• Korean Journal of Microbiology
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• v.39 no.1
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• pp.45-50
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• 2003

The diversity and change of microbial communities during kimchi fermentation at $4^{\circ}C$ were analyzed by denaturing gradient gel electrophoresis (DGGE). Kimchi samples were taken every 5 days over the fermentation periods (for 60 days) to extract total DNA for DGGE analysis. Touchdown polymerase chain reaction was performed to amplify the V3 region of 16S rRNA gene. Sequencing results of partial 16S rDNA amplicons from DGGE profiles revealed that lactic acid bacteria (LAB), especially Weissella koreensis, Lactobacillus sakei and Leuconostoc gelidum were dominants in kimchi fermentation at $4^{\circ}C$. And we knew that W. koreensis steadily existed throughout the whole fermentation period, also Lb. sakei and Leuc. gelidum appeared from 10th day and 30th day of fermentation time, respectively and then these species were to be dominant microorganisms.

• Korean Journal of Microbiology
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• v.44 no.1
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• pp.29-36
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• 2008

Nitrogen is one of the major pollutants that should be removed by wastewater treatment systems. Biological nitrogen removal (BNR) is a key technology in advanced wastewater treatment systems operated by bacterial populations. Nitrification is the first step of microbiological processes in BNR system. Ammonia is oxidized to nitrite by ammonia-oxidizing bacteria (AOB) and then nitrite is subsequently oxidized to nitrate by nitrite-oxidizing bacteria (NOB). The diversity of NOB in nitrification reactors of 3 BNR systems, Edited biological aerated filter system, Nutrient removal laboratory system, and the Rumination type sequencing batch reactor system, was investigated by terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes. Cluster analysis of T-RF profiles showed that communities of Nitrobacter group in each system were different depending upon the process of systems. However, the clusters of Nitrospira group were divided by the habitat of aqueous and solid samples.

• Microbiology and Biotechnology Letters
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• v.39 no.2
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• pp.133-139
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• 2011

In this study, we determined the changes in microbial numbers in solar salts according to the manufacturing process and storage duration. The salt samples were harvested from salt farms in Shinan (area 2) and Yeonggwang (area 1). They were serially diluted ten-fold and then placed on 4 kinds of cultivable media (mannitol salt agar, eosin methylene blue, plate count agar, and trypticase soy agar). After incubation, we obtained 62 halophilic isolates from the salt samples. Coliform and general bacteria were not detected in all salt samples. By 16S rRNA sequencing analysis, we found 12 kinds of halophilic bacteria belonging to the genera Halobacillus, Halomonas, Bacillus, Idiomarina, Marinobacter, Pseudoalteromonas, Vibrio, Salinivibrio, Virgibacillus, Alteromonas, Staphylococcus and some un-known stains. In our study, we discovered two novel species that have a 16S rDNA sequence similarity below 97%.

• Korean Journal of Environmental Biology
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• v.28 no.4
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• pp.223-230
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• 2010

To investigate the variations of physico-chemical factors in four stations (Hanlim, Aewol, Sinchon, Hamdeok) at Jeju coastal area, Water temperature, Salinity, dissolved oxygen (DO), pH, chemical oxygen demand (COD), suspended solid (SS), ammonia-nitrogen ($NH_4-N$), nitrite-nitrogen ($NO_3-N$), nitrate-nitrogen ($NO_2-N$) were analysed. The ranges of water temperature were from 26.23 to $28.6^{\circ}C$, the salinity were from 31.4 to 32.88‰, the pH were from 8.15 to 8.35, the chemical oxygen were from 0.48 to 0.91 mg $L^{-1}$. A total of 52 strains of marine actinomycetes was isolated from Jeju Island coastal area. They were characterized by determining morphological and physio-biochemical properties, the API kit and confirmed by molecular methods including partial sequencing of 16S rRNA. A neighbor-joining tree of partial 16S rRNA sequences divided the 52 isolates in 2 major groups, 22 strains of Gram positive bacteria/Actinobacteria (division)/Actinomycetales (order)/Streptomycineae (suborder)/Streptomycetaceae (family)/Streptomyces (93.1%) and 2 strains of Streptospotangineae (suborder)/Nocardiopsaceae (family)/Nocardiopsis (6.9%).

• 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.

• Asian-Australasian Journal of Animal Sciences
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• v.15 no.7
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• pp.1057-1065
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• 2002

The antagonistic activities of 30 strains of lactobacilli against Helicobacter pylori were determined and Lactobacillus helveticus CU631 has been selected as the strain which possesses the strongest inhibitory effect in the disc diffusion assay showing inhibition zone diameter of $10{\pm}1.5mm$, whereas those of L. plantarum and L. fermentum have been shown to be $4.0{\pm}0.6mm$. H. pylori G88016 revealed the highest vacuolating toxin producing activity among the 8 strains, the inhibitory activity of L. helveticus CU631 in vacuolating toxin producing activity of H. pylori manifested in the co-culture of two strains and in the 5:5 mixture of supernatant of the two strains. Both L. helveticus CU631 and cell free culture supernatant had a strong inhibitory activities in urease and cytotoxin producing activities of H. pylori NCTC11637 and CJH12. An accelerated proteolytic activity of water soluble peptides by L. helveticus CU631 during the refrigeration storage has been manifested in the cream cheese. DNA seqences of 16S-23S ribosomal RNA spacer region showed typical pattern among the various strains of L. helveticus, which could be used in the identification of L. helveticus CU 631.

