• Asian-Australasian Journal of Animal Sciences
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• v.30 no.8
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• pp.1198-1205
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• 2017

Objective: An experiment was conducted to isolate and identify new methanogens in Korea from an anaerobic digester that uses pig slurry. Methods: An anaerobic digestate sample was collected from an anaerobic digester using pig slurry. Pre-reduced media were used for the growth and isolation of methanogens. Growth temperature range, pH range, NaCl concentration range, substrate utilization, and antibiotic tolerance were investigated to determine the physiological characteristics of isolated methanogens. The isolates were also examined microscopically for their morphology and Gram-stained. Polymerase chain reaction of 16S rRNA and mcrA gene-based amplicons was used for identification purpose. Results: Four strains, designated KOR-3, -4, -5, and -6, were isolated and were non-motile, irregular coccoid, and 0.5 to $1.5{\mu}m$ in diameter. Moreover, the cell walls of isolated strains were Gram-negative. KOR-3 and KOR-4 strains used acetate for methane production but did not use $H_2+CO_2$, formate, or methanol as a growth substrate KOR-5 and KOR-6 strains utilized acetate, methanol, and trimethylamine for methanogenesis but did not use $H_2+CO_2$ or formate as a growth substrate. The optimum temperature and pH for growth of four strains were $39^{\circ}C$ and 6.8 to 7.2, respectively. The optimum concentration of NaCl for growth of KOR-3, KOR-5, and KOR-6 were 1.0% (w/v). The optimum NaCl concentration for KOR-4 was 0.5% (w/v). All of the strains tolerated ampicillin, penicillin G, kanamycin, streptomycin, and tetracycline; however, chloramphenicol inhibited cell growth. Phylogenetic analysis of 16S rRNA and mcrA genes demonstrated that strains KOR-3, -4, -5, and -6 are related to Methanosarcina mazei (M. mazei, 99% sequence similarity). Conclusion: On the basis of physiological and phylogenetic characteristics, strains KOR-3, -4, -5, and -6 are proposed to be new strains within the genus Methanosarcina, named M. mazei KOR-3, -4, -5, and -6.

• Journal of Microbiology and Biotechnology
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• v.16 no.10
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• pp.1554-1560
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• 2006

A Gram-positive, aerobic or facultative anaerobic, non motile, endospore-forming bacterial strain, designated Gsoil $114^T$, was isolated from a soil sample of a ginseng field in Pocheon Province (South Korea), and was characterized taxonomically by using a polyphasic approach. It grew well on nutrient agar medium and utilized a limited number of organic substrates as sole carbon sources, including D-xylose and some other carbohydrates, but did not utilize L-amino acids and organic acids. The isolate was positive for oxidase test but negative for catalase, and negative for degradation of macromolecules such as starch, cellulose, xylan, casein, chitin, and DNA. The G+C content of the genomic DNA was 41.8 mol%. The predominant isoprenoid quinone was menaquinone 7 (MK-7). The major fatty acids were $anteiso-C_{15:0}$ (32.1%), $iso-C_{15:0}$ (30.5%), and $anteiso-C_{17:0}$ (30.2%). Comparative 16S rRNA gene sequence analysis showed that strain Gsoil $114^T$ fell within the radiation of the cluster comprising Bacillus species and joined Bacillus shackletonii LMG $18435^T$ with a bootstrap value of 95%. The highest 16S rRNA gene sequence similarities were found with Bacillus shackletonii LMG $18435^T$ (97.6%), Bacillus acidicola DSM $14745^T$ (96.9%), Bacillus sporothermodurans DSM $10599^T$ (96.5%), and Bacillus oleronius DSM $9356^T$ (96.5%). The phylogenetic distance from any other validly described species within the genus Bacillus was less than 96%. DNA-DNA hybridization experiments showed that the DNA-similarities between strain Gsoil $114^T$ and closest phylogenetic neighbors were less than 39%. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil $114^T$ (=KCTC $13944^T$=DSMZ $18134^T$) was classified in the genus Bacillus as the type strain of a novel species, for which the name Bacillus ginsengihumi sp. nov. is proposed.

