• The Plant Pathology Journal
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• 제29권4호
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• pp.465-470
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• 2013

In January 2012, spreading type petunia cv. Wave Pink plants showing an abnormal growth habit of sprouting unusual multiple plantlets from the lateral buds were collected from a greenhouse in Gwacheon, Gyeonggi Province, Korea. The presence of phytoplasma was investigated using PCR with the primer pairs P1/P6, and R16F1/R1 for nested-PCR. In the nested PCR, 1,096 bp PCR products were obtained, and through sequencing 12 Pet-Stol isolates were identified. Comparison of the nucleotide sequences of 16S rRNA gene of the 12 Pet-Stol isolates with other phytoplasmas belonging to aster yellows or Stolbur showed that Pet-Stol isolates were members of Stolbur. The presence of phytoplasma in petunia was also confirmed by microscopic observation of the pathogens. In this study, Stolbur phytoplasma was identified from spreading type petunia cultivars by sequence analysis of 16S rRNA gene of phytoplasma and microscopic observation of phytoplasma bodies. This is the first report of Stolbur phytoplasma in commercial Petunia hybrida cultivars.

• The Plant Pathology Journal
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• 제40권2호
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• pp.171-191
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• 2024

Identification of Helicotylenchus species is very challenging due to phenotypic plasticity and existence of cryptic species complexes. Recently, the use of rDNA barcodes has proven to be useful for identification of Helicotylenchus. Molecular markers are a quick diagnostic tool and are crucial for discriminating related species and resolving cryptic species complexes within this speciose genus. However, DNA barcoding is not an error-free approach. The public databases appear to be marred by incorrect sequences, arising from sequencing errors, mislabeling, and misidentifications. Herein, we provide a comprehensive analysis of the newly obtained, and published DNA sequences of Helicotylenchus, revealing the potential faults in the available DNA barcodes. A total of 97 sequences (25 nearly full-length 18S-rRNA, 12 partial 28S-rRNA, 16 partial internal transcribed spacer [ITS]-rRNA, and 44 partial cytochrome c oxidase subunit I [COI] gene sequences) were newly obtained in the present study. Phylogenetic relationships between species are given as inferred from the analyses of 103 sequences of 18S-rRNA, 469 sequences of 28S-rRNA, 183 sequences of ITS-rRNA, and 63 sequences of COI. Remarks on suggested corrections of published accessions in GenBank database are given. Additionally, COI gene sequences of H. dihystera, H. asiaticus and the contentious H. microlobus are provided herein for the first time. Similar to rDNA gene analyses, the COI sequences support the genetic distinctness and validity of H. microlobus. DNA barcodes from type material are needed for resolving the taxonomic status of the unresolved taxonomic groups within the genus.

• 한국미생물·생명공학회지
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• 제32권2호
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• pp.195-198
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• 2004

Molec-ular analysis was performed on the microflora found In the necrotic pulpal tissue collected from 5 infected root canals that were diagnosed as a periapical abscess. 16S rRNA coding gene (rDNA) library construction and sequencing were performed in order to identify the microflora, The 16S rDNA sequences from 278 clones were identified by a comparison with the database sequence in GenBank. Three phylum and 31 species, which were related to the oral microflora, were identified from the 3 samples (No. 87, 105, and 115). Dialister invisus (5.6％), Peptostreptococcus micron (18.3％), and Veillonella sp. (3.3％) were the organism present in all tee samples. Lac-tobacillusfementum (2.8％),Eubacterumsp./E. infirmum (6.7％), Shuttleworthiasatelles (3.9％), Psudorarnihacfer alactoiyticus (13.3％), Bulleidia moorei (2.8％), and Prevotella denticola (1.1％) were found in two samples. Two phylum and low species of environmental microflora were identified from 2 samples (No.95 and 101). The reason for this might be contamination of the samples with dental water. These results showed that molecular analysis could reveal more diverse microflora that are associated with endodontic infections than that revealed by conventional cultural methods. In addition, these results may of for the basic data to epidemiological studies related with endodontic infection.

