• Journal of Yeungnam Medical Science
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• 제19권1호
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• pp.1-10
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• 2002

With the establishment of rapid sequence analysis of 16S rRNA and the recognition of its potential to determine the phylogenetic position of any prokaryotic organism, the role of 16S rRNA similarities in the present species definition in bacteriology need to be clarified. Comparative studies clearly reveal the limitations of the sequence analysis of this conserved gene and gene product in the determination of relationship at the pathogenic strain level for which DNA-DNA reassociation experiments still constitute the superior method. Since today the primary structure of 16S rRNA is easier to determine than hybridization between DNA strands, the strength of the sequence analysis is to recognize the level at which DNA pairing studies need to be performed, which certainly applies to similarities of 97% and higher.

• 식물병연구
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• 제9권4호
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• pp.189-195
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• 2003

참외의 발효과를 유발하는 세균은 16S rDNA 염기분석에 의해 3 group으로 분류되었다. CM2105균주의 16S rDNA 염기서열은 Microbacterium phyllosphaerae의 염기서열과 99.6%의 높은 상동성을 나타냈고, M. holiorum과도 99.5%의 높은 상동성을 나타냈다. CM2101과 CM2121균주의 16S rDNA 염기서열은 "P. pavonaceae"와 각각 98.9%, 98.8, CM2126균주는 P. costantinii와 99.5%, P. grimontii와 99.0%의 높은 상동성을 나타냈다. CM21131균주의 16S rDNA 염기서열은 Enterobacter cloacae와 99.7%의 높은 상동성 나타냈다. 검정균주의 생리적, 생화학적 특성과 16S rDNA의 염기분석에 따라 CM2105 균주는 M. phyllosphaerae, CM2101, CM2121, CM2126 균주는 Pseudomonas spp., 그리고 CM2113 균주는 E. cloacae로 동정하였다.

• 미생물학회지
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• 제46권4호
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• pp.405-408
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• 2010

점액세균의 16S rDNA에 특이적으로 부착하는 프라이머를 사용한 중합효소연쇄반응(PCR)을 통해 아산시와 우포늪에서 채취한 다섯 토양시료 내 점액세균의 다양성을 조사하였다. 점액세균의 16S rDNA을 갖는 76개 PCR 조각의 서열분석 결과, 표준균주와 95% 미만의 상동성을 보이는 5개의 신속 추정 점액세균이 관찰되어 국내 토양에 아직까지 분리되지 않은 많은 새로운 점액세균들이 존재함을 보여주었다.

• Journal of Microbiology and Biotechnology
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• 제10권5호
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• pp.643-650
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• 2000

A new aniline-utilizing microorganism, strain HY1 obtained from an orchard soil, was characterized by using the BIOLOG system, an analysis of the total cellular fatty acids, and a 16S rDNA sequence. Strain HY1 was identified as a Burkholderia species, and was designated Burkholderia sp. HY1. GC and HPLC analyses revealed that Burkholderia sp. HY1 was able to degrade aniline to produce catechol, which was subsequently converted to cis,cis-muconic acid through an ortho-ring fission pathway under aerobic conditions. Strain HY1 exhibited a drastic reduction in the rate of aniline degradation when glucose was added to the aniline media. However, the addition of peptone or nitrate to the aniline media dramatically accelerated the rate of aniline degradation. A fatty acid analysis showed that strain HY1 was able to produce lipids 16:0 2OH, and 11 methyl 18:1 ${\omega}7c$ approximately 3.7-, 2.2-, and 6-fold more, respectively, when grown on aniline media than when grown on TSA. An analysison the alignment of a 1,435 bp fragment. A phylogenetic analysis of the 16S rDNA sequence based on a 1,420 bp multi-alignment sowed of the 16s rDNA sequence revealed that strain HY1 was very closely related to Burkholderia graminis with 95% similarity based that strain HY1 was placed among three major clonal types of $\beta$-Proteobacteria, including Burkholderia graminis, Burkholderia phenazinium, and Burkholderia glathei. The sequence GAT(C or G)${\b{G}}$, which is highly conserved in several locations in the 16S rDNA gene among the major clonal type strains of $\beta$-Proteobacteria, was frequently replaced with GAT(C or G)${\b{A}}$ in the 16S rDNA sequence from strain HY1.

