• Korean Journal of Ecology and Environment
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• v.41 no.1
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• pp.11-18
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• 2008

Seasonal succession and community composition of planktonic ciliates were studied in Kyungan Stream from December 2000 to December 2001. Oligotrichs accounted for 53% of total ciliates. Total abundance of ciliates peaked in spring (30 March, 6 April) and in summer (8 June, 20 July) reaching values up to $1.9\times10^4$ cells $L^{-1}$. Seasonal succession of dominant species occurred obviously. Large-sized $(>50{\mu}m)$ species (Stylonychia sp1, Phascolodon vorticella and Codonella cratera) dominanted from winter to spring. Small sized $(<30{\mu}m)$ species (Vorticella spp., Rimostrombidium hyalinum and Halteria grandinella) dominanted in summer and autumn. Total abundance of large-sized species coincided with the Chl-${\alpha}$ concencetation during the study (r=0.33, p<0.05, n=39). Among the small-sized species Halteria grandinella was a significant relationship with bacterial abundance (r=0.35, p<0.05, n=39).

• Journal of Life Science
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• v.31 no.10
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• pp.922-928
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• 2021

To profile the microbial compositions of Korean traditional fermented paste made from whole soybeans, Doenjang and Cheonggukjang, and compare their taxonomic differences, we analyzed the V3-V4 region of 16S rRNA of naturally fermented foods by using next generation sequencing. α-Diversity results showed that values indicating bacterial community abundances (OTUs) and richness (ACE, Chao1) were statistically significant (p=0.0001) in Doenjang and Cheonggukjang. Firmicutes was the most common phylum in both groups, representing 97.02% and 99.67% in the Doenjang and Cheonggukjang groups, respectively. Bacillus was the most dominant genus, accounting for 71.70% and 59.87% in both groups. Linear discriminant (LDA) effect size (LEfSe) analysis was performed to reveal the significant ranking of abundant taxa in different fermented foods. A size-effect threshold of 2.0 on the logarithmic LDA score was used for discriminative functional biomarkers. On the species level, Bacillus subtilis, Tetragenococcus halophilus, and Clostridium arbusti were significantly more abundant in Doenjang than in Cheonggukjang, whereas Bacillus thermoamylovorans, Enterococcus faecium, and Lactobacillus sakei were significantly more abundant in Cheonggukjang than in Doenjang. Permutational multivariate analysis of variance (PERMANOVA) showed that the statistical difference in microbial clusters between the two groups was significant at the confidence level of p=0.001. This research could be used as basic research to identify the correlation between the biochemical characteristics of Korean fermented foods and the distribution of microbial communities.

• Asian-Australasian Journal of Animal Sciences
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• v.26 no.8
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• pp.1144-1151
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• 2013

In this study, protein domains with cellulase activity in goat rumen microbes were investigated using metagenomic and bioinformatic analyses. After the complete genome of goat rumen microbes was obtained using a shotgun sequencing method, 217,892,109 pair reads were filtered, including only those with 70% identity, 100-bp matches, and thresholds below $E^{-10}$ using METAIDBA. These filtered contigs were assembled and annotated using blastN against the NCBI nucleotide database. As a result, a microbial community structure with 1431 species was analyzed, among which Prevotella ruminicola 23 bacteria and Butyrivibrio proteoclasticus B316 were the dominant groups. In parallel, 201 sequences related with cellulase activities (EC.3.2.1.4) were obtained through blast searches using the enzyme.dat file provided by the NCBI database. After translating the nucleotide sequence into a protein sequence using Interproscan, 28 protein domains with cellulase activity were identified using the HMMER package with threshold E values below $10^{-5}$. Cellulase activity protein domain profiling showed that the major protein domains such as lipase GDSL, cellulase, and Glyco hydro 10 were present in bacterial species with strong cellulase activities. Furthermore, correlation plots clearly displayed the strong positive correlation between some protein domain groups, which was indicative of microbial adaption in the goat rumen based on feeding habits. This is the first metagenomic analysis of cellulase activity protein domains using bioinformatics from the goat rumen.

• Journal of Microbiology and Biotechnology
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• v.26 no.1
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• pp.130-138
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• 2016

The use of antibiotics in aquaculture raises environmental and food safety concerns because chronic exposure of an aquatic ecosystem to antibiotics can result in the spread of antibiotic resistance, bioaccumulation of antibiotics in the organisms, and transfer of antibiotics to humans. In an attempt to overcome these problems, high-concentration red clay was applied as an alternative antibiotic against the following common fish pathogens: Aeromonas salmonicida, Vibrio alginolyticus, and Streptococcus equinus. The growth of A. salmonicida and V. alginolyticus was retarded by red clay, whereas that of S. equinus was promoted. Phase contrast and scanning electron microscopy analyses confirmed the attachment of red clay on cell surfaces, resulting in rapid gravitational removal and cell surface damage in both A. salmonicida and V. alginolyticus, but not in S. equinus. Different cell wall properties of grampositive species may explain the unharmed cell surface of S. equinus. Significant levels of oxidative stress were generated in only the former two species, whereas significant changes in membrane permeability were found only in S. equinus, probably because of its physiological adaptation. The bacterial communities in water samples from Oncorhynchus mykiss aquacultures supplemented with red clay showed similar structure and diversity as those from oxytetracycline-treated water. Taken together, the antibiotic effects of high concentrations of red clay in aquaculture can be attributed to gravitational removal, cell surface damage, and oxidative stress production, and suggest that red clay may be used as an alternative for antibiotics in aquaculture.

• Journal of Digital Convergence
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• v.14 no.10
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• pp.349-354
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• 2016

The emergence and dissemination of extended-spectrum ${\beta}$-lactamse (ESBL) producing Klebsiella pneumoniae isolates make it more difficult to treatment of bacterial infections. In our study, we detected ESBL genes and investigated antimicrobial susceptibility of K. pneumoniae isolates in Chungcheong province. In addition, clonality among the isolates was analyzed by repetitive element sequence (REP)-PCR. Twenty-one of 102 K. pneumoniae isolates produced CTX-M-14 and/or CTX-M-15 and showed high level (over 70%) resistance to third cephalosporins. CTX-M type ESBL producing K. pneumoniae strains isolated in our study showed diverse clonality and some of the isolates have been disseminated in the community. Enhancing infection control will be needed to prevent dissemination of the K. pneumoniae isolates. In addition, for more effective control of resistant bacteria it is considered necessary to monitor the database constructed through convergence of biological investigation and statistical analysis of antimicrobial resistance genes.

• ALGAE
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• v.29 no.4
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• pp.249-265
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• 2014

As with land crops, cultivated algae are affected by various diseases ranging from large outbreaks of a disease to chronic epiphytes, which may downgrade the value of the final product. The recent development of intensive and dense mariculture practices has enabled some new diseases to spread much faster than before. A new disease is reported almost every year, and the impact of diseases is expected to increase with environmental change, such as global warming. We observed the incidence of diseases in two Pyropia sea farms in Korea from 2011 to 2014, and estimated the economic loss caused by each disease. Serious damage is caused by the oomycete pathogens, Pythium porphyrae and Olpidiopsis spp., which decreased the productivity of the Pyropia sea farms. In Seocheon sea farms, an outbreak of Olpidiopsis spp. disease resulted in approximately US $1.6 million in loss, representing approximately 24.5% of total sales during the 2012-2013 season. The damage caused by green-spot disease was almost as serious as oomycete diseases. An outbreak of green-spot disease in the Seocheon sea farms resulted in approximately US $1.1 million in loss, representing 10.7% of total sales in the 2013-2014 season in this area. However, the causative agent of green-spot disease is still not confirmed. "Diatom felt" is regarded as a minor nuisance that does not cause serious damage in Pyropia; however, our case study showed that the economic loss caused by "diatom felt" might be as serious as that of oomycete diseases. Bacteria and cyanobacteria are indigenous members of epiphytic microbial community on Pyropia blades, but can become opportunistic pathogens under suitable environmental conditions, especially when Pyropia suffers from other diseases. A regular acid wash of the Pyropia cultivation nets is the most common treatment for all of the above mentioned diseases, and represents approximately 30% of the total cost in Pyropia sea farming. However, the acid wash is ineffective for some diseases, especially for Olpidiopsis and bacterial diseases.

• Biomedical Science Letters
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• v.10 no.3
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• pp.309-315
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• 2004

Methicillin resistant Staphylococcus aureus (MRSA) is one of the most common nosocomial pathogens. Many hospitals are facing the problems which they have to use expensive antibiotics and suffer from long term hospital study of patients due to MRSA. This study is to survey MRSA nasal colonization of patients and doctors, and to investigate the mode of transmission of MRSA by pulsed field gel electrophoresis (PFGE) and then use these data to prevent further spread of cross infection and reduce nosocomial infection. Subjects of this study were 201 patients with MRSA infection at an university hospital in Busan from Sept. 1997 to Aug. 1998. Bacterial genotypes of MRSA strains isolated from nares and wound of patients (14 cases) and nares of doctors (8 cases) were analyzed by PFGE. Nasal cultures of 20 I patients for detecting nasal colonization of MRSA were performed and incidence rate of nasal colonization was 40％ (80/201). Among 201 patients MRSA were acquired from hospital in 140 (70％) patients and were acquired from community 61 (30％) patients. Among 14 pairs of MRSA from colonized or infected sites and anterior nares, DNA patterns of 10 pairs (71.4％) were equal. 86％ (12/14) MRSA strains isolated from patients and 12.5％ (1/8) MRSA strains isolated from doctors show same pattern. DNA patterns were changed in some doctors after nasal oint. Treatment. It could be inferred that the most sources of MRSA in hospital are the endemically existing MRSA. Therefore, we believe that it would be necessary to control MRSA nasal colonization of the patients and the related medical teams to reduce the medical cost and to improve the efficacy of medical cares.

• Korean Journal of Microbiology
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• v.46 no.1
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• pp.33-37
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• 2010

Rhizobacterial strain isolated from barren soil, Bacillus subtilis RFO41 exhibits a high level of phosphate solubilizing activity and produces some phytohormones. Its promoting effect on the growth of Xanthium italicum Moore, a wild plant growing at lakeside barren land and thus a good candidate plant for revegetation of barren lakeside was evaluated in the in situ test for 19 weeks at Lake Paro, Kangwon-do. Strain RFO41 could enhance the dry weight of X. italicum by 67.7%. It also increased the shoot length of X. italicum plant by 21.1% compared to that of uninoculated control. Both growth enhancements had statistical significance. However, the inoculation did not show any effect on the root growth, which might be due to the breakage of tiny root. Denaturing gradient gel electrophoresis analysis showed that the inoculated bacteria were maintained in the soils, and the indigenous bacterial community did not exhibit any significant change. This plant growth promoting capability may be utilized as an environment-friendly and low cost revegetation method, especially for the sensitive areas such as barren lakeside lands.

• Journal of Environmental Health Sciences
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• v.39 no.5
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• pp.447-455
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• 2013

Objectives: This study aims to understand the concentration, diversity, and antibiotic characteristics of staphylococci present in the indoor air of child-care facilities. Methods: Air sampling was performed from October 2012 to January 2013 in 120 child-care facilities in Seoul, Korea. Methicillin-resistant bacteria were selected from the total obtained airborne bacteria and subjected to 16S rRNA analysis for methicillin-resistant staphylococcal species determination. Identified staphylococcal strains were tested for resistance to a range of antibiotics. Results: Average total airborne bacterial concentration was $508.9{\pm}246.3CFU/m^3$. Indoor concentration of total airborne bacteria had a significant positive correlation with the $CO_2$ concentration in the child-care facilities. Methicillin-resistant staphylococci were present in 13.3% of the child-care facilities studied. A total of four species (S. epidermidis, S. cohnii, S. saprophyticus, S. sp.) and 55 strains were identified from the indoor air of the child-care facilities. Staphylococcus cohnii was the most common species (54.5%), followed by S. epidermidis (38.2%). All of the isolated staphylococcal strains exhibited high resistance to oxacillin, erythromycin, mupