• Korean Journal of Microbiology
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• v.45 no.2
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• pp.208-214
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• 2009

To avoid ambiguity in counting the number of colony, about 1,500 of colonies grown on B. cereus selective agar plates were grouped into 12 types by morphological difference and then identified by biochemical and 16S rDNA nucleotide sequence. Among them, seven colony types with 11 to 15 mm diameters of halo were identified as B. cereus or B. cereus subsp. cytotoxis. Five mm sized colonies with no halo, which have not been considered as B. cereus according to the manufacturer's manual, were identified as B. cereus. A colony type with double halos of only 6 mm in diameter was also B. cereus. Other three types were proven to be Enterococcus sp., Brevibacillus sp., and B. subtilis, respectively. PCR results showed that only 9 types that are identified as B. cereus strains harbor at least one of B. cereus toxin genes.

• Korean journal of applied entomology
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• v.55 no.4
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• pp.459-464
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• 2016

An outbreak of the migratory locust, Locusta migratoria, in the environment-friendly reclaimed plantations of forage crops in Sanyimyeon, Haenam-gun, Jellanam-do, Korea in August 2014 caused severe damages to various crops. Owing to its first occurrence in the Korean history, the causes underlying the outbreak and phase-transition of the migratory locust were not known. It is critical to establish the genetic relationship of the migratory locust in Sanyimyeon, Haenam-gun with the other previously reported strains in the world in order to understand the mechanisms responsible for its outbreak. The gene sequences of the 16S ribosomal RNA (rRNA) and displacement-loop (D-loop) of the mitochondria of various regional species of the migratory locust were used to perform the phylogenetic analysis. Our results suggested that the migratory locusts in Sanyimyeon, Haenam-gun are closely related with the Eurasian strains of the northern lineage. In future, these two mitochondrial genes can be used for elucidating the genetic population structures in migratory locusts in various regions. In addition, the sequence information of these genes can be used to enhance our understanding of the genetic basis of the outbreak of migratory locusts.

• Microbiology and Biotechnology Letters
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• v.34 no.3
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• pp.204-210
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• 2006

Ethyl (S)-4-chloro-3-hydroxybutyrate is a useful intermediate for the synthesis of Atorvastatin, a chiral drug to hypercholesterolemia. In this research, two 4-chloro-3-hydroxybutyro-nitrile-degrading strains were isolated from soil sample. They were identified as Rhodococcus erythropolis strains by 16S rRNA analysis. The nitrile-degrading enzyme(s) were suggested to be nitrile hydratase and amidase rather than nitrilase from the result of thin layer chromatography analysis. The corresponding genes were obtained by PCR cloning method. The predicted protein sequences had identities more than 96% with nitrile hydratase ${\alpha}-subunit$, nitrile hydratase ${\beta}-subunit$, and amidase of R. erythropolis. The 4-chloro-3-hydroxybutyronitrile-hydrolyzing activities in both strains were increased dramatically by ${\varepsilon}-caprolactam$ which was known as good inducer for nitrile hydratase. Both intact cells and cell-free extract could hydrolyze the nitrile compound. So, the intact cell and the enzymes could be used as potential biocatalyst for the production of 4-chloro-3-hydroxybutyric acid.

• Journal of Life Science
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• v.27 no.4
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• pp.435-441
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• 2017

Perchlorate ($ClO_4^-$) is an emerging contaminant detected in soil, groundwater, and surface water. Previous study revealed bacterial community in the enrichment culture tdegraded perchlorate using elemental sulfur as an electron donor. Quantitative and qualitative molecular methods were employed in this study to investigate archaeal community in the enrichment culture. Real-time qPCR showed that archaeal 16S rRNA gene copy number in the culture was about 1.5% of bacterial 16S rRNA gene copy number. This suggested that less archaea were adapted to the environment of the enrichment culture and bacteria were dominant. DGGE banding pattern revealed that archaeal community profile of the enrichment culture was different from that of the activated sludge used as an inoculum for the enrichment culture. The most dominant DGGE band of the enrichment culture was affiliated with Methanococci. Further research is necessary to investigate metabolic role of the dominant archaeal population to better understand microbial community in the perchlorate-reducing enrichment culture.

• Journal of Korean Society of Environmental Engineers
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• v.33 no.11
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• pp.847-854
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• 2011

To deal with issues from global climate changes, renewable bioenergy has become important. Algae have been regarded as a good resource for biorefinery and bioenergy, and also have potential capability to remove nutrient and non-decompositional pollutants for wastewater advanced treatment. Although algal-bacterial ecological interaction would be a crucially important factor in using algae for wastewater advanced treatment and resource recovery from wastewater, very little is known about ecological interaction between algae and bacteria in a real wastewater environment. In this study, under a real municipal wastewater condition, we characterized wastewater pollutant treatability and bacterial communities in response to growth of Ankistrodesmus gracilis SAG278-2, which can grow in wastewater and has a high lipid contents. The growth of algal population using the wastewater was inhibited by increase in wastewater bacteria while bacterial survival and cellular decay rate were not influenced by the algal growth. Removals of recalcitrant organic matters and total nitrogen were improved in the presence of algal growth. According to T-RFLP and statistical analysis, algal growth affected time-course changes in bacterial community structures. The following 16S rRNA gene amplicon, cloning results showed that the algal growth changes in bacterial community structure, and that bacterial populations belonging to Sediminibacterium, Sphingobacterium, Mucilaginibacter genera were identified as cooperative with the algal growth in the wastewater.

