• Title/Summary/Keyword: 16S rDNA

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Identification of Bacteria Causing Fermentation of Oriental Melon in Korea (참외 발효과를 유발하는 세균의 동정)

  • Choi, Jae-Eul;Cha, Sun-Kyung;Kim, Jin-Hee;Yuk, Jin-Ah;Hwang, Yong-Soo;Kwon, Soon-Wo
    • Research in Plant Disease
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    • v.9 no.4
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    • pp.189-195
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    • 2003
  • Bacteria causing fermentation in Oriental melon were identified as three independent groups on the basis of 16S rDNA sequence analysis. The 16S rDNA sequence of the strain CM2105 showed the highest identity (99.6%) with that of Microbacterium phyllosphaerae, and also indicated high sequence identity to that of M. holiorum (99.5%). The 16S rDNA sequences of the strain CM2101 and CM2121 matched at the high sequence similarity (98.9%, 98.8, respectively), to that of Pseudomonas pavonacea, and the DNA sequence of CM2126 showed high sequence identity to that of P. costantinii (99.5%), and P. grimontii (99.0%). The 16S rDNA sequence of the strain CM2113 showed the highest identity (99.7%) with that of Enterobacter cloacae. The 16S rDNA sequences, the physiological and biochemical analysis suggested that the strain CM2105 belonged to Microbacterium phyllosphaerae, CM2101, CM2121 and CM2126 to Pseudomonas spp., CM2113 to Enterobacter cloacae.

Molecular Identification of Anginosus Group Streptococci Isolated from Korean Oral Cavities

  • Park, Soon-Nang;Choi, Mi-Hwa;Kook, Joong-Ki
    • International Journal of Oral Biology
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    • v.38 no.1
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    • pp.21-27
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    • 2013
  • Anginosus group streptococci (AGS) were classified based on the nucleotide sequences of the 16S rRNA gene (16S rDNA) and comprised Streptococcus anginosus, Streptococcus intermedius, and Streptococcus constellatus. It is known that AGS is a causative factor of oral and systematic diseases. The purpose of this study was to discriminate the 56 clinical strains of AGS isolated from Korean oral cavities using phylogenetic analysis of 16S rDNA and species-specific PCR at the species-level. The 16S rDNA of clinical strains of AGS was sequenced using the dideoxy chain termination method and analyzed using MEGA version 5 software. PCR was performed to identify the clinical strains using species-specific primers described in previous studies and S. intermedius-specific PCR primers developed in our laboratory. The resulting phylogenetic data showed that the 16S rDNA sequences can delineate the S. anginosus, S. intermedius, and S. constellatus strains even though the 16S rDNA sequence similarity between S. intermedius and S. constellatus is above 98%. The PCR data showed that each species-specific PCR primer pair could discriminate between clinical strains at the species-level through phylogenetic analysis of 16S rDNA nucleotide sequences. These results suggest that phylogenetic analysis of 16S rDNA and PCR are useful tools for discriminating between AGS strains at the species-level.

Diversity of Myxobacteria in Soil Samples from Asansi and Uponeup in Korea (아산시와 우포늪 토양의 점액세균 다양성)

  • Chung, Jin-Woo;Kim, Jin-Woo;Cho, Kyung-Yun
    • Korean Journal of Microbiology
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    • v.46 no.4
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    • pp.405-408
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    • 2010
  • Diversity of myxobacteria in five soil samples from Asansi and Uponeup in Korea was explored by means of polymerase chain reaction (PCR) using primers that specifically bind 16S rDNA of myxobacteria. DNA sequence analysis of 76 PCR fragments containing myxobacterial 16S rDNA revealed five putative novel myxobacterial genera whose 16S rDNA sequences shared <95% sequence identity with those of the type strains. This finding indicates the presence of many uncultured and unidentified myxobacterial species in Korean soil.