• Korean Journal of Clinical Laboratory Science
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• v.47 no.4
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• pp.286-291
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• 2015

Equol has beneficial effects on human health. Fermented soy products contain equol, and many microbes participate in the equol production process. This study investigated fermented Korean soybean paste, doenjang. Thirty seven doenjang samples collected from different manufacturers were examined. Equol was detected in 3 samples (D2, D13, and D19) at the maximum content of 507 ng/100 g by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Fifteen microbial species were isolated and identified by 16S rRNA gene sequence analysis and by matrix assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS). Bacillus spp, Paenibacillus spp, Tetragenococcus spp, Stapylococcus spp, and Clostridium species were the predominant bacteria in equol containing doenjang samples.

• Journal of Mushroom
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• v.13 no.4
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• pp.305-309
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• 2015

In order to isolate compost-promoting bacteria with high activity of cellulase and xylanase, spent mushroom substrates with sawdust were collected from mushroom cultivation farm, Jinju, Gyeongnam in Korea. Among of the isolates, one strain, designated CA105 was selected by agar diffusion method. The strain CA105 was identified as members of the Bacillus subtilis by biochemical characteristics using VITEK 2 system. Comparative 16S rRNA gene sequence analysis showed that isolate CA105 formed a distinct phylogenetic tree within the genus Bacillus and was most closely related to Bacillus subtilis with 16S rRNA gene sequence similarity of 98.9%. On the basis of its physiological properties, biochemical characteristics and phylogenetic distinctiveness, isolate CA105 was classified within the genus Bacillus subtilis, for which the name Bacillus subtilis CA105 is proposed. The cellulase and xylanase activity of B. subtilis CA105 was slightly increased according to bacterial population from exponential phase to stationary phase in growth curve for Bacillus sp. CA105.

• Journal of Practical Agriculture & Fisheries Research
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• v.22 no.2
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• pp.51-58
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• 2020

Continuous mortality in commercially cultured Japanese eel (Anguilla japonica), showing symptoms of dermal ulcerations and focal hemorrhages on the body, occurred on a private farm in November, 2019 in Korea. A series of mortality had been described in one local eel culture farm from November to December in 2019. From the three cases, three isolates of Vibrio spp. were recovered from the blood, ascitic fluid, and kidney of the dead fish, respectively. Based on the 16S rRNA sequence comparisons, the Vibrio isolates from the 1^st and 3^rd cases (strain named 1E1-2 and 3K1-2) were identified as V. fluvialis and the isolate from the 2^nd case was identified as V. plantisponsor (strain named 2A3-1). Moreover, the 16S rRNA-based phylogenetic analysis revealed that strain 1E1-2 and 3K1-2 were most similar to V. fluvialis NBRC 103150^T, and strain 2A3-1 was most similar to V. plantisponsor NBRC103148^T. According to the results of the antibiotic resistance determination, V. fluvialis 1E1-2 showed intermediate resistance to tetracycline and chloramphenicol, and was resistant to trimethoprim-sulfamethoxazole. V. plantisponsor 2A3-1 showed intermediate resistance to ciprofloxacin and levofloxacin, and was resistant to trimethoprim-sulfamethoxazole. V. fluvialis 3K1-2 showed intermediate resistance to tetracycline, and was resistant to ampicillin and trimethoprim-sulfamethoxazole. These results have provided the evidences on the occurrence of antibiotic-resistant Vibrio infection in commercially cultured Japanese eels are present in Korea.

• Journal of Microbiology and Biotechnology
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• v.27 no.9
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• pp.1566-1575
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• 2017

MicroRNAs (miRNAs) are abundant in bovine milk and milk derived from other livestock, and they have functional roles in infants and in the secretion process of mammary glands. However, few studies have evaluated miRNAs in dairy processes, such as during cheese making and ripening. Thus, we investigated the characteristics of milk-derived miRNAs during the manufacturing and ripening of Camembert cheese as well as the microbiota present using the quantitative reverse transcription polymer chain reaction (RT-qPCR) and 16S rRNA pyrosequencing, respectively. Pyrosequencing showed that the cheese microbiota changed dramatically during cheese processing, including during the pasteurization, starter culture, and ripening stages. Our results indicated that the RNA contents per $200mg/200{\mu}l$ of the sample increased significantly during cheese-making and ripening. The inner cheese fractions had higher RNA contents than the surfaces after 12 and 22 days of ripening in a time-dependent manner (21.9 and 13.2 times higher in the inner and surface fractions than raw milk, respectively). We performed a comparative analysis of the miRNAs in each fraction by RT-qPCR. Large amounts of miRNAs (miR-93, miR-106a, miR-130, miR-155, miR-181a, and miR-223) correlated with immune responses and mammary glands were present in aged cheese, with the exception of miR-223, which was not present on the surface. Considerable amounts of miRNAs were also detected in whey, which is usually disposed of during the cheese-making process. Unexpectedly, there were no significant correlations between immune-related miRNAs and the microbial populations during cheese processing. Taken together, these results show that various functional miRNAs are present in cheese during its manufacture and that they are dramatically increased in amount in ripened Camembert cheese, with differences according to depth.

