• Research in Plant Disease
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• v.24 no.2
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• pp.138-144
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• 2018

In December 2016, stem rot symptoms were observed on Persian buttercup (Ranunculus asiaticus) plants in Chilgok, Gyeongbuk, Korea. In the early stage of the disease, several black spots appeared on the stem of infected plants. As the disease progressed, the infected stem cleaved and wilted. The causal agent was isolated from a lesion and incubated on Reasoner's 2A (R2A) agar at $25^{\circ}C$. Total genomic DNA was extracted for phylogenetic analysis. Based on the 16S rRNA gene analysis, the isolated strain was found to belong to the genus Pseudomonas. To identify the isolated bacterial strain at the species level, the nucleotide sequences of the gyrase B (gyrB) and RNA polymerase D (rpoD) genes were obtained and compared with the sequences in the GenBank database. As the result, the causal agent of the stem rot disease was identified as Pseudomonas marginalis. To determine the pathogenicity of the isolated bacterial strain, it was inoculated into the stem of healthy R. asiaticus plant, the inoculated plant showed a lesion with the same characteristics as the naturally infected plant. Based on these results, this is the first report of bacterial stem rot on R. asiaticus caused by P. marginalis in Korea.

• YAKHAK HOEJI
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• v.55 no.1
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• pp.22-31
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• 2011

This systematic review was conducted to assess the clinical effect of ocular fluoroquinolones used for the treatment of bacterial conjunctivitis. A literature search for randomized controlled clinical trials registered up to January 2010 based on PubMed database, using the following search terms: conjunctivitis and fluoroquinolones (besifloxacin, moxifloxacin, gatifloxacin, levofloxacin, lomefloxacin, ciprofloxacin and ofloxacin) were performed. Pooled data on the clinical resolution and bacterial eradication rates derived from selected 16 studies were reported as the relative risk (RR) and 95% confidence interval (95% CI) compared with placebo. Early clinical resolution and microbiological eradication rates in placebo were 28% and 62% respectively. Fluoroquinolones were significantly effective comparing to placebo: early RR 1.94 (95% CI 1.60~2.34) and late RR 1.30 (1.19~1.43) in clinical resolution rates, and early RR 1.75 (1.58~1.94) and late RR 1.28 (1.18~1.39) in microbiological eradication rates. Besifloxacin, ciprofloaxain and moxifloxacin in clinical resolution, and besifloxacin and levofloxacin in microbiological eradication showed higher RRs than pooled overall fluoroquinolones' RRs. New quinolones had higher antibacterial potencies for all pathogens isolated from bacterial conjunctivitis and resistant isolates than old generation quinolones. In conclusion, ocular 7 fluoroquinolones were all effective than placebo for bacterial conjunctivitis and there were differences between quinolones in early and late clinical resolutions and microbiological eradications, and no differences in safety comparing to placebo.

• Genomics & Informatics
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• v.4 no.4
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• pp.182-187
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• 2006

6-Phosphogluconolactonase (6PGL) is one of the key enzymes in the ubiquitous pathways of central carbon metabolism, but bacterial 6PGL had been long known as a missing enzyme even after complete bacterial genome sequence information became available. Although recent experimental characterization suggests that there are two types of 6PGLs (DevB and YbhE), their phylogenetic distribution is severely biased. Here we present that proteins in COG group previously described as 3-oarboxymuconate cyclase (COG2706) are actually the YbhE-type 6PGLs, which are widely distributed in Proteobacteria and Fimicutes. This case exemplifies how erroneous functional description of a member in the reference database commonly used in transitive genome annotation cause systematic problem in the prediction of genes even with universal cellular functions.

• Korean Journal of Microbiology
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• v.49 no.4
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• pp.377-382
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• 2013

The bacterial community structures of the marine sponge, Dactylospongia metachromia, collected from Chuuk of Micronesia on February 2012, were analyzed by denaturing gradient gel electrophoresis (DGGE). The DGGE fingerprints of two individuals of D. metachromia, CH607 and CH840 showed the same band patterns. The sequences derived from DGGE bands revealed 93~100% similarities with known bacterial species in the public database and high similarity with uncultured bacterial clones. The bacterial community structures of both D. metachromia sponges (CH607, CH840) were composed of 6 phyla, 8 classes: Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Acidobacteria, Actinobacteria, Chloroflexi, Cyanobacteria, Spirochaetes. DGGE fingerprint - based phylogenetic analysis revealed that the bacterial community profiles were identical in two individuals of the same sponge species collected from the same geographical location.