• Korean Journal of Microbiology
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• v.42 no.1
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• pp.19-25
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• 2006

This study was undertaken to develop PCR primers for the identification and detection of Streptococcus mutans (by)using species-specific forward and universal reverse primers. These primers targeted the variable regions of the 16S ribosomal RNA coding gene (rDNA). The primer specificity was tested against 11S. mutans strains and 10 different species (22 strains) of oral bacteria. The primer sensitivity was determined by testing serial dilutions of the purified genomic DNA of S. mutans ATCC $25175^T$. The data showed that species-specific amplicons were obtained from all the S. mutans strains tested, which was not observed in the other species. The direct and nested PCR could detect as little as 2 pg and 2 fg of the chromosomal DNA from S. mutans ATCC $25175^T$, respectively. This shows that the PCR primers are highly sensitive and applicable to the detection and identification of S. mutans.

• Korean Journal of Environmental Biology
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• v.29 no.3
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• pp.126-137
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• 2011

Although Sumunmulbangdui wetland at the Halla Mountain in Jeju Island, a kind of montane wetlands, has been considered to bear high biodiversity, no study has been reported on the bacterial diversity. In this study, soil and water samples were collected from the wetland in order to isolate novel bacterial species. Bacterial strains belonging to the phyla Bacteroidetes, Firmicutes, and Actinobacteria were isolated after spreading soil and water samples onto solid agar media. The 16S rRNA gene sequences of the strains assigned to the three phyla were compared to those of type strains of the species in the phyla. The strains that showed less than 98.7% 16S rRNA gene sequence similarity to the validly published species were considered to be novel species candidates. A total of 32 strains were regarded as novel species candidates in the phyla Bacteroidetes, Firmicutes, and Actinobacteria. Diversity of novel species candidates was very low; the candidates were confined to only few genera. In the Bacteroidetes, 13 novel candidate species were affiliated with the genera Mucilaginibacter, Sphingobacterium, Pedobacter, Flavobacterium, and Chryseobacterium. A total of 13 novel candidate species that assigned to the genera Paenibacillus Lysinibacillus, and Bacillus were identified in the phylum Firmicutes. Only two candidate species that belonged to the genera Mycobacterium and Nocardia were excavated in the Actinobacteria. Cultural, physiological, and chemotaxonomic characteristics have been determined for the novel species candidates, and the characteristics are described in this study.

• Korean Journal of Clinical Laboratory Science
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• v.49 no.4
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• pp.413-419
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• 2017

Four imipenem-resistant bacteria were isolated from the clinical specimens of a patient with pneumonia. To identify the isolates, we used the GN card of Vitek II system and performed a phylogenetic analysis based on 16S rRNA gene sequence. The isolates were identified as P. aeruginosa (2 strains), P. monteilii (1 strain), and P. putida (1 strain), and were tested for antibiotic resistance after determining the MIC of imipenem to be $${\geq_-}8{\mu}g/mL$$ using the AST-N225 card of Vitek II system. The imipenem-resistant genotypes were determined using PCR products amplified using specific ${\beta}-Lactamase$ gene primers. The MBL gene was identified in all four isolates. One strain of P. aeruginosa exhibited the VIM and SHV-1 type genes, while the other strain exhibited both VIM and OXA group II genes. According to the antimicrobial susceptibility test, the bacteria were more susceptible to amikacin than other antibiotics. DNA fingerprint analysis using ERIC-PCR to analyze the epidemiological relationship between strains estimated that both the P. aeruginosa isolates were similar, but exhibited different DNA band types. It is uncommon to find four strains of imipenem-resistant bacteria with different DNA band types in a single patient.

• Journal of Life Science
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• v.26 no.6
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• pp.711-720
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• 2016

To determine the degree of common genes and the phylogenetic relationships among genome-sequenced 680 prokaryotes, the similarities among 4,631 clusters of orthologous groups of protein (COGs)’ presence/ absence and gene content trees were analyzed. The number of COGs was in the range of 103–2,199 (mean 1377.1) among 680 prokaryotes. Candidatus Nasuia deltocephalinicola str. NAS-ALF, an obligate symbiont with insects, showed the minimum COG, while Pseudomonas aeruginosa PAO1, an opportunistic pathogen, represented the maximum COG. The similarities between two prokaryotes were 49.30–99.78 % (mean 72.65%). Methanocaldococcus jannaschii DSM 2661 (hyperthermophilic and autotrophic, Euryarchaeota phylum) and Mesorhizobium loti MAFF303099 (mesophilic and symbiotic, alpha-Proteobacteria class) had the minimum amount of similarities. As gene content may represent the potential for an organism to adapt to each habitat, this may represent the history of prokaryotic evolution or the range of prokaryotic habitats at present on earth. COG content trees represented the following. First, two members of Chloroflexi phylum (Dehalogenimonas lykanthroporepellens BL-DC-9 and Dehalococcoides mccartyi 195) showed a greater relationship with Archaea than other Eubacteria. Second, members of the same phylum or class in the 16S rRNA gene were separated in the COG content tree. Finally, delta- and epsilon-Proteobacteria were in different lineages with other Proteobacteria classes in neighbor-joining (NJ) and maximum likelihood (ML) trees. The results of this study would be valuable to identifying the origins of organisms, functional relationships, and useful genes.

• Microbiology and Biotechnology Letters
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• v.31 no.4
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• pp.429-434
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• 2003

The 16S rDNA sequences of nine strains, two type strains of validated Microbispora species and a strain of invalidated Microbispora species, and six soil isolates, were determined and compared with those of representatives of the family Streptosporangiaceae. The phylogenetic analysis indicated that all of the validated species of the genus Microbispora consistently formed a monophyletic unit and were well separated from the other genera of the family Streptosporangiaceae. All the isolates were placed to the genus Microbispora, whereas an invalidated Microbispora species, Microbispora griseoalba IMSNU $22049^{T}$ (= KCTC $9314^{T}$), was closely related to members of the genus Nocardia.