• Korean Journal of Veterinary Research
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• v.38 no.2
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• pp.304-313
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• 1998

Sixteen Korean field transmissible gastroenteritis viruses (TGEVs) were isolated using swine testicular cell (STC) and the genomic diversity of them was analyzed. All TGEV isolates produced a typical cytopathic effect in STC and were confirmed as TGEV by immunofluorescence assay using monoclonal antibody against TGEV and PCR using TGEV specific primers. RNAs from TGEV field isolates and vaccine TGEV were extracted and amplified by RT and PCR. The RT-PCR products were digested with selected restriction enzymes and analyzed RFLP patterns. The N-terminal end region of S gene and ORF 3 and 3-1 genes of TGEV amplified by TGEV specific primer pairs seemed to be conserved. Most specific variations were detected in S gene amplified by TGEV 4/6 primer pairs which includes antigenic sites A and D. When the PCR products were treated with Sau3AI and Ssp I, Bvac(vaccine strain), field isolates 133 and 347 were differentiated from Miller and Purdue types. In the case of D5 field isolates, it was classified into Purdue type by Sau 3AI but classified into independent TGEV by Ssp I. Two different TGEV strains from D2 sample were confirmed by plaque purification and RT-PCR-RFLP analysis. To investigate the change occurring in TGEV genome after serial passage, the TGEV P44 strain was passaged through STC. There were specific changes in S gene and a large deletion was observed in ORF 3 and 3-1 genes. These studies showed that a distinct difference in genome exists among TGEV field isolates.

• Journal of Species Research
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• v.4 no.2
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• pp.109-126
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• 2015

As a subset study to discover indigenous prokaryotic species in Korea, a total of 39 bacterial strains assigned to the classes Betaproteobacteria and Gammaproteobacteria were isolated from diverse environmental samples collected from soil, tidal flat, freshwater, seawater, seaweed, wetland, plant roots, guts of insects, and fermented foods. From the high 16S rRNA gene sequence similarity (>99.1%) and formation of a robust phylogenetic clade with the closest species, it was determined that each strain belonged to each independent and predefined bacterial species. There is no official report that these 39 species have been described in Korea; therefore 4 species of 4 genera in the order Burkholderiales and 1 species in the order Neisseriales within the class Betaproteobacteria, and 10 species of 6 genera in the order Alteromonadales, 11 species of 3 genera in the order Pseudomonadales, 4 species of 4 genera in the order Enterobacteriales, 2 species of 2 genera in the order Vibrionales, 1 species in the order Aeromonadales, 3 species of 3 genera in the order Oceanospirillales, 2 species of 2 genera in the order Xanthomonadales, and 1 species in the order Chromatiales within the Gammaproteobacteia are reported for proteobacterial species found in Korea. Gram reaction, colony and cell morphology, basic biochemical characteristics, isolation source, and strain IDs are also described in the species description section.

• Journal of Species Research
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• v.4 no.2
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• pp.97-108
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• 2015

As a subset study to discover indigenous prokaryotic species in Korea, a total of 29 bacterial strains assigned to the classes Alphaproteobacteria were isolated from various environmental samples collected from plant root, ginseng soil, forest soil, marsh, mud flat, freshwater and seawater. From the high 16S rRNA gene sequence similarity (>99.1%) and formation of a robust phylogenetic clade with the closest species, it was determined that each strain belonged to each independent and predefined bacterial species. There is no official report that these 29 species included in Alphaproteobacteria is have been described in Korea; therefore 14 species of 9 genera in the order Rhizobiales, 7 species of 6 genera in the order Sphingomonadales and 4 species of 2 genera in the order Caulobacterales and 3 species in the order Rhodobacterales and 1 species in the order Rhodospirillales found in Korea. Gram reaction, colony and cell morphology, basic biochemical characteristics, isolation source, and strain IDs are also described in the species description section.