Mixed Infection of 16S rDNA I and V Groups of Phytoplasma in a Single Jujube Tree

  • Lee, Sang-Hun;Han, Sang-Sub;Cha, Byeong-Jin
    • The Plant Pathology Journal
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    • v.25 no.1
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    • pp.21-25
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    • 2009
  • Jujube trees infected with phytoplasma exhibit symptoms of typical witches' broom, such as yellowing, abnormally small leaves, short internodes and proliferation of shoots. A 1.2 kb fragment of the 16S rDNA from jujube phytoplasma was generated by R16F2n/R16R2 primer pair from earlier amplified P1/P7 PCR products of cloned jujube witches' broom phytoplasmas. Enzymatic restriction fragment length polymorphism (RFLP) and sequence analysis of 16S rDNA revealed that the jujube tree was infected with 16S rDNA I and V groups of phytoplasmas. Extensive comparative analyses of restriction enzyme profiles from Alu I, Hha I, Msp I, and Rsa I clearly classified the two into different phytoplasma groups. The phylogenie analyses based on 16S rDNA showed that the similarity of the two different clones was 87.5%. This is the first report of a mixed phytoplasmal infection in a single jujube tree.

Comparison of metabolic diversity by sole carbon source utilization and genetic diversity by restriction patterns of amplified 16S rDNA (ARDRA)in soil bacterial communities. (토양세균 군집의 대사 다양성과 16S rDNA의 제한효소 지문분석에 의한 유전적 다양성의 비교)

  • 송인근;최영길;김유영;조홍범
    • Korean Journal of Microbiology
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    • v.35 no.1
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    • pp.72-77
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    • 1999
  • To investigate soil bacterial diversity according to vegelalioo types, utilizing ability of sole carbon sources and restriction enzyme patterns of 16s rDNA were analyzed. From the both results; five kinds of soil microbial communities were grouped as forest soil (Quercus mongolica and Pinus densi&ra vegetation), grass-agricultured soil and microbial communities of naked soil. But, both soil microbial communities of directily exlracted from ths soil and indirectly extracted from heterotrophic bacteria that cultured soil in LB medium showed very different similarity.

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Isolation of Lactococci Inhibiting Listeria monocytogenes from Kimchi Habitat and Its Identification by 16S rDNA Analysis (김치 서식처에서 Listeria monocytogenes를 억제하는 lactococci의 분리와 16S rDNA분석에 의한 동정)

  • 박은주;한홍의;민봉희
    • The Korean Journal of Ecology
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    • v.22 no.1
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    • pp.45-50
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    • 1999
  • A bacteriocin-producing strain was isolated from kimchi at the early stage of kimchi fermentation. It was identified as Lactococcus lactis by morphological, cultural and physiological characteristics and partial sequence of 16S rDNA. The bacteriocin from isolate had antimicrobial activity against gram positive pathogenic bacteria, such as Listeria monocytogenes. Staphylococcus aureus and several strains of lactic acid bacteria but not to gram negative bacteria, Yersinia enterocolitica. The bacteriocin was sensitive to protease, protease ⅩⅣ, a-chymotrypsin and pepsin but not to lipase, trypsin and lysozyme. The bacteriocin activity was stable at pH 2-11 and temperature of 100 for 10 min. Thus, Listeria monocytogenes could be inhibited by Lactococcus lactis at early stage of fermentation.

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Phylogenetic Relationship Among Four Species of Korean Oysters Based on Mitochondrial 16S rDNA and COI Gene (미토콘드리아 16S rDNA와 COI유전자에 근거한 한국산 굴류 4종의 유연관계)

  • 이상엽;박두원;안혜숙;김상해
    • Animal Systematics, Evolution and Diversity
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    • v.16 no.2
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    • pp.203-211
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    • 2000
  • Partial mitochondrial 16S rDNA and COI gene were amplified using PCR and sequenced for four species of oysters in Korea. Phylogenetic relationships among them were inferred from their aligned sequences by neighbor-joining method. The sequence comparison data of two mitochondrial genes showed that the genetic distinction between two oyster genera (Crassostreo and Ostrea) was obvious. Phylogenetic analysis based on the nucleotide sequences and A+T percentage of two genes indicates that C. gigas and C. nippona strongly formed a sister group and then C. ariakensis was clustered with the clade although that based on amino acid sequences of COI gene by neighbor-joining method represented different phylogenetic tree.