• Food Science and Preservation
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• v.17 no.2
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• pp.301-306
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• 2010

We identified microorganisms causing skin disease in slaughtered chickens. Ten microbial strains were isolated from skin wound regions on the back and legs of chickens. Fatty acid composition analysis of the cell membranes of isolated bacteria identified five isolates of Shigella sonnei, Proteus mirabilis (2), and Escherichia coli (2). In addition, 16S rRNA sequencing indicated that S. sonnei (99%), P. mirabilis (99%), and E. coli (99%) were the strains responsible for skin wounds in chickens. Therefore, these three species may be the major pathogenic bacteria causing skin wounds on the back and legs of chickens.

• Fisheries and Aquatic Sciences
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• v.3 no.1
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• pp.64-70
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• 2000

DNA probes for the l6S rRNA have been designed for the detection of Edwardsiella tarda. In order to accomplish this purpose, the l6S rRNA gene from E. tarda has been cloned and sequenced. Two highly feasible oligonucleotide probe sites have been determined by the database analysis programs presented by PCGENE and BLAST. These two probes have been evaluated by slot blot hybridization analysis. Hetero- and homo-trimeric templates have been synthesized using these two probe sites. The templates have been further multimerized by PCR to generate between 150 and 300 bp long DIG-11-dUTP labeled probes. Unlike 3' end labeled oligonucleotide probes or templates, multimerized probes showed no cross­hybridization in the given experimental condition. Furthermore, a significant increase in sensitivity has been observed with these probes. This method, we presented here, may be useful for the designing of probes for the detection of other fish pathogenic microorganisms also.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.11
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• pp.1715-1724
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• 2019

Objective: As laying hens become aged, laying performance and egg quality are generally impaired. One of the practical methods to rejuvenate production and egg quality of aged laying hens with decreasing productivity is a forced molting. However, the changes in intestinal microbiota after forced molting of aged hens are not clearly known. The aim of the present study was to analyze the changes in excreta bacterial communities after forced molting of aged laying hens. Methods: A total of one hundred 66-wk-old Hy-Line Brown laying hens were induced to molt by a 2-d water removal and an 11-d fasting until egg production completely ceased. The excreta samples of 16 hens with similar body weight were collected before and immediately after molting. Excreta bacterial communities were analyzed by high-throughput sequencing of bacterial 16S rRNA genes. Results: Bacteroidetes, Firmicutes, and Proteobacteria were the three major bacterial phyla in pre-molting and immediate post-molting hens, accounting for more than 98.0%. Lactobacillus genus had relatively high abundance in both group, but decreased by molting (62.3% in premolting and 24.9% in post-molting hens). Moreover, pathogenic bacteria such as Enterococcus cecorum and Escherichia coli were more abundant in immediate post-molting hens than in pre-molting hens. Forced molting influenced the alpha diversity, with higher Chao1 (p = 0.012), phylogenetic diversity whole tree (p = 0.014), observed operational taxonomic unit indices (p = 0.006), and Simpson indices (p<0.001), which indicated that forced molting increased excreta bacterial richness of aged laying hens. Conclusion: This study improves the current knowledge of bacterial community alterations in the excreta by forced molting in aged laying hens, which can provide increasing opportunity to develop novel dietary and management skills for improving the gastrointestinal health of aged laying hens after molting.

• Microbiology and Biotechnology Letters
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• v.38 no.3
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• pp.322-328
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• 2010

Fermented skate is a traditional Korean food popular in Southwestern area of Korea. It has a characteristic flavor and alkaline pH. In this study we tried to determine the microbial flora in fermented skate using two different approaches. In culture-independent method, we amplified V2 region of 16S rRNA gene by PCR and cloned them into pUC18 plasmid to construct 16S rDNA fragment library. BLAST searches for the sequences obtained from this library revealed that uncultured bacterium clone 054E11.b was the most dominant flora in this fermented fish. In culture-dependent method, we diluted suspension of skate and spreaded on MRS, PCA, and MacConkey plates. We identified colonies grown on those plates by using PCR amplification of V2 region of 16S rRNA and DNA sequencing. BLAST searches of those DNA sequences resulted in totally different species with the observations from the 16S rDNA library analysis. Discrepancies of results obtained from both approaches suggest that the agar plates used in culture-dependent method may be different from the real condition of fermented skate. Therefore, results from culture-independent approach using 16S rDNA fragment library analysis may reflect real microbial flora in fermented skate.