• The Plant Pathology Journal
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• v.29 no.4
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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.

• Microbiology and Biotechnology Letters
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• v.32 no.2
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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.

• The Plant Pathology Journal
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• v.40 no.2
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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.

• Microbiology and Biotechnology Letters
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• v.30 no.2
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• pp.129-134
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• 2002

To isolate probiotic lactic acid bacteria having superior inhibitory activities against animal gastro-intestinal pathogenic bacteria such as Salmonella gallinarum, Staphylococcus aureus and Escherichia coli, 130 strains were initially isolated from the small intestines of Korean native chickens and 7 lactic acid bacteria were finally selected. By using API CHL kit and 16S rRNA sequencing method, the selected lactic acid bacteria were found to be belonged to genus Lactobacillus except BD14 identified as Pediococcus pentosaceus. Especially, Lactobacillus pentosus K34 showed the highest resistancy to both of HCl and bile salt, as well as the highest inhibitory activities against S. gallinarum, S. aureus and E. coli. All the selected strains were sensitive to various antibiotics such as neomycin, erythromycin, cephalosporin, amoxicillin/clavulanic acid, ampicillin, oxytetracycline, but resistant to ciprofloxacin. All the selected strains except BL strain were resistant to colistin and streptomycin, and BD14, BD16, K34 strains were resistant to gentamicin.

• Journal of Marine Bioscience and Biotechnology
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• v.2 no.4
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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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• v.29 no.9
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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.

• Microbiology and Biotechnology Letters
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• v.39 no.3
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• pp.287-293
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• 2011

The purpose of this study was to isolate and characterize fungal deteriogens, which induce discoloration of the cement tunnel, and calcite forming bacteria (CFBs), which have antifungal activity against fungal deteriogens. Isolation of mold, bacteria and yeast was performed using several solid media and partially identified using internal transcribed spacer (ITS); 5.8S rRNA gene sequencing and 16s rDNA sequencing. A total of 19 microbial strains were identified with the most widely distributed fungal strain being Cladospirum sphaerospermum. In addition, five bacteria derived from the tunnel were identified as CFBs. Amongst the latter, Bacillus aryabhatti KNUC205 exhibited antifungal activity against Cladospirum sphaerospermum KNUC253 and Aspergillus niger KCTC6906 as concentrated filtered supernatants.

• Genomics & Informatics
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• v.10 no.4
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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.

• Research in Plant Disease
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• v.28 no.1
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• pp.54-56
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• 2022

A peanut plant showing wilt and browned symptom was found in the field of Gochang, Korea, in July 2021. The symptomatic peanut plant was collected from the field and isolation of the pathogen caused the wilt symptom was performed using the collected sample on TZC media. The dominated colony on media was isolated colony on media was isolated and subcultured of purification. The pure cultured bacteria was identified as Ralstonia solanacearum by sequencing of 16S rRNA gene. Multiplex polymerase chain reaction using phylotype-specific primer set identified isolate as phylotype I (R. pseudosolanacearum). Phylogenetic tree was constructed based on 16S rRNA sequence and it was closed with R. pseudosolanacearum. Pathogenicity of the isolates was assessed by soil drenching inoculation on 4-week-old peanut plant. The wilt symptom was successfully reproduced by inoculation of the isolates after 14 days. This is first report of bacterial wilt caused by R. pseudosolanacearum on peanut in Korea.

• Journal of Microbiology and Biotechnology
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• v.14 no.1
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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.