• Journal of Species Research
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• v.7 no.2
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• pp.161-180
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• 2018

Fourteen bacterial strains, low10-4-1, J11015, 17J27-22, 17G22-9, 17G9-4, 17Bio_15, 17gy_33, 17SD1_21, Strain8, 17Sr1_17, J21014T, H31021, 17J49-9, and 17J80-6 assigned to the phylum Actinobacteria, Bacteroidetes, Deinococcus-Thermus, and Firmicutes were isolated from soil samples. Phylogenetic analysis based on 16S rRNA gene sequence revealed that strains low10-4-1, J11015, 17J27-22, 17G22-9, 17G9-4, 17Bio_15, 17gy_33, 17SD1_21, Strain8, 17Sr1_17, J21014T, H31021, 17J49-9, and 17J80-6 were most closely related to Marmoricola aurantiacus (98.9%), Calidifontibacter indicus (99.8%), Gordonia soli (98.8%), Rhodococcus globerulus (99.5%), Pseudarthrobacter siccitolerans (99.1%), Hymenobacter qilianensis (98.7%), Hymenobacter terrae (99.0%), Deinococcus yunweiensis (99.2%), Deinococcus proteolyticus (99.7%), Domibacillus indicus (99.2%), Exiguobacterium mexicanum (100.0%), Kurthia senegalensis (99.1%), Lysinibacillus composti (99.6%), and Bacillus loiseleuriae (99.3%). These fourteen species have never been reported in Korea, therefore we report them here for the first time.

• The Journal of Korean Society of Virology
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• v.29 no.2
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• pp.65-74
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• 1999

Reovirus was found to inhabit both the respiratory and the enteric tract of human and animals. The genome of reovirus comprises 10 segments of double-stranded RNA, total size 24 kbp. Nine strains of reovirus were isolated from human and field mice in Korea. Aseptically collected sera from human and lung tissues from field mice were used for virus isolation. For serotype determination, hemagglutination inhibition test was used, and three strains were confirmed to type 2 and six strains to type 3. To determine the genomic diversity and molecular phylogeny of reoviruses isolated in Korea, part of S4 genomic segment of reovirus was enzymatically amplified and directly sequenced. In nucleotide level, Apo98-35 strain showed 15.4%, 19.3%, and 14.4% differences compared to type 1 (T1L, Lang), type 2 (T2J), and type 3 reference strains, respectively. In amino acid level, Apo98-35 strain showed 10.5%, 13.7%, and 9.5% differences compared to type 1, type 2, and type 3 reference strains, respectively. Using the maximum parsimony method based on 285 bp spaning region of the S4 genomic segment, phylogenetic analysis indicated that Apo98-35 from Korea formed different phylogenetic branch. Our data obtained by sequence and phylogenetic analyses of reoviruses are consistent with the distinct geographically dependent evolution of reoviruses in Korea.

• Journal of Species Research
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• v.5 no.2
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• pp.241-253
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• 2016

In 2014, as a subset study to discover indigenous prokaryotic species in Korea, a total of 33 bacterial strains assigned to the class Gammaproteobacteria were isolated from diverse environmental samples collected from soil, tidal flat, freshwater, seawater, oil-contaminated soil, and guts of animal. From the high 16S rRNA gene sequence similarity (>98.5%) and formation of a robust phylogenetic clade with the closest species, it was determined that each strain belonged to each independent and predefined bacterial species. There is no official report that these 33 species have been described in Korea; therefore, 1 strain of the Aeromonadales, 6 strains of the Alteromonadales, 3 strains of the Chromatiales, 5 strains of the Enterobacteriales, 4 strains of the Oceanospirillales, 11 strains of the Pseudomonadales, and 3 strains of the Xanthomonadales within the Gammaproteobacteria are described for unreported bacterial species in Korea. Gram reaction, colony and cell morphology, basic biochemical characteristics, and isolation sources are also described in the species description section.

• Journal of Species Research
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• v.5 no.2
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• pp.206-219
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• 2016

As a subset study to discover indigenous prokaryotic species in Korea, a total of 42 bacterial strains assigned to the class Alphaproteobacteria were isolated from diverse environmental habitats including plant roots, ginseng soil, forest soil, marsh, mud flat, freshwater, and seawater. From the high 16S rRNA gene sequence similarity (>99.1%) and formation of a robust phylogenetic clade with the closest species, it was determined that each strain belonged to each independent and predefined bacterial species. There is no official report that these 42 species have been described in Korea; therefore 4 species of 1 genera in the order Caulobacterales, 18 species of 10 genera in the order Rhizobiales, 7 species of 5 genera in the order Sphingomonadales and 13 species of 11 genera in the order Rhodobacterales within the Alphaproteobacteria are reported for alphaproteobacterial species found in Korea. Gram reaction, colony and cell morphology, basic biochemical characteristics, isolation source, and strain IDs are also described in the species description section.

