• Journal of Species Research
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• 제11권4호
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• pp.321-329
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• 2022

Four species of cyanobacteria that are unrecorded in Korea were isolated from freshwater and brackish water. These four species are Laspinema thermale of Laspinemaceae, Planktothricoides raciborskii and Planktothrix spiroides of Microcoleaceae, and Cephalothrix lacustris of Phormidiaceae, all belonging to the order Oscillatoriales. Laspinema thermale is morphologically characterized as apical cells that are longer than other cells. In this strain, the similarity of the 16S rRNA gene sequence with the previously reported L. thermale strains were 99.30-99.50%. Planktothricoides raciborskii, which is characterized by bluntly conical morphology of apical cells, showed 98.80-99.50% of similarity of the 16S rRNA gene sequence to the previously reported P. raciborskii strains. Planktothrix spiroides are characterized by floating due to gas vacuoles. In this strain, the similarity of the 16S rRNA gene sequence with the previously reported P. spiroides strains were 99.80-99.90%. Cephalothrix lacustris, characterized by having calyptra in apical cells, showed 99.80-99.90% similarity of the 16S rRNA gene sequence to previously reported C. lacustris strains. Also, these species were clustered in the same clade in phylogenetic analysis using 16S rRNA gene sequences with each corresponding species.

• 한국동물위생학회지
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• 제37권3호
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• pp.157-164
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• 2014

Clostridium chauvoei is the etiologic agent of blackleg, a high mortality rated disease infection mainly cattle. In the present study, the partial sequences of 16S rRNA and flagellin gene of C. chauvoei isolated in Jeonbuk, Korea were determined and compared with those of reference strain. Oligonucleotide primers were designed to amplify a 811 bp fragment of 16S rRNA gene and 1229 bp fragment of flagellin gene. Sequencing analysis of 16S rRNA gene showed high homology to the reference strains ranging 82.3% to 100%, while flagellin gene were different from published foreign clostridia, showing 98.7% to 72.0% nucleotide sequence homology. Phylogenetic analysis based on 16S rRNA gene revealed the close phylogenetic relationship of C. chauvoei and C. septicum in cluster I, which includes C. carnis, C. tertium, C. quinii, C. celatum, C. perfringens, C. absonum, C. botulinum B. Phylogentic analysis also revealed that flagellin gene formed a single cluster with C. chauvoei, C. septicum, C. novyi A, C. novyi B, C. tyrobutylicum, C. acetobutylicum. The genetic informations obtained from this study could be useful for the molecular study of C. chauvoei.

• ALGAE
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• 제17권3호
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• pp.153-159
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• 2002

Partial 16S rRNA gene sequences of seven cyanophycean strains from the National Instiute of Environmental Research of Korea - Microcystis aeruginosa, M. aeruginosa f. aeruginosa, M. ichthyoblade, M. viridis, Anabaena flos-aquae, and Oscillatoria sancta - were analyzed and the phylogenetic relationship of Microcystis among Cyanophyceae were evaluated. Based on sequence analysis results, Microcystis is monophyletic, the clade of which supported 100% bootstrap tress, and distinguished clearly from the other taxa. Therefore, the partial 16S rRNA gene sequences can be a useful and efficient tool for distinguishing Microcystis from other cyanophycean without axenic culture or cloning.

• 미생물학회지
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• 제43권3호
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• pp.232-235
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• 2007

해양 및 토양에서의 암모니아 산화는 세균에 비해 Crenarchaeota 그룹의 archaea에 의해 우세하게 일어나고 있음이 알려졌다. 서해 갯벌에서, 배양에 의존하지 알고, 특정 암모니아 산화유전자(amoA)를 가진 archaea을 동정하고자 디지털 PCR법을 응용한 nested PCR법을 개발하였다. amoA와 16S rRNA유전자가 동시에 증폭된 샘플의 분석결과, 16S rRNA유전자에 비해 amoA 유전자의 다양성 이 높았으며, I.1a 그룹의 crenarchaea가 I.1b 그룹의 crenarchaea보다 갯벌지역에서 암모니아 산화에 우점적으로 기여하고 있음을 알 수 있었다. 본 연구에서 시도된, 디지털 PCR과 multiplex-nested PCR을 접목한 접근법을 이용하면 특정 기능유전자를 가진 미생물을 환경에서 검증하는데 응용할 수 있을 것이다.

• 한국식품과학회지
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• 제32권6호
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• pp.1331-1335
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• 2000

김치 젖산균인 WL6는 API kit 또는 Biolog system방법에 의하여 동정한 결과, Leuconostoc mesenteroides ssp. cremoris, Leu. mesenteroides ssp. dextranicum 또는 Lactobacillus bifermentans로 나타나 동정되지 않았다. 그러나, pepN gene과 16S rRNA gene으로부터 2개의 specific-sequence primer set을 제조하여 PCR 방법으로 증폭한 후에 표준균주들과 비교한 결과, WL6는 Lactobacillus bifermentans로 추정되었다.