• 한국미생물·생명공학회지
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• 제30권2호
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• pp.129-134
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• 2002

토종닭 소장으로부터 가축 소화기 병원성 유해세균의 분리를 위하여 무작위 선별법과 중층-도말법을 사용하여 총130주의 유산균을 1차 분리하였다. 1차 분리한 130주를 paper disc법을 사용하여 최종적으로 살모넬라 균, 포도상구균, 대장균에 대하여 저해능이 우수한 7주를 분리하였다. 분리 균주의 동정을 위하여 1차로 API CHL kit를 사용하였고, 동정의 정확성을 높이기 위하여 2차로 16S rRNA sequencing 방법을 사용하였다. 그 결과 BD14 균주는 Pediococcus pentosaceus로 동정되었으며 나머지 6주는 Lactobacillus sp.로 동정되어 모두 안전성 있는 유산균임을 확인하였다. 여러 병원균에 가장 항균력이 큰 유산균은 L. pentosus K34이었으며, 이 유산균은 염산과 담즙산에 대한 내성에서도 가장 우수한 균주로 나타났다. 10종의 항생제에 대한 감수성을 조사한 결과 ciprofloxacin에 대하여 모든 균주가 내성을 보였고, BL 균주를 제외하고 모든 균주가 colistin, streptomycin에 대하여 내성을 보였다. 또한 BD14, BD16, K34 균주가 gentamicin에 대한 내성을 보였다.

• 한국해양바이오학회지
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• 제2권4호
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• pp.238-244
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• 2007

Nowadays many people are concerned about being healthy, and many dairy products are taken as health supplementary foods. Among dairy products, kefir, also called as Tibet mushroom, is a yogurt fermented by kefir grain, which is a mixture of lactic acid bacteria and yeasts. Although there are many empirical evidences that kefir is very influential for human body, the exact reason is not definitively discovered. Therefore, it would be useful to understand characteristics of a kefir grain and to categorize bacteria in a kefir grain. In this paper, molecular biological apparatus such as PCR, electrophoresis, PCR purification, DNA sequencing were used to identify and classify the species of lactic acid bacteria and yeast in a kefir grain. We used PCR-based identification method using 16S rRNA primer and Internal Transcribed Spacer (ITS) primer. We identified 6 different species which were selected on different medium. In addition, observation with scanning electron microscope (SEM) enabled us to grasp an external shape of the kefir grain. Although we found a limited number of microbial species, more intensive research are needed for extensive identification of microorganism species in Korean kefir grain.

• Asian-Australasian Journal of Animal Sciences
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• 제29권9호
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• pp.1345-1352
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• 2016

The hindgut of horses is an anaerobic fermentative chamber for a complex and dynamic microbial population, which plays a critical role in health and energy requirements. Research on the gut microbiota of Mongolian horses has not been reported until now as far as we know. Mongolian horse is a major local breed in China. We performed high-throughput sequencing of the 16S rRNA genes V4 hypervariable regions from gut fecal material to characterize the gut microbiota of Mongolian horses and compare them to the microbiota in Thoroughbred horses. Fourteen Mongolian and 19 Thoroughbred horses were used in the study. A total of 593,678 sequence reads were obtained from 33 samples analyzed, which were found to belong to 16 phyla and 75 genera. The bacterial community compositions were similar for the two breeds. Firmicutes (56% in Mongolian horses and 53% in Thoroughbred horses) and Bacteroidetes (33% and 32% respectively) were the most abundant and predominant phyla followed by Spirochaete, Verrucomicrobia, Proteobacteria, and Fibrobacteres. Of these 16 phyla, five (Synergistetes, Planctomycetes, Proteobacteria, TM7, and Chloroflexi) were significantly different (p<0.05) between the two breeds. At the genus level, Treponema was the most abundant genus (43% in Mongolian horses vs 29% in Thoroughbred horses), followed by Ruminococcus, Roseburia, Pseudobutyrivibrio, and Anaeroplasma, which were detected in higher distribution proportion in Mongolian horses than in Thoroughbred horses. In contrast, Oscillibacter, Fibrobacter, Methanocorpusculum, and Succinivibrio levels were lower in Mongolian horses. Among 75 genera, 30 genera were significantly different (p<0.05) between the two breeds. We found that the environment was one of very important factors that influenced horse gut microbiota. These findings provide novel information about the gut microbiota of Mongolian horses and a foundation for future investigations of gut bacterial factors that may influence the development and progression of gastrointestinal disease in horses.

• 한국미생물·생명공학회지
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• 제39권3호
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• pp.287-293
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• 2011

본 연구는 터널표면의 퇴색 및 변색을 초래할 것으로 생각되는 주요 균사형진균을 결정하고, 그 진균을 방제하기 위해 부근 장소에서 분리된 세균들이 항진균 길항능을 가지는 동시에 탄산칼슘 형성을 확인하였다. 이 균주를 이용하여 모르타르에 적용했을 때 항진균 및 압축강도 증진효과를 가진 세균자원을 확보하는데 그 목적이 있다. 터널내의 오염된 지역에서 시료를 취하여 다양한 배지를 이용하여 곰팡이, 효모 및 세균을 분리하였고, 분리된 진균의 ITS-5.8S rRNA gene sequene와 세균의 16s rDNA sequence를 이용해 부분동정을 실시했다. 분리된 미생물의 터널 내 분포를 결정하였으며, 분리된 세균 5종의 탄산칼슘 형성능력을 확인하였다. 터널내 오염지역에서 가장 널리 분포하는 곰팡이인 C. sphaerospermum KNUC253 과 감수성 시험에 널리 이용되는 공시균인 A. niger KCTC6906을 대상으로 항진균 시험을 실시하였다. 터널 분리세균 5종 모두 urea-$CaCl_2$ 고체배지에서 배양했을 때 콜로니 주변부 에서 종 특이적으로 다양한 크기와 형태의 탄산칼슘을 형성함을 확인하였다. 그 중 B. aryabhatti KNUC205는 감수성 곰팡이를 대상으로 뛰어난 항진균 길항능을 보였다.

• 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.

• 식물병연구
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• 제28권1호
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• pp.54-56
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• 2022

2021년 7월, 고창 땅콩 재배포장에서 시들음 증상을 보이는 땅콩 지상부를 발견하였다. 병징은 잎이 갈색으로 시들어 말라 죽은 것처럼 보였으며, 채집한 식물체의 지제부를 잘라 표면소독 후 멸균수에 넣었을 때 ooze 현상을 관찰하였다. 땅콩에서 순수분리된 병원균은 16s rRNA 유전자 염기서열과 phylotype 분류, 유연관계 분석을 통해 분리된 균주가 Ralstonia pseudosolanacearum이라는 것을 확인하였다. 현재까지 국내에 보고된 풋마름병은 고추, 토마토, 감자 등을 기주로 발생한다고 알려져 있다. 본 연구는 국내 처음으로 R. pseudosolanacearum에 의해 발생한 땅콩 풋마름병을 보고하고자 한다.

• Journal of Microbiology and Biotechnology
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• 제14권1호
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• pp.205-211
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• 2004

A 16S rDNA clone library was generated to investigate the bacterial diversity in tidal flat sediment in Ganghwa Island, Republic of Korea. A total of 103 clones were sequenced and analyzed by comprehensive phylogenetic analyses. No clones were identical to any of known 16S rRNA sequences in public databases. Sequenced clones fell into thirteen lineages of the domain Bacteria: the alpha, beta, gamma, delta, and epsilon Proteobacteria, Actinobacteria, CFB group, Chloroflexi, Acidobacteria, Planctomycetes, Verrucomicrobia, and known uncultured candidate divisions (OP11, BRC1, KSB1, and WS1). Two clones were not associated with any known bacterial divisions. The majority of clones belonged to the gamma and delta Proteobacteria (46.7%). Clones of Actinobacteria were distantly related to known taxa. It is evident from 16S rDNA-based community analysis that the bacterial community in tidal flat sediment is remarkably diverse and unique among other marine environments examined so far.