• 식물병연구
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• 제10권1호
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• pp.63-68
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• 2004

벼에서 문제시되는 도열병과 잎집무의마름병을 생물학적으로 방제하기 위해 병원균과 생태학적 지위가 비슷한 벼 뿌리에서 내생하는 S. marcescens 23 균주를 분리하였다. 선발 균주들을 공시하여 R. solani와 P. grisea에 대한 길항능력을 검정하여 R. solani와 P. grisea에 각각 83.9％. 88.3％의 높은 억제율을 보인 RSm220 균주를 선발하였다. 선발된 RSm220은 생리ㆍ생화학적 특성 검정결과 S. marcescens type strain과 높은 상관성을 나타내었고. 16S rDNA sequencing에 의한 계통 분석에 의해 S. marcescens의 16S rDNA sequence에 98.2％ 유사성을 나타내어 S. marcescens로 동정되었다 내생성 S. marcescens RSm220은 벼 도열병과 잎집무늬마름병에 대한 생물학적 방제제로의 사용이 가능할 것으로 사료된다.

• Journal of Microbiology and Biotechnology
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• 제16권5호
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• pp.740-747
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• 2006

Amplification by universal consensus sequences in pathogenic bacterial DNA would allow rapid identification of pathogenic bacteria, and amplification of genus-specific and species-specific sequences of pathogenic bacterial DNA might be used for genotyping at the genus and species levels. For design of probes for molecular diagnostics, several tools are available as stand-alone programs or as Web application. However, since most programs can design only a few probe sets at one time, they are not suitable for large-scale and automatic probes design. Therefore, for high-throughput design of specific probes in diagnostic array development, an automated design tool is necessary. Thus, we developed a Web-based automatic system for design of genus-specific and species-specific probes for pathogen detection. The system is available at http://www.miprobe.com.

• 한국미생물·생명공학회지
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• 제43권1호
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• pp.65-78
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• 2015

순천만의 염생식물 근권에서 정주하는 세균의 분리를 위해 순천만에서 우점하는 자생식물인 칠면초 군락 3개 지점을 선발하여 샘플링 하였다. 시료는 marine broth, tryptic soy broth 한천배지를 통해 분리되었으며, 형태학적인 구분을 통해 순수분리되었다. 분리주의 16S rDNA를 분석하여 총 92 균주가 동정되었다. 이들의 유연관계 확인을 위한 계통수 작성 결과, 각각 firmicutes (56.5%), gamma-proteobacteria (29.3%), alpha-proteobacteria (5.4%), actinobacteria (5.4%), bacteroidetes (3.3%)에 속하였다. Shannon’s Diversity index (H')를 산출하였을 때 각각 1.675, 1.924, 2.04로, 채취 지점별로 종 다양성의 차이를 보였다.

• Journal of Microbiology and Biotechnology
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• 제16권3호
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• pp.431-437
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• 2006

Aero-tolerant microorganisms were isolated from healthy Koreans over the age of 95 years. The microorganisms were then identified based on their morphological and biochemical characteristics and 16S rDNA sequences. The growth properties of the isolated strains were investigated in kimchi. The characteristics of kimchi containing the microorganisms were studied microscopically, physicochemically, and organoleptically. Among 7 aero-tolerant strains, a strain with a 16S rDNA sequence exhibiting 99% homology with Bifidobacterim animalis strain B83 was selected and named B. animalis DY-64. The new strain showed a better acid resistance and salt resistance (p<0.05) than B. animalis ATCC 25527. After 15 days of fermentation in kimchi, the viability of B. animalis DY-64 was about 10%, and the kimchi had a better overall edible quality than conventional kimchi. Thus, it was found that the application of B. animalis DY-64 to kimchi preparation produced a good overall edible quality.

