• Journal of Microbiology and Biotechnology
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• v.15 no.2
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• pp.388-394
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• 2005

In order to investigate the distribution of dominant Bifidobacterium species in intestinal microflora of Korean adults and seniors, SDS-PAGE profiles of whole cell proteins were used for the identification of bifidobacteria. To confirm the reliability of SDS-PAGE, the Bifidobacterium species identified by SDS-PAGE of whole cell proteins were validated by using 16S rDNA sequencing analysis. The results of SDS­PAGE corresponded well with those determined by the analysis of 16S rDNA sequencing. Based on the analysis of SDS-PAGE patterns on unidentified fecal strains which showed positive in fructose-6-phosphate phosphoketolase activity, B. adolescentis, B. longum, and B. bifidum were identified in the feces of adults, and B. adolescentis, B. longum, B. bifidum, B. breve, and B. dentium were identified in those of seniors. In most of the fecal samples tested, the predominant Bifidobacterium species consisted of only a few species, and differences in the distribution and numbers of Bifidobacterium species were observed between adults and seniors. B. adolescentis and B. longum were found to be the most common species in feces of adults, but not in seniors. Accordingly, the distribution and abundance of bifidobacteria in the human intestinal microflora varied depending on the age of hosts.

• The Journal of Korean Medicine
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• v.32 no.5
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• pp.41-49
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• 2011

Objectives: To optimize the preservation method of herbal decoction, we investigated the content of principle components of Pyungwi-san, liquiritin, glycyrrhizin, and hesperidin according to preservation temperature and period. We also investigated the changing patterns of pH and microbial population in Pyungwi-san decoction as a model case. Methods: With samples preserved at different temperatures, the content of liquiritin, glycyrrhizin, and hesperidin was determined using HPLC and microbial population was determined as viable counting method up to 8 times every month. Identification of isolated bacteria was performed by 16S rDNA analysis. Results: The content of liquiritin and glycyrrhizin did not change according to the preservation temperature and period, but that of hesperidin was severely decreased at room temperature. The isolate from the decoction was identified as Bacillus licheniformis by 16S rDNA sequence analysis. Microbial population appeared after 3 months' preservation and reached maximum value at 4 months; at all tested temperatures, the pH showed the lowest value (4.4-4.5) simultaneously. Conclusion: From the results, it seems to be that the microbial growth affects the pH of preserved decoction but not the change of liquiritin and glycyrrhizin content.

• KSBB Journal
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• v.26 no.5
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• pp.407-411
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• 2011

Microbial fuel cell (MFC) wes enriched using sludge in wastewater treatment. The microbial community of activated sludge and enriched MFC were analyzed by FISH (fluorescent in situ hybridization) and 16S rDNA sequencing. Bacteroidetes group were pre-dominant in activated sludge by FISH. ${\alpha}$ group, ${\gamma}$ group and Acintobacter group were dominant and they were similar to distribution. The average value of 10 peak of MFC is 0.44C. When MFC wase enriched by sludge, ${\gamma}$-Proteobacteria, Plantomycetes group increased 70% and 60%, respectively. In results of 16S rDNA sequencing, Sphiringomonas sp. was comprised in ${\alpha}$ proteobacteria and Enterobacter sp., Klebsiella sp., Acinetobacter sp., Bacillus sp. were comprised in ${\gamma}$ proteobacteria and Chryseobacterium sp. was comprised in Flavobacteria were isolated from sludge.