• Journal of Marine Bioscience and Biotechnology
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• v.7 no.2
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• pp.42-51
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• 2015

The community structure of cultivable bacteria associated with the marine sponge, Petrosia corticata, collected from Jeju Island in summer (September) of 2012 and winter (January) of 2013, were compared by the PCR-ARDRA method. Bacterial strains were cultured for 4 days at $26^{\circ}C$ on Zobell medium and marine agar medium. After PCR amplification of 16S rRNA gene of individual strains, the restriction enzymes MspI and HaeIII were used to make restriction patterns. As a result, 24 ARDRA patterns from the summer sponge and 20 ARDRA patterns from the winter sponge were obtained. The sequencing result of 1-3 selected strains from each pattern showed over 98% similarities with the known sequences from the public database. At the phylum level, the bacterial community structures of both sponges (summer and winter) were identical qualitatively and composed of 4 phyla : Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. Alphaproteobacteria accounted for 42.5% of total in summer sponge and 25.2% in winter, decreasing in the winter sample. Gammaproteobacteria accounted for 27.5% of total in summer sponge and 35.2% in winter, increasing in the winter sample. At the genus and species level, summer sponge had more diverse bacterial communities than winter sponge. Actinobacteria, Bacteroidetes, and Firmicutes increased in the winter sample.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2003.10a
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• pp.245-250
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• 2003

There are currently about 6000 bacterial species with validly published names, but scientists assume that these may be less than 1% of bacterial species present on the earth. Microbial resource is one of the most important bioresources in bioinderstry and provides us with high economic values. To find missing ones, the studies of metagenome, metabolome, and proteome about microbes have started recently in developed countries. We construct the information system that integrates information on microbial genome resources and manages the information to support efficient research of microbial genome application, and name this system 'Bio-Meta Information System (Bio-MIS)'. Bio-MIS consists of integrated microbial genome resources database, microbial genome resources input system, integrated microbial genome resources search engine, microbial resources on-line distribution system, portal service and management via internet. In the future, we will include public database connection and implement useful bioinformatics software for analyzing microbial genome resources. The web-site is accessible at http://biomis.probionic.com

• Journal of Veterinary Science
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• v.22 no.3
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• pp.37.1-37.14
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• 2021

Background: Ticks are one of the most common external parasites in dogs, and are associated with the transmission of a number of major zoonoses, which result in serious harm to human health and even death. Also, the increasing number of pet dogs and pet owners in China has caused concern regarding human tick-borne illnesses. Accordingly, studies are needed to gain a complete understanding of the bacterial composition and diversity of the ticks that parasitize dogs. Objectives: To date, there have been relatively few reports on the analysis of the bacterial community structure and diversity in ticks that parasitize dogs. The objective of this study was to investigate the microbial composition and diversity of parasitic ticks of dogs, and assessed the effect of tick sex and geographical region on the bacterial composition in two tick genera collected from dogs in China. Methods: A total of 178 whole ticks were subjected to a 16S ribosomal RNA (rRNA) next generation sequencing analysis. The Illumina MiSeq platform targeting the V3-V4 region of the 16S rRNA gene was used to characterize the bacterial communities of the collected ticks. Sequence analysis and taxonomic assignment were performed using QIIME 2 and the GreenGene database, respectively. After clustering the sequences into taxonomic units, the sequences were quality-filtered and rarefied. Results: After pooling 24 tick samples, we identified a total of 2,081 operational taxonomic units, which were assigned to 23 phyla and 328 genera, revealing a diverse bacterial community profile. The high, moderate and low prevalent taxa include 46, 101, and 182 genera, respectively. Among them, dominant taxa include environmental bacterial genera, such as Psychrobacter and Burkholderia. Additionally, some known tick-associated endosymbionts were also detected, including Coxiella, Rickettsia, and Ricketssiella. Also, the potentially pathogenic genera Staphylococcus and Pseudomonas were detected in the tick pools. Moreover, our preliminary study found that the differences in microbial communities are more dependent on the sampling location than tick sex in the tick specimens collected from dogs. Conclusions: The findings of this study support the need for future research on the microbial population present in ticks collected from dogs in China.

• Mycobiology
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• v.45 no.3
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• pp.160-171
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• 2017

Larvae of Bradysia agrestis, an insect vector that transports plant pathogens, were sampled from geographically isolated regions in Korea to identify their cutaneous fungal and bacterial flora. Sampled areas were chosen within the distribution range of B. agrestis; each site was more than 91 km apart to ensure geographical segregation. We isolated 76 microbial (fungi and bacteria) strains (site 1, 29; site 2, 29; site 3, 18 strains) that were identified on the basis of morphological differences. Species identification was molecularly confirmed by determination of universal fungal internal transcribed spacer and bacterial 16S rRNA gene sequences in comparison to sequences in the EzTaxon database and the NCBI GenBank database, and their phylogenetic relationships were determined. The fungal isolates belonged to 2 phyla, 5 classes, and 7 genera; bacterial species belonged to 23 genera and 32 species. Microbial diversity differed significantly among the geographical groups with respect to Margalef's richness (3.9, 3.6, and 4.5), Menhinick's index (2.65, 2.46, and 3.30), Simpson's index (0.06, 0.12, and 0.01), and Shannon's index (2.50, 2.17, and 2.58). Although the microbial genera distribution or diversity values clearly varied among geographical groups, common genera were identified in all groups, including the fungal genus Cladosporium, and the bacterial genera Bacillus and Rhodococcus. According to classic principles of co-evolutionary relationship, these genera might have a closer association with their host insect vector B. agrestis than other genera identified. Some cutaneous bacterial genera (e.g., Pseudomonas) displaying weak interdependency with insect vectors may be hazardous to agricultural environments via mechanical transmission via B. agrestis. This study provides comprehensive information regarding the cutaneous microflora of B. agrestis, which can help in the control of such pests for crop management.

• Asian-Australasian Journal of Animal Sciences
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• v.28 no.6
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• pp.888-895
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• 2015

Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and subsequent sub-cloning and sequencing were used in this study to analyze the molecular phylogenetic diversity and spatial distribution of bacterial communities in different spatial locations during the cooling stage of composted swine manure. Total microbial DNA was extracted, and bacterial near full-length 16S rRNA genes were subsequently amplified, cloned, RFLP-screened, and sequenced. A total of 420 positive clones were classified by RFLP and near-full-length 16S rDNA sequences. Approximately 48 operational taxonomic units (OTUs) were found among 139 positive clones from the superstratum sample; 26 among 149 were from the middle-level sample and 35 among 132 were from the substrate sample. Thermobifida fusca was common in the superstratum layer of the pile. Some Bacillus spp. were remarkable in the middle-level layer, and Clostridium sp. was dominant in the substrate layer. Among 109 OTUs, 99 displayed homology with those in the GenBank database. Ten OTUs were not closely related to any known species. The superstratum sample had the highest microbial diversity, and different and distinct bacterial communities were detected in the three different layers. This study demonstrated the spatial characteristics of the microbial community distribution in the cooling stage of swine manure compost.

• The Journal of Korean Obstetrics and Gynecology
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• v.32 no.2
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• pp.50-70
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• 2019

Objectives: The purpose of this study was to show effectiveness of Korean medicine external treatment on bacterial vaginosis by analyzing randomized controlled clinical trials. Methods: We searched randomized controlled clinical trials related with Korean external treatment on bacterial vaginosis through national and overseas database and analyzed them in detail. Results: 15 articles were included according to our selection criteria and 2,176 women were involved. 1. All treatment groups were treated with intervention including Korean medicine external treatment and their results were statistically more effective than control groups. 2. External washing was the most frequently used method followed by vaginal tablet, fumigation and powder. 3. The most frequently used herbal medicine was Sophorae Radix followed by Phellodendri Cortex, Cindi Fructus, Dictamni Radicix Cortex and Kochiae Fructusa. 4. There were 4 studies reporting side effects of treatment and no significant side effects were observed. Conclusions: There was significant difference in the effectiveness of the intervention including Korean external therapy. Based on the analysis, it could be an effective way for the treatment of bacterial vaginosis in clinical practice.