• 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 Microbiology and Biotechnology
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• 제18권2호
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• pp.194-198
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• 2008

A newly designed Cytophaga-Flavobacteria-specific 16S rRNA gene primer pair was employed to investigate the CF community structure in the Bering Sea, revealing a previously unknown and unexpected high CF diversity in this high latitude cold sea. In total, 56 clones were sequenced and 50 unique CF 16 rRNA gene fragments were obtained, clustering into 16 CF subgroups, including nine cosmopolitan subgroups, five psychrophilic subgroups, and two putatively autochthonous subgroups. The majority of sequences (82%) were closely related to uncultured CF species and could not be classified into known CF genera, indicating the presence of a large number of so-far uncultivated CF species in the Bering Sea.

• 미생물학회지
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• 제47권3호
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• pp.268-274
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• 2011

남조세균 Anabaena (Cyanobacteria, Nostocales)는 담수 생태계에서 녹조 현상을 유발하거나 일부 종은 간독소(hepatotoxin)를 갖고 있어 수질관리 차원에서 주목 받아 왔다. 본 연구는 Anabaena RNA polymerase beta subunit (rpoB) 유전자 염기서열을 규명하였으며, 분류학적 분자 마커로 사용하기 위하여 이들 염기서열의 특성을 평가하였다. Anabaena rpoB 유전자는 16S rRNA 유전자와 비교하여 염기 유사도가 낮으며 유전자 변이가 큰 것으로 분석되었으며, 통계적으로 유의한 차이를 보였다(Student t-test, p<0.01). Parsimony 분석을 통해 rpoB 유전자가 4.8배의 속도로 빠르게 진화하는 것으로 파악되었다. 또한 rpoB 유전자 phylogeny 분석에서 16S rRNA tree보다 높은 해상도로 Anabaena 균주를 명확하게 구분해 주었다. 본 연구 결과는 Anabaena의 종 식별, 분자계통 분류, 분자적 검출을 위해 rpoB 유전자가 매우 효과적이라는 것을 제시해 준다.

• 한국축산시설환경학회지
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• 제21권3호
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• pp.93-98
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• 2015

The objective of this study was to review application of next-generation sequencing (NGS) to investigate microbiome in the livestock sector. Since the 16S rRNA gene is used as a phylogenetic marker, unculturable members of microbiome in nature or managed environments have been investigated using the NGS technique based on 16S rRNA genes. However, few NGS studies have been conducted to investigate microbiome in the livestock sector. The 16S rRNA gene sequences obtained from NGS are classified to microbial taxa against the 16S rRNA gene reference database such as RDP, Greengenes and Silva databases. The sequences also are clustered into species-level OTUs at 97% sequence similarity. Microbiome similarity among treatment groups is visualized using principal coordinates analysis, while microbiome shared among treatment groups is visualized using a venn diagram. The use of the NGS technique will contribute to elucidating roles of microbiome in the livestock sector.

• Parasites, Hosts and Diseases
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• 제51권4호
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• pp.401-412
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• 2013

Because of an increased number of Acanthamoeba keratitis (AK) along with associated disease burdens, medical professionals have become more aware of this pathogen in recent years. In this study, by analyzing both the nuclear 18S small subunit ribosomal RNA (18S rRNA) and mitochondrial 16S rRNA gene loci, 27 clinical Acanthamoeba strains that caused AK in Japan were classified into 3 genotypes, T3 (3 strains), T4 (23 strains), and T5 (one strain). Most haplotypes were identical to the reference haplotypes reported from all over the world, and thus no specificity of the haplotype distribution in Japan was found. The T4 sub-genotype analysis using the 16S rRNA gene locus also revealed a clear subconformation within the T4 cluster, and lead to the recognition of a new sub-genotype T4i, in addition to the previously reported sub-genotypes T4a-T4h. Furthermore, 9 out of 23 strains in the T4 genotype were identified to a specific haplotype (AF479533), which seems to be a causal haplotype of AK. While heterozygous nuclear haplotypes were observed from 2 strains, the mitochondrial haplotypes were homozygous as T4 genotype in the both strains, and suggested a possibility of nuclear hybridization (mating reproduction) between different strains in Acanthamoeba. The nuclear 18S rRNA gene and mitochondrial 16S rRNA gene loci of Acanthamoeba spp. possess different unique characteristics usable for the genotyping analyses, and those specific features could contribute to the establishment of molecular taxonomy for the species complex of Acanthamoeba.