• Parasites, Hosts and Diseases
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• 제43권1호
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• pp.7-13
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• 2005

The taxonomy of Acanthamoeba spp., an amphizoic amoeba which causes granulomatous amoebic encephalitis and chronic amoebic keratitis, has been revised many times. The taxonomic validity of some species has yet to be assessed. In this paper, we analyzed the morphological characteristics, nuclear 18s rDNA and mitochondrial 16s rDNA sequences and the Mt DNA RFLP of the type strains of four Acanthamoeba species, which had been previously designated as A. divionensis, A. parasidionensis, A. mauritaniensis, and A. rhysodes. The four isolates revealed characteristic group II morphology. They exhibited 18S rDNA sequence differences of $0.2-1.1\%$ with each other, but more than $2\%$ difference from the other compared reference strains. Four isolates formed a different clade from that of A. castellanii Castellani and the other strains in morphological group lion the phylogenetic tree. In light of these results, A. paradivionensis, A. divionensis, and A. mauritaniensis should be regarded as synonyms for A. rhysodes.

• Asian-Australasian Journal of Animal Sciences
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• 제16권12호
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• pp.1816-1821
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• 2003

Reliable PCR based identification of lactobacilli has been described utilizing the sequence of 16S-23S rRNA intergenic spacer region. Those sequence comparisons showed a high degree of difference in homology among the strains of L. rhamnosus, L. casei, L. acidophilus and L. helveticus whose 16S-23S rRNA intergenic small SR's sizes were 222 bp, 222 bp, 206 bp and 216 bp respectively. The sequence of 16S-23S rRNA intergenic spacer region of L. rhamnosus ATCC 53103 revealed the close relatedness to those of L. casei strains by the homology ranges from 95.4% to 97.2%. 16S-23S rRNA intergenic spacer region nucleotide sequence of L. acidophilus showed some distant relatedness with L. rhamnosus ATCC 53103 with the homology ranges from 40.3% to 41.8% and that with L. helveticus was shown to be 30% of homology, which exists at the most distant phylogenetic relatedness. The identification of species and strain of lactobacilli was possible on the basis of these results. The common sequences among the 17 strains were CTAAGGAA located in the initiating position of the DNA and some discrepancies were found between the same strains based on these results.

• 미생물학회지
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• 제51권4호
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• pp.398-406
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• 2015

제주도에서 채집한 해양 해면 Halichondria panicea의 공생세균 군집구조를 배양에 의한 ARDRA와 비배양에 의한 DGGE 분석 방법에 의하여 조사하였다. 16S rRNA gene-ARDRA 분석을 위해 변형된 Zobell 배지와 Marine agar를 이용하여 120균주를 선별하고 제한효소, HaeIII와 MspI을 사용하여 ARDRA type을 구분하였다. ARDRA type으로부터 유래한 16S rRNA gene 염기서열 분석 결과, 알려진 세균 종과 96% 이상의 유사도를 나타내었으며 Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes, Firmicutes 등 3문 4강이 관찰되었다. 그 중 Alphaproteobacteria가 우점하였다. 같은 해면, H. panicea의 DGGE 분석을 위해 total genomic DNA로부터 16S rRNA gene를 증폭하여 DGGE fingerprinting을 수행한 결과 14개의 밴드가 관찰되었다. 각 밴드의 16S rRNA gene 염기서열은 알려진 세균의 염기서열과 100%의 유사성을 나타내었으며 대부분의 염기서열은 uncultured bacteria에 속하였다. DGGE 분석으로부터 미생물의 군집은 Alphaproteobacteria, Gammaproteobacteria, Acidobacteria, Actinobacteira, Bacteroidetes, Cyanobacteria, Chloroflexi 등 6문 7강으로 나타났다. ARDRA와 DGGE 방법에 의해 Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes가 공통적으로 발견되었으나 전체적인 공생세균의 군집구조는 분석방법에 따라 차이를 나타내었다. 배양에 의한 방법보다 비배양 방법에서 더 다양한 세균군집구조를 나타내었다.