• Journal of Microbiology
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• v.42 no.2
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• pp.152-155
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• 2004

Pseudomonas sp. K82 has been reported to be an aniline-assimilating soil bacterium. However, this strain can use not only aniline as a sole carbon and energy source, but can also utilize benzoate, p-hydroxybenzoate, and aniline analogues. The strain accomplishes this metabolic diversity by using dif-ferent aerobic pathways. Pseudomonas sp. K82, when cultured in p-hydroxybenzoate, showed extradiol cleavage activity of protocatechuate. In accordance with those findings, our study attempted the puri-fication of protocatechuate 4,5-dioxygenase (PCD 4,5). However the purified PCD 4,5 was found to be very unstable during purification. After Q-sepharose chromatography was performed, the crude enzyme activity was augmented by a factor of approximately 4.7. From the Q-sepharose fraction which exhibited PCD 4,5 activity, two subunits of PCD4,5 (${\alpha}$ subunit and ${\beta}$ subunit) were identified using the N-terminal amino acid sequences of 15 amino acid residues. These subunits were found to have more than 90％ sequence homology with PmdA and PmdB of Comamonas testosteroni. The molecular weight of the native enzyme was estimated to be approximately 54 kDa, suggesting that PCD4,5 exists as a het-erodimer (${\alpha}$$_1$${\beta}$$_1$). PCD 4,5 exhibits stringent substrate specificity for protocatechuate and its optimal activity occurs at pH 9 and 15 $^{\circ}C$. PCR amplification of these two subunits of PCD4,5 revealed that the ${\alpha}$ subunit and ${\beta}$ subunit occurred in tandem. Our results suggest that Pseudomonas sp. K82 induced PCD 4,5 for the purpose of p-hydroxybenzoate degradation.

• Journal of Species Research
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• v.7 no.3
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• pp.222-230
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• 2018

Six bacterial strains 18JY42-3, 18SH, 18JY76-11, 17J11-11, 18JY14-14, and 18JY15-11 assigned to the phylum Proteobacteria, Firmicutes, and Actinobacteria were isolated from soil samples in Korea. The Cohnella species, strain 18JY42-3 was Gram-stain-positive, short rod-shaped and beige-colored. The Methylobacterium species, strains 18SH and 18JY76-11 were Gram-stain-negative, short rod-shaped and pink-colored. The Microterricola species, strain 17J11-11 was Gram-stain-positive, short rod-shaped and yellow-colored. The Paenarthrobacter species, strains 18JY14-14 and 18JY15-11 were Gram-stain-positive, short rod-shaped and white-colored. Phylogenetic analysis based on 16S rRNA gene sequence showed that strains 18JY42-3, 18SH, 18JY76-11, 17J11-11, 18JY14-14, and 18JY15-11 were most closely related Cohnella rhizosphaerae (MH497628; 98.8%), Methylobacterium goesingense (MH497632; 99.1%), Methylobacterium populi (MH497635; 99.9%), Microterricolagilva (MH504108; 98.4%), Paenarthrobacter nicotinovorans (MH497641; 100%), and Paenarthrobacter nitroguajacolicus (MH497646; 99.2%), respectively. All the six unrecorded strains showed resistance to UV radiation. This is the first report of these six species in Korea.

• Mycobiology
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• v.47 no.2
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• pp.230-241
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• 2019

The Great Sebkha of Oran is a closed depression located in northwestern of Algeria. Despite the ranking of this sebkha among the wetlands of global importance by Ramsar Convention in 2002, no studies on the fungal community in this area have been carried out. In our study, samples were collected from two different regions. The first region is characterized by halophilic vegetation and cereal crops and the second by a total absence of vegetation. The isolated strains were identified morphologically then by molecular analysis. The biotechnological interest of the strains was evaluated by testing their ability to grow at different concentration of NaCl and to produce extracellular enzymes (i.e., lipase, amylase, protease, and cellulase) on solid medium. The results showed that the soil of sebkha is alkaline, with the exception of the soil of cereal crops that is neutral, and extremely saline. In this work, the species Gymnoascus halophilus, Trichoderma gamsii, the two phytopathogenic fungi, Fusarium brachygibbosum and Penicillium allii, and the teleomorphic form of P. longicatenatum observed for the first time in this species, were isolated for the first time in Algeria. The halotolerance test revealed that the majority of the isolated are halotolerant. Wallemia sp. and two strains of G. halophilus are the only obligate halophilic strains. All strains are capable to secrete at least one of the four tested enzymes. The most interesting species presenting the highest enzymatic index were Aspergillus sp. strain A4, Chaetomium sp. strain H1, P. vinaceum, G. halophilus, Wallemia sp. and Ustilago cynodontis.