• Journal of Animal Science and Technology
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• v.47 no.3
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• pp.465-474
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• 2005

A two-step broad-range PCR method detecting gram-negative bacteria at the level as low as 2 CFU was developed by using primers of GNFI and GNRI and then semi-nested primer of GNF2 and GNRI. The nucleotide sequences of the primers were determined based on l6S rRNA gene. The DNA fragments of 1173 bp and 169 bp were amplified in one-step PCRs with primer sets of GNFI-GNRI and GNF2-GNRl, respectively, using template DNA from seven strains of gram-negative bacteria including Escherichia coli, Enterobacter aerogenes, Klebsiella pneumoniae, Pseudomonas spp., and Acinetobacter baumaii but not from Achromobacter lyticus, Alca/igens faecalis, and five strains of gram-positive bacteria. DNA fragments of 180 bp were amplified from LTLT-pasteurized milk and UHf-pasteurized milk in the two-step PCR. The DNA fragments were amplified from LTLT-pasteurized milk which was added with Pseudomonas j/uorescens and subsequently heated at 65 $^{\circ}C$, 80 $^{\circ}C$, and 100 $^{\circ}C$ for 30 min but they were not amplified from the milk autoclaved at 121$^{\circ}C$ for 15 min. It was suggested in PCR that Pseudomonas fluorescens heated at 65 $^{\circ}C$ for 30 min in milk was more sensitive to DNase treatment than viable bacteria.

• Food Science and Preservation
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• v.17 no.3
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• pp.410-417
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• 2010

Several extracellular protease-producing bacteria were isolated from Chungkookjang, a traditional Korean food of fermented soybeans, on skim milk agar plates. Among these bacteria, strain D14 exhibited the highest production (15.2 U/mL) and specific activity (40.0 U/mg protein) of extracellular protease activity as assessed on growth in a protease induction medium composed of 1% (w/v) soluble starch, 1.5% (w/v) skim milk, 0.5% (w/v) yeast extract, and 2% (w/v) NaCl. The bacterium was identified as Bacillus subtilis based on morphological and physiological characteristics and 16S rDNA sequence. A BLAST search of 16S rDNA sequences revealed that the isolate was most closely related to Bacillus subtilis subsp. subtilis strain NCIB 3610. The 16S rDNA sequence homology was 99.9%. Our isolate produced the highest level of protease when grown in a protease induction medium containing 1% (w/v) sorbitol and 0.5% (w/v) yeast extract. Fructose and glucose reduced enzyme production to 12.7% and 35.9%, respectively, of the level seen when the strain was grown in medium containing soluble starch. Soytone also reduced enzyme production to 61.4% of the level noted when the strain was grown in medium containing yeast extract.

• Korean Journal of Ecology and Environment
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• v.47 no.4
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• pp.342-349
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• 2014

This study was conducted to identify the bloom-forming Anabaena strains with two phenotypes (straight-type and coil-type) isolated from North Han River (Sambong-ri Joam-myun) using 16S rDNA sequence. The odor material producing potential was also examined using the geosmin-synthesizing gene cluster. Despite of striking morphological difference of the two stains, resembling A. circinalis and A. crassa species, the phylogenetic analysis using 16S rDNA identified the both strains as a single species of A. circinalis with high genetic similarity (98%~100%). Also, two Anabaena strains showed to possess the geosmin-synthesizing gene cluster, indicating that they are capable of producing the odor substance. This study is the first report that provides the direct evidence of geosmin production in the gene level by A. circinalis in Korea, and provides important basic information to identify the source alga of geosmin increase and its management in North Han River.

• Molecules and Cells
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• v.25 no.4
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• pp.510-522
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• 2008

To construct the molecular systematics of the genus Megoura (Hemiptera: Aphididae), DNA based-identification was performed using four mitochondrial and three nuclear DNA regions: partial cytochrome c oxidase I (COI), partial tRNA-leucine + cytochrome c oxidase II (tRNA/COII), cytochrome b (CytB), partial 12S rRNA + tRNA-valine + 16S rRNA (12S/16S), elongation factor-1 alpha ($EF1{\alpha}$), and the internal transcribed spacers 1 and 2 (ITS1, ITS2). Pairwise sequence divergences between taxa were compared, and phylogenetic analyses were performed based on each DNA region separately, and the combined datasets. COI, CytB, $EF1{\alpha}$, ITS1, and ITS2 were relatively effective in determining species and resolving their relationships. By contrast, the sequences of tRNA/COII and 12S/16S were not able to separate the closely related species. CytB and $EF1{\alpha}$ gave better resolution with higher average sequence divergences (4.7% for CytB, 5.2% for $EF1{\alpha}$). The sequence divergence of COI (3.0%) was moderate, and those of the two ITS regions (1.8% for ITS1, 2.0% for ITS2) were very low. Phylogenetic trees were constructed by minimum evolution, maximum parsimony, maximum likelihood, and Bayesian phylogenetic analyses. The results indicated that the phylogenetic relationships between Megoura species were associated with their host preferences. Megoura brevipilosa and M. lespedezae living on Lespedeza were closely related, and M. nigra, monophagous on Vicia venosa, was rather different from M. crassicauda, M. litoralis, and M. viciae, which are oligophagous on Lathyrus and Vicia. The three populations of M. crassicauda formed a clade separated from M. litoralis and M. viciae. Nevertheless M. litoralis and M. viciae, which are morphologically similar, were not separated due to negligible sequence divergence. We discuss the phylogenetic relationships of the Megoura, and the usefulness of the seven DNA regions for determining the species level phylogeny of aphids.

• Animal cells and systems
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• v.16 no.5
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• pp.415-424
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• 2012

Four species of ophichthid leptocephali were identified using 12S rDNA sequences, and their morphological descriptions were first provided based on six individuals (S1-S3,M1, and E1-E2) collected from the East Sea and the Korea Strait between September 2008 and October 2010. Mitochondrial 12S rDNA 859-861 base pairs of ophichthid leptocephali were compared with those of 16 ophichthids adult and 2 outgroups (Anguilla japonica and Conger myriaster). Leptocephali of S1 and E1 were very closely clustered with adult of Scolecenchelys borealis (D=0.002) and Echelus uropterus (D=0.000), respectively. However, leptocephali of S2-S3 andM1 were slightly far clustered with leptocephalus of S1 (D=0.006) and adult of Muraenichthys gymnopterus (0.034), respectively. We believe that S1 and E1 are S. borealis and E. uropterus, respectively, in which the former is unrecorded species in Korea. However, S2-S3 and M1 may be undescribed species belonging to genus Scolecenchelys and Muraenichthys, respectively, because total numbers of myomeres for S2-S3 (148-158) and M1 (151) were not consistent with total numbers of vertebrae or distribution for any adult of Scolecenchelys spp. and Muraenichthys spp. in the world. We propose the new Korean name 'Dong-hae-mul-baem' for S. borealis.

• Parasites, Hosts and Diseases
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• v.43 no.1 s.133
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• pp.7-13
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• 2005

The taxonomy of Acanthamoeba spp., an amphizoic amoeba which causes granulomatous amoebic encephalitis and chronic amoebic keratitis, has been revised many times. The taxonomic validity of some species has yet to be assessed. In this paper, we analyzed the morphological characteristics, nuclear 18s rDNA and mitochondrial 16s rDNA sequences and the Mt DNA RFLP of the type strains of four Acanthamoeba species, which had been previously designated as A. divionensis, A. parasidionensis, A. mauritaniensis, and A. rhysodes. The four isolates revealed characteristic group II morphology. They exhibited 18S rDNA sequence differences of $0.2-1.1\%$ with each other, but more than $2\%$ difference from the other compared reference strains. Four isolates formed a different clade from that of A. castellanii Castellani and the other strains in morphological group lion the phylogenetic tree. In light of these results, A. paradivionensis, A. divionensis, and A. mauritaniensis should be regarded as synonyms for A. rhysodes.

• Microbiology and Biotechnology Letters
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• v.35 no.4
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• pp.347-351
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• 2007

Potato scab is prevalent in all potato-growing areas of Jeju Island and causes economically significant losses. Streptomyces species are known as pathogens of potato scab. In this study, we analyzed the 16S rRNA sequences of Streptomyces spp, which are isolated from potato scab lesions in Jeju Island, and constructed 16S rRNA phylogenetic tree. All isolates were clearly differentiated into the genus Streptomyces, and the tree also showed that new scab-causing Streptomyces spp or not yet named species of Streptomyces are existed in Jeju Island, Korea.