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Genetic identification of Aeromonas species using a housekeeping gene, rpoD, in cultured salmonid fishes in Gangwon-Do (강원도 양식 연어과 어류에서 분리된 에로모나스 종의 유전학적 동정)

  • Lim, Jongwon;Koo, Bonhyeong;Kim, Kwang Il;Jeong, Hyun Do;Hong, Suhee
    • Journal of fish pathology
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    • v.30 no.2
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    • pp.79-88
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    • 2017
  • At the present, fish farms are suffering a lot of economic losses due to infectious diseases caused by various pathogens including aeromonad. Aeromonad is ubiquitous bacteria that causes infectious diseases. At least 26 species in the genus Aeromonas have been reported to cause fatal infections not only in salmonid fishes, but also in other freshwater and seawater fishes. Molecular techniques based on nucleic acid sequences of 16S rDNA and housekeeping genes can be used to identify the Aeromonas species. In this study, The genus Aeromonas was isolated from salmonid fishes of sixteen fish farms in Gangwon-Do, Korea and phylogenetically identified based on the sequences of 16S rDNA and housekeeping genes for Aeromonad, i.e. RNA polymerase sigma factor ${\sigma}^{70}$ (rpoD) or DNA gyrase subunit B (gyrB). Consequently, 96 strains were collected from Atlantic salmon (Salmo salar), coho salmon (Oncorhynchus kisutch), masou salmon (Oncorhynchus masou) and rainbow trout (Oncorhynchus mykiss), and 36 isolates were identified as the genus Aeromonas by 16S rDNA analysis. Thirty six Aeromonad isolates were further analysed based on rpoD or gyrB gene sequences and found Aeromonas salmonicida (24 isolates), A. sobria (10 isolates), A. media (1 isolates) and A. popoffii (1 isolates), indicating that A. salmonicida is a main infectious bacteria in Salmonid fishes in Gangwon-Do. It was also proved that the phylogenetic identification of Aeromonas species based on the sequences of housekeeping gene is more precise than the 16S rDNA sequence.

Diversity of Pigment-Producing Halophilic Bacteria Isolated from Coastal Seawater and Solar Saltern in Korea (한국 근해와 염전에서 분리한 색소 생성 호염성 세균의 다양성)

  • Yong Hae-Young;Park Jin-Sook
    • Korean Journal of Microbiology
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    • v.40 no.4
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    • pp.302-306
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    • 2004
  • A total of forty strains of pigment-producing halophilic bacteria were isolated from the solar saltern and coastal seawater in Korea. The diversity of those bacteria were determined on the basis of PCR-RFLP and 16S rDNA sequences. The isolated strains were clssified into nine genera: Pseudoalteromonas, Photobacterium, Vibrio, Halobacillus, Bacillus, Paracoccus, Salinicoccus, Tenacilbaculum, and Flavobacterium. While more than $80\%$ of the pigment-producing halophilic bacteria isolated from the coastal seawater were classified as gram-negative Pseudolateromonas, most of the strains isolated from the solar saltern were classified into gram-positive Halo­bacillus. The other strain was KK7, which may be identified as novel species belonging to the genus, Salini­coccus.

Molecular Differentiation of Bacillus spp. Antagonistic Against Phytopathogenic Fungi Causing Damping-off Disease

  • Cho, Min-Jeong;Kim, Young-Kwon;Ka, Jong-Ok
    • Journal of Microbiology and Biotechnology
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    • v.14 no.3
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    • pp.599-606
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    • 2004
  • Gram-positive antagonistic bacilli were isolated from agricultural soils for possible use in biocontrol of plant pathogenic fungi, Fusarium oxysporum, Rhizoctonia solani, and/or Pythium ultimum. Among the 65 antagonistic Gram-positive soil isolates, 22 strains were identified as Bacillus species by 16S rDNA sequence analyses. Four strains, including DF14, especially exhibited multiple antagonistic properties against the three damping-off fungi. Genotypic properties of the Bacillus isolates were characterized by rapid molecular fingerprinting methods using repetitive extragenic palindromic-PCR (REP-PCR), ribosomal intergenic spacer-length polymorphisms (RIS-LP), 16S rDNA PCR-restriction fragment length polymorphisms (PCR-RFLP), and strain-specific PCR assays. The results indicated that the REP-PCR method was more valuable than the RIS-LP and 16S rDNA PCR-RFLP analyses as a rapid and reliable approach for bacilli typing and identification. The use of strain-specific primers designed based on 16S rDNA sequence comparisons enabled it to be possible to selectively detect a strain, DF14, which is being used as a biocontrol agent against damping-off fungi.