• Journal of Microbiology
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• 제41권3호
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• pp.183-188
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• 2003

We isolated and cultured bacteria that inhabited marine biofilms, and identified them by phylogenetic analysis using 16S rDNA sequences. In the marine environment, biofilms cover most subtidal and intertidal solid surfaces such as rocks, ships, loops, marine animals, and algae. The bacteria in most biofilms are embedded in extracellular polymeric substances that comprise mainly of exopolysaccharides. The exopolysaccharides are excreted from multiple bacterial species; therefore, biofilms are a good source for screening exopolysaccharide-producing bacteria. Thirty-one strains were cultured, and a total of 17 unique strains were identified. Phylogenetic analysis using 16S rDNA sequences indicated that the 17 strains belonged to ${\alpha}$-Proteobacteria (Ochrobactrum anthropi, Paracoccus carotinifaciens); ${\gamma}$-Proteobacteria (Pseudoalteromonas agarovorans, P. piscicida, Pseudomonas aeruginosa, Shewanella baltica, Vibrio parahaemolyticus, V. pomeroyi); CFB group bacteria (Cytophaga latercula, Tenacibaculum mesophilum); high GC, Gram-positive bacteria (Arthrobacter nicotianae, Brevibacterium casei, B. epidermidis, Tsukamurella inchonensis); and low GC, Gram-positive bacteria (Bacillus macroides, Staphylococcus haemolyticus, S. warneri).

• Genomics & Informatics
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• 제10권4호
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• pp.249-255
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• 2012

In this study, fosmid cloning strategies were used to assess the microbial populations in water from the International Space Station (ISS) drinking water system (henceforth referred to as Prebiocide and Tank A water samples). The goals of this study were: to compare the sensitivity of the fosmid cloning strategy with that of traditional culture-based and 16S rRNA-based approaches and to detect the widest possible spectrum of microbial populations during the water purification process. Initially, microbes could not be cultivated, and conventional PCR failed to amplify 16S rDNA fragments from these low biomass samples. Therefore, randomly primed rolling-circle amplification was used to amplify any DNA that might be present in the samples, followed by size selection by using pulsed-field gel electrophoresis. The amplified high-molecular- weight DNA from both samples was cloned into fosmid vectors. Several hundred clones were randomly selected for sequencing, followed by Blastn/Blastx searches. Sequences encoding specific genes from Burkholderia, a species abundant in the soil and groundwater, were found in both samples. Bradyrhizobium and Mesorhizobium, which belong to rhizobia, a large community of nitrogen fixers often found in association with plant roots, were present in the Prebiocide samples. Ralstonia, which is prevalent in soils with a high heavy metal content, was detected in the Tank A samples. The detection of many unidentified sequences suggests the presence of potentially novel microbial fingerprints. The bacterial diversity detected in this pilot study using a fosmid vector approach was higher than that detected by conventional 16S rRNA gene sequencing.

• 한국어병학회지
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• 제17권3호
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• pp.159-169
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• 2004

2003년 5월과 2003년 10월동안에 제주도내 5개소의 넙치 종묘배양장에서 초기 먹이로 공급 되어지는 동물성 플랑크톤인 rotifer와 20-30일령 넙치 자어에서 장관백탁증 원인균으로 알려진 V. ichthyoenteri를 분리하기 위해 실험한 결과 총 71개의 Vibrio sp. 분리가 되었고, 생화학적 동정결과 2개의 그룹에서 24개의 V ichthyoenteri가 동정 되었다. V. ichthyoenteri의 신속한 검출을 위한 종특이적 primer를 V. ichthyoenteri(KCCM 40870)ISR의 특이적인 서열을 이용하여 제작하였다. V. ichthyoenteri를 포함한 20종의 Vibrio속 균주의 genomic DNA와 18group 분리균주 genomic DNA를 PCR한 결과 V. ichthyoenteri 만의 특이적인 band가 생성됨을 알 수가 있다. 따라서 V. ichthyoenteri(KCCM 40870) ISR의 서열로 제작한 primer가 넙치 자치어에 발병하는 장관백탁증 원인균인 Vibrio ichthyoenteri의 신속한 검출과 정확한 동정을 할 수 있는 molecular marker로 이용할 수 있음을 확인하였다.