolific disease which continuously damages olive flounder aquaculture. A bacterial disease survey was performed from January to June 2017 on 20 olive flounder farms on Jeju Island. A total of 1710 fish were sampled, and bacteria from the external and internal organs of 560 fish were collected. Bacterial strains were identified using 16 s rRNA sequencing. Twenty-seven species and 184 strains of Vibrio were isolated during this survey, and phylogenetic analysis was performed. Bacterial isolates were investigated for the distribution of pathogenic and non-pathogenic species, as well as bacterial presence in tested organs was characterized. V. gigantis and V. scophthalmi were the dominant non-pathogenic and pathogenic strains isolated during this survey, respectively. This study provides data on specific Vibrio spp. isolated from cultured olive flounder in an effort to provide direction for future research and inform aquaculture management practices.

• Journal of Species Research
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• 제12권2호
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• pp.158-164
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• 2023

In March 2021, marine sediment from East Sea samples were suspended in a 2% NaCl solution, and serial dilution was performed in fresh marine and Reasoner's 2A agar. Isolated bacterial strains were identified based on 16S rRNA gene sequences, and showed at least 98.7% sequence similarity with previously reported bacterial species. Finally, seven bacterial strains which were validly published but not reported in Korea, were obtained. These isolates were allocated to the orders Bacillales and Flavobacteriales. The three Flavobacteriales strains are classified into the family Flavobacteriaceae. The other four Bacillales belong to the families Bacillaceae and Paenibacillaceae. The seven unrecorded bacterial strains in this study are classified into seven different genera, which are assigned to Mesobacillus, Paenibacillus, Gramella, Gillisia, Arenibacter, Fictibacillus, and Brevibacillus. During the investigation, the possibility of excavation of various unrecorded species in domestic marine sediment was confirmed. Gram-staining, cell morphology, physiological and basic biochemical characteristics, and phylogenetic analysis were performed in this study and provided in the description of each strain.

• Journal of Species Research
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• 제12권spc2호
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• pp.23-32
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• 2023

During screening for indigenous prokaryotic species in Republic of Korea in 2021, a total of 21 bacterial strains assigned to the phylum Bacteroidota were isolated from a variety of environmental habitats including pine cone, seaweed, soil, sea sediment, brackish water and moss. Based on the 16S rRNA gene sequence similarity value of more than 98.7% and formation of a robust phylogenetic clade with the type strain of the closest bacterial species, it was found that the 21 strains belong to independent and recognized bacterial species. There has been no official report that the identified 21 species have been isolated in Republic of Korea up to date. Therefore, 16 species in six genera of two families in the order Flavobacteriales, two species in two genera of two families in the order Cytophagales, one species in one genus of one family in the order Chitinophagales and two species in one genus of one family in the order Sphingobacteriales are proposed as unrecorded species of the phylum Bacteroidota isolated in Republic of Korea. Their Gram reaction, colony and cell morphology, basic phenotypic characteristics, isolation source, taxonomic status, strain ID and other information are described in the species descriptions.

• 대한수의학회지
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• 제55권3호
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• pp.205-208
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• 2015

Ten dogs were enrolled in this study: two healthy dogs, two obese dogs without other medical issues and six obese dogs with underlying diseases including pemphigus, chronic active hepatitis, hyperadrenocorticism, narcolepsy, otitis media and heartworm infection. Pyrosequencing of the 16S rRNA gene to explore the gut bacterial diversity revealed that distal gut bacterial communities of samples from patients with pemphigus, otitis media and narcolepsy consisted primarily of Firmicutes, while the major phylum of the distal gut bacterial communities in patients with chronic active hepatitis and hyperadrenocorticism was Fusobacteria. Proteobacteria were the dominant phylum in heartworm infected obese patients.

• 환경생물
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• 제41권3호
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• pp.215-222
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• 2023

In 2022, research for native prokaryotic species in Korea reported 10 unrecorded bacterial strains affiliated to phyla Actinomycetota, Bacillota, and Pseudomonadota. The strains formed monophyletic clades with the most closely related species (with ≥98.7% sequence similarity) in the 16S rRNA gene sequencing. Among them, four species of the phylum Actinomycetota, two species of the phylum Bacillota, and four species of the phylum Pseudomonadota have not been reported in Korea, suggesting unrecorded species in Korea. Information on strains such as Gram staining reaction, colony and cell morphology, biochemical characteristics, and isolation sources were provided in the species description.

• Journal of Species Research
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• 제10권3호
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• pp.191-200
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• 2021

To study the biodiversity of bacterial species, here we report indigenous prokaryotic species of Korea. A total of 23 bacterial strains affiliated to the class Alphaproteobacteria were isolated from various environmental sources including seaweeds, seawater, fresh water, wetland/marsh, tidal sediment, plant roots, sewage and soil. Considering higher than 98.8% 16S rRNA gene sequence similarities and formation of a well-defined phylogenetic clade with named species, it was confirmed that each strain belonged to the predefined bacterial species of the class Alphaproteobacteria. There is no official report of these 23 species in Korea; 20 species of 16 genera (Mameliella, Yangia, Paracoccus, Ruegeria, Loktanella, Phaeobacter, Dinoroseobacter, Tropicimonas, Lutimaribacter, Litoreibacter, Sulfitobacter, Roseivivax, Labrenzia, Hyphomonas, Maricaulis, Thalassospira) in the order Rhodobacterales and 3 species of a single genus (Brevundimonas) in the order Caulobacterales. Gram-staining, cell morphology, basic biochemical characteristics, isolation sources, optimum temperature, growth media, and strain IDs are detailed in the species description as well as Table 1.

• 미생물학회지
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• 제45권2호
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• pp.170-176
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• 2009

제주도에 서식하는 2종의 해양 해면, Dictyonella sp.와 Spirastrella abata의 공생세균 군집구조를 16S rDNA-DGGE(denaturing gradient gel electrophoresis) 방법에 의해 분석하였다. 해면으로부터 total genomic DNA를 추출하여 GC clamp가 추가된 세균에 특이적인 341f primer와 518r primer를 이용하여 16S rRNA gene의 V3 부위를 증폭한 후 DGGE 전기 영동하고 재증폭하여 염기서열을 분석하였다. 그 결과 Dictyonella sp.에서 8개, Spirastrella abata에서 7개의 band를 확인할 수 있었다. 공통된 주요 band가 없는 패턴을 나타내었으며, DGGE band로부터 DNA를 추출하여 부분 염기서열을 분석한 결과, NCBI에 등록된 서열들과 93%~98%의 유사도를 나타내었다. Dictyonella sp.의 주요 해면 공생세균은 uncultured Gammaproteobacteria, Spirastrella abata의 경우 uncultured Alphaproteobacteria, Firmicutes에 각각 포함되어 해면 종에 따른 숙주 특이적 분포를 보이는 것으로 나타났다.