• The Korean Journal of Ecology
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• 제22권1호
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• pp.45-50
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• 1999

김치 발효 초기에 bacteriocin 생성 유산균을 분리하고자 하였다. 분리 유산균은 형태, 배양 및 생리학적인 특징과 16S rDNA의 부분적인 염기서열로부터 Lactococcus lactis로 동정되었다. 분리균주가 생성한 bacteriocin은 Listeria monocytogenes, Staphylococcus aureus와 같은 그람 양성 병원성 세균과 몇몇 유산균에 대해 항균활성이 있었고, 그람음성균인 Yesinia에는 활성이 없었다. bacteriocin의 활성은 protease, protease ⅩⅣ, a-chymotrypsin과 pepsin에 대해서 활성이 소실되었으나, lipase, trypsin, lysozyme에 대해서는 활성이 유지되었다. bacteriocin의 활성은 pH 2∼11에서 안정적이며 l00℃에서 10분간 열처리시에도 변하지 않았다. 따라서 L. monocytogenes는 발효초기에 L. lactis에 의하여 억제될 수 있다.

• Parasites, Hosts and Diseases
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• 제46권3호
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• pp.157-164
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• 2008

Three Acanthamoeba isolates (KA/E9, KA/E17, and KA/E23) from patients with keratitis were identified as Acanthamoeba triangularis by analysis of their molecular characteristics, a species not previously recognized to be a corneal pathogen. Epidemiologic significance of A. triangularis as a keratopathogen in Korea has been discussed. Morphologic features of Acanthamoeba cysts were examined under a microscope with differential interference contrast (DIC) optics. Mitochondrial DNA (mtDNA) of the ocular isolates KA/E9, KA/E17, and KA/E23 were digested with restriction enzymes, and the restriction patterns were compared with those of reference strains. Complete nuclear 188 and mitochondrial (mt) 16S rDNA sequences were subjected to phylogenetic analysis and species identification. mtDNA RFLP of 3 isolates showed very similar patterns to those of SH621, the type strain of A. triangularis. 16S and 18S rDNA sequence analysis confirmed 3 isolates to be A. triangularis. 18S rDNA sequence differences of the isolates were 1.3% to 1.6% and those of 16S rDNA, 0.4% to 0.9% from A. triangularis SH621. To the best of our knowledge, this is the first report, confirmed by 18S and 16S rDNA sequence analysis, of keratitis caused by A. triangularis of which the type strain was isolated from human feces. Six isolates of A. triangularis had been reported from contaminated contact lens cases in southeastern Korea.

• Journal of Microbiology and Biotechnology
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• 제18권5호
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• pp.815-820
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• 2008

Two culture-independent methods, namely ribosomal DNA libraries and denaturing gradient gel electrophoresis (DGGE), were adopted to examine the microbial community of a Malaysian light crude oil. In this study, both 16S and 18S rDNAs were PCR-amplified from bulk DNA of crude oil samples, cloned, and sequenced. Analyses of restriction fragment length polymorphism (RFLP) and phylogenetics clustered the 16S and 18S rDNA sequences into seven and six groups, respectively. The ribosomal DNA sequences obtained showed sequence similarity between 90 to 100% to those available in the GenBank database. The closest relatives documented for the 16S rDNAs include member species of Thermoincola and Rhodopseudomonas, whereas the closest fungal relatives include Acremonium, Ceriporiopsis, Xeromyces, Lecythophora, and Candida. Others were affiliated to uncultured bacteria and uncultured ascomycete. The 16S rDNA library demonstrated predomination by a single uncultured bacterial type by >80% relative abundance. The predomination was confirmed by DGGE analysis.