• Korean Journal of Microbiology
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• v.42 no.1
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• pp.26-33
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• 2006

To understand the efficient process of biological nitrogen removal (BNR) system, the structure of bacterial communities in nitrification reactors was analyzed using PCR and terminal restriction fragment length poly morphism (I-RFLP) methods. In this study, we used an advanced treatment system with plotting media, Nutrient Removal Laboratory system, or the rumination type sequencing batch reactor (SBR) system. The terminal restriction fragments of ammonia-oxidizing bacteria (AOB) and other $\beta-proteobacteria$ were observed in all of three BNR systems. The nucleotide sequence analysis of terminal restriction fragments showed that Nitrosomonas and Nitrosolobus were major populations of AOB in SBR system, whereas uncultured $\beta-proteobacteria$ and Cardococcus australiensis were the predominant groups in other two BNR systems. Also the SBR system may be more efficient to enrich AOB. These results indicate that the different structure of bacterial community may be developed depending on the wastewater treatment systems, although the same influent is used.

• 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.

• Journal of Environmental Health Sciences
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• v.48 no.3
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• pp.176-182
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• 2022

Background: The risk of imported infectious diseases has been increasing with the annual rise in the number of international travelers. Objectives: This study aims to analyze the distribution and characteristics of intestinal bacteria isolated in 2019 from residents of Chungcheongnam-do Province with experience of travelling overseas. Methods: Twenty-three former overseas travelers with diarrhea were analyzed to detect viruses and bacteria according to the Manual for Detection of Foodborne Pathogens at Outbreaks. Additionally, antibiotic susceptibility tests and 16s rRNA sequencing were performed. Results: Twenty-five strains of ten pathogens were isolated from 18 samples. Pathogenic E. coli was the most common at 57.7%, followed by Clostridium perfringens (15.4%), Campylobacter spp. (7.7%), and Salmonella spp. (7.7%). The serotype of Salmonella was confirmed as Salmonella Braenderup, II 9,46:g,[m],[s],t:[e,n,x]. Conclusions: It was confirmed that the major enteric bacterial pathogens isolated from overseas travelers in Chungcheongnam-do Province were pathogenic E. coli, as found in other studies. The study on Plesiomonas shigelloides is meaningful in that it is reported as a rare case of infection in Korea. Antibiotic resistance and 16s rRNA analysis were performed, which is expected to provide important basic data for the prevention of traveler's diarrhea.

• Mycobiology
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• v.50 no.6
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• pp.439-447
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• 2022

Two strains, YP344 and YP579 were isolated from soil samples in Pocheon City, Gyeonggi Province, South Korea. The strains YP344 and YP579 belong to the genus Vishniacozyma and Dioszegia, respectively. The molecular phylogenetic analysis showed that the strain YP344 was closely related to Vishniacozyma peneaus. Strain YP344T differed by four nucleotide substitutions with no gap (0.70%) in the D1/D2 domain of the LSU rRNA gene and 16 nucleotide substitutions with 8 gaps (5.76%) in the ITS region. On the other hand, the strain YP579^T varied from the type strain of the most closely related species, Dioszegia zsoltii var. zsoltii, by 6 nucleotide substitutions with four gaps (1.64%) in the D1/D2 domain of LSU rRNA gene and 26 nucleotide substitutions with 14 gaps (8.16%) in the ITS region. Therefore, the name Vishniacozyma terrae sp. nov. and Dioszegia terrae sp. nov. are proposed, with type strains YP344T (KCTC27988^T) and YP579^T (KCTC 27998^T), respectively.