• Journal of Microbiology and Biotechnology
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• 제30권9호
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• pp.1335-1342
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• 2020

The identification of bacterial pathogens to humans is critical for environmental microbial risk assessment. However, current methods for identifying pathogens in environmental samples are limited in their ability to detect highly diverse bacterial communities and accurately differentiate pathogens from commensal bacteria. In the present study, we suggest an improved approach using a combination of identification results obtained from multiple databases, including the multilocus sequence typing (MLST) database, virulence factor database (VFDB), and pathosystems resource integration center (PATRIC) databases to resolve current challenges. By integrating the identification results from multiple databases, potential bacterial pathogens in metagenomes were identified and classified into eight different groups. Based on the distribution of genes in each group, we proposed an equation to calculate the metagenomic pathogen identification index (MPII) of each metagenome based on the weighted abundance of identified sequences in each database. We found that the accuracy of pathogen identification was improved by using combinations of multiple databases compared to that of individual databases. When the approach was applied to environmental metagenomes, metagenomes associated with activated sludge were estimated with higher MPII than other environments (i.e., drinking water, ocean water, ocean sediment, and freshwater sediment). The calculated MPII values were statistically distinguishable among different environments (p < 0.05). These results demonstrate that the suggested approach allows more for more accurate identification of the pathogens associated with metagenomes.

• 한국식물병리학회지
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• 제13권2호
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• pp.125-128
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• 1997

Reactions of Pseudomonas syringae pv. actinidiae to 95 carbon sources in a 96-well microplate (BiOLOG GN MicroPlateTM) were investigated. The bacterium used 9 carbon sources such as D-mannitol, sucrose, etc., but did not use 62 carbon sources such as $\alpha$-cyclodextrin, dextrin, etc. Based on the reactions, a user data base for identification of P. syringae pv. actinidiae was constructed in Biolog program (BiOLOG MicroLogTM 2 system). P. syringae pv. actinidiae isolates collected from kiwifruits could be identified automatically with high similarity using the user data base, which could diagnose rapidly and easily whether the tree was infected with bacterial canker or not.

• 치위생과학회지
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• 제9권2호
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• pp.249-255
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• 2009

본 연구는 성인성 치주염 환자의 치은연하 치면세균막을 총 60개 치아에서 채취하여 F. nucleatum과 A. actinomycetemcomitans의 동정을 위해 세균배양법, single PCR법 및 mutliplex PCR법을 실시하였고, 세균 동정법간의 비교를 통해 다음과 같은 결과를 얻었다. 1. F. nucleatum과 A. actinomycetemcomitans의 동정을 위해 세균배양법, single PCR 및 multiplex PCR을 실시한 결과 F. nucleatum은 각각 12개(20.0%), 45개(75.0%), 43개(71.7%) 치아에서 양성반응을 보였지만, A. actinomycetemcomitans는 각각 0개(0.0%), 4개(6.7%), 1개(1.7%) 치아에서 양성반응이 나타났다. 2. F. nucleatum은 세균배양법에 비해 single PCR법 및 multiplex PCR법에서 높은 검출 빈도를 보여 좀 더 효율적인 세균 동정법으로 생각되었지만, 통계적으로는 유의한 차이가 없었다. 3. A. actinomycetemcomitans는 세균배양법에서 전혀 검출되지 않아 통계적으로 검정할 수 없었고, 세균 동정법간의 비교도 어려웠다. 4. F. nucleatum과 A. actinomycetemcomitans의 동정을 위한 single PCR법과 multiplex PCR법 간의 비교에서 두 세균 모두 검출 빈도에 있어서는 큰 차이를 보이지 않았지만, 통계적으로는 유의한 차이를 보였다.

• Fisheries and Aquatic Sciences
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• 제22권7호
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• pp.14.1-14.8
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• 2019

Olive flounder (Paralichthys olivaceus) is the major species developed for aquaculture in South Korea. Over the long history of olive flounder aquaculture, complex and diverse diseases have been a major problem, negatively impacting industrial production. Vibriosis is a prolific disease which continuously damages olive flounder aquaculture. A bacterial disease survey was performed from January to June 2017 on 20 olive flounder farms on Jeju Island. A total of 1710 fish were sampled, and bacteria from the external and internal organs of 560 fish were collected. Bacterial strains were identified using 16 s rRNA sequencing. Twenty-seven species and 184 strains of Vibrio were isolated during this survey, and phylogenetic analysis was performed. Bacterial isolates were investigated for the distribution of pathogenic and non-pathogenic species, as well as bacterial presence in tested organs was characterized. V. gigantis and V. scophthalmi were the dominant non-pathogenic and pathogenic strains isolated during this survey, respectively. This study provides data on specific Vibrio spp. isolated from cultured olive flounder in an effort to provide direction for future research and inform aquaculture management practices.

• 대한수의학회지
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• 제33권1호
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• pp.119-123
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• 1993

The present study was intended to use the avidin-biotin-peroxidase-antiperoxidase complex (ABPAP) method for the identification of Mycobacterium bovis in the tissue sections of infected cattle. Antibodies and linksera for ABPAP procedure used in incubated order were rabbit anti-Mycobacterium polyvalent antibodies, goat anti-rabbit IgG, rabbit peroxidase-antiperoxidase complex, biotinyl-horse anti-rabbit IgG, and avidin-biotin-peroxidase complex. Where the bacterial antigen was localized by ABPAP, a dark brown deposit occurred in the cytoplasms of macrophages and Langerhans' giant cells of the granulomatous lesions. The method approved to be highly specific for the identification of the bacteria and allowed a precise localization of the bacterial antigen in infected cells.