• 산업식품공학
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• 제14권1호
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• pp.7-13
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• 2010

호열성 미생물을 검토하기 위하여 전국 각지로부터 토양과 두엄을 채취하여 그로부터 호열성 미생물을 분리하였다. 토양과 두엄으로부터 분리된 호열성 미생물 1250여 균주를 선별하였고, 이들을 대상으로 미생물이 생산하는 효소 활성을 검토하여 호열성 전분 분해 효소를 생산하는 1주의 미생물을 확인하였다. 확인된 1주의 미생물을 strain 2719라 명명하였다. Strain 2719 균주는 형태학적으로 gram 양성 간균의 특징을 나타냈고, 균주의 표면은 매끄럽지 않았으며, 비교적 다양한 길이를 가지고 있었다. 또한 다른 gram 양성 간균들에 비해서 많은 수의 균사들이 각 균주들 사이에 복잡하게 얽혀있었다. 생화학적 특성을 확인한 결과 catalase 양성, glucose 발효, arabinose 발효, mannitol 발효, casein gelatin starch 가수분해의 특징을 가지고 있었으며, 이는 Bacillus sp.로 추정되었다. 생육 pH의 범위는 pH 6-pH 8범위에서 생육이 가능했으며, 생육 온도의 범위는 50-70${^{\circ}C}$였다. 16S rDNA sequence 분석결과 Bacillus thermoglucosidasius의 16S rDNA와 99.52%가 일치하였으나, sequence의 일부분이 다른 부분이 있고, 생육 특성에서 약간의 차이를 보였다. 또한 gene bank에 등록되어 있는 균주들의 16S rDNA sequence들과 비교하여도 일치하는 균주는 확인되지 않았다. 이와 같은 실험결과에 따라 2719 균주는 기존에 발표되지는 않았으나, Bacillus thermoglucosidasius와 매우 유사한 균주로 판단되어 Bacillus thermoglucosidasius 2719로 명명하였다.

• Journal of Microbiology and Biotechnology
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• 제22권1호
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• pp.13-24
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• 2012

The genetic diversity of plant growth-promoting rhizobacterial (PGPR) fluorescent pseudomonads associated with the sugarcane (Saccharum officinarum L.) rhizosphere was analyzed. Selected isolates were screened for plant growthpromoting properties including production of indole acetic acid, phosphate solubilization, denitrification ability, and production of antifungal metabolites. Furthermore, 16S rDNA sequence analysis was performed to identify and differentiate these isolates. Based on 16S rDNA sequence similarity, the isolates were designated as Pseudomonas plecoglossicida, P. fluorescens, P. libaniensis, and P. aeruginosa. Differentiation of isolates belonging to the same group was achieved through different genomic DNA fingerprinting techniques, including randomly amplified polymorphic DNA (RAPD), amplified ribosomal DNA restriction analysis (ARDRA), repetitive extragenic palindromic (REP), enterobacterial repetitive intergenic consensus (ERIC), and bacterial repetitive BOX elements (BOX) analyses. The genetic diversity observed among the isolates and rep-PCR-generated fingerprinting patterns revealed that PGPR fluorescent pseudomonads are associated with the rhizosphere of sugarcane and that P. plecoglossicida is a dominant species. The knowledge obtained herein regarding the genetic and functional diversity of fluorescent pseudomonads associated with the sugarcane rhizosphere is useful for understanding their ecological role and potential utilization in sustainable agriculture.

• The Plant Pathology Journal
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• 제20권4호
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• pp.283-288
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• 2004

Four Erwinia carotovora strains isolated from potatoes showing blackleg symptoms and rotted Chinese cabbage were analysed by biochemical tests and sequence analysis of 16S rDNA and 16S-23S rRNA intergenic spacer (IGS) regions, and the data were compared to related E. carotovora strains. Based on the results of the biochemical tests and sequence analysis, 2 of the 4 strains were identified as E. carotovora subsp. carotovora (Ecc), whereas the rest strains were distinct from Ecc. The last two strains, HCC3 and JEJU, were biochemically similar to E, carotovora subsp. atroseptica (Eca). However, the results of sequence analysis and Eca-specific PCR assays showed that the strains were distinct from Eca. On the basis of 16S rDNA sequence analysis, HCC3 and JEJU strains were placed in E. carotovora subsp. odorifera and E. carotovora subsp. wasabiae, respectively. The results of sequence analysis and specific PCR assay for Eca indicated that Asian Eca strains were distinct from European Eca strains, although they were phenotycally homogeneous.