• Journal of Ginseng Research
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• 제46권1호
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• pp.1-10
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• 2022

Ginseng has been well-known as a medicinal plant for thousands of years. Bacterial endophytes ubiquitously colonize the inside tissues of ginseng without any disease symptoms. The identification of bacterial endophytes is conducted through either the internal transcribed spacer region combined with ribosomal sequences or metagenomics. Bacterial endophyte communities differ in their diversity and composition profile, depending on the geographical location, cultivation condition, and tissue, age, and species of ginseng. Bacterial endophytes have a significant effect on the growth of ginseng through indole-3-acetic acid (IAA) and siderophore production, phosphate solubilization, and nitrogen fixation. Moreover, bacterial endophytes can protect ginseng by acting as biocontrol agents. Interestingly, bacterial endophytes isolated from Panax species have the potential to produce ginsenosides and bioactive metabolites, which can be used in the production of food and medicine. The ability of bacterial endophytes to transform major ginsenosides into minor ginsenosides using β-glucosidase is gaining increasing attention as a promising biotechnology. Recently, metabolic engineering has accelerated the possibilities for potential applications of bacterial endophytes in producing beneficial secondary metabolites.

• International Journal of Oral Biology
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• 제40권1호
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• pp.41-50
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• 2015

The aim of this study was to identify bacteria isolated from the oral cavities and to determine their antimicrobial susceptibility against eight antibiotics. The bacterial strains were obtained from the Korean Collection for Oral Microbiology (KCOM). The bacteria were identified by comparing 16S rDNA sequences at the species level. The data showed that 77 bacterial strains were predominantly identified as streptococci (49.4%) and staphylococci (14.3%). Minimum inhibitory concentrations (MIC) were determined using a broth dilution assay to test the sensitivity of the bacterial strains. The MIC values of the oral bacterial strains against antibiotics were different. Streptococci were sensitive to clindamycin, cefuroxime axetil, and vancomycin, and they were resistant to tetracycline. Staphylococci also were sensitive to clindamycin, cefuroxime axetil, and vancomycin, and they were resistant to penicillin antibiotics. Gramnegative bacterial strains were sensitive to tetracycline and were resistant to clindamycin. These results suggest that the antimicrobial susceptibility test is necessary in deciding the prescription for antibiotics, to prevent the misuse or abuse of antibiotics.

• Fisheries and Aquatic Sciences
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• 제26권10호
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• pp.593-604
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• 2023

Post-harvest handling and hygienic level of aquatic products significantly affect the quality and level of safety. Cold chain control is one of the determining factors for the quality of fish and the bacterial community that grows on the fish. Identification of spoilage bacteria and pathogens in aquatic products must be made because it will determine the physical and chemical quality. A molecular identification method with high sensitivity is the solution. This study aims to identify the quality of fish and bacterial communities that grow. The research procedures included sample collection, pH measurement, drip loss measurement, transportation and cold storage treatment, DNA extraction, DNA sequencing, sequence analysis, and bioinformatics analysis. The conclusion obtained from this study is that the simulation of the cold chain system applied to eastern little tuna does not significantly affect changes in the water activity value, pH, and drip loss. The insignificant change indicates that the eastern little tuna samples are still in good quality. The bioinformatics analysis showed the highest diversity and abundance of the bacterial community came from the Gammaproteobacterial class.

• 식물병연구
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• 제29권1호
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• pp.39-44
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• 2023

To diagnose lily fasciation, lily bulbs showing fasciation were collected from several greenhouses in Jeju Island, South Korea. Bacteria were isolated from the lily bulbs and amplified with both primers for fasA in plasmid and for putative glycosyltransferase epsH gene in chromosome of Rhodococcus fascians. Three bacterial isolates were detected with the P450 primer set and identified as R. fascians by NCBI blast analysis. Twelve bacterial isolates were identified as R. fascians using RS02785 primer set, including the three bacterial isolates identified as the same pathogen using the P450 primer set. Pathogenicity of these bacterial strains identified as R. fascians was demonstrated. Apparent symptoms were observed on wounded lily leaves after inoculation with each bacterial suspension whereas no symptom was found on lily leaves treated with H₂O. Furthermore, bacteria re-isolated from wounded sites were identified as R. fascians. Based on the results, these two sets of primers are recommended for quarantine of R. fascians.

• Genomics & Informatics
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• 제20권4호
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• pp.47.1-47.13
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• 2022

Klebsiella pneumoniae is a gram-negative bacterium that is known for causing infection in nosocomial settings. As reported by the World Health Organization, carbapenem-resistant Enterobacteriaceae, a category that includes K. pneumoniae, are classified as an urgent threat, and the greatest concern is that these bacterial pathogens may acquire genetic traits that make them resistant towards antibiotics. The last class of antibiotics, carbapenems, are not able to combat these bacterial pathogens, allowing them to clonally expand antibiotic-resistant strains. Most antibiotics target essential pathways of bacterial cells; however, these targets are no longer susceptible to antibiotics. Hence, in our study, we focused on a hypothetical protein in K. pneumoniae that contains a DNA methylation protein domain, suggesting a new potential site as a drug target. DNA methylation regulates the attenuation of bacterial virulence. We integrated computational-aided drug design by using a bioinformatics approach to perform subtractive genomics, virtual screening, and fingerprint similarity search. We identified a new potential drug, koenimbine, which could be a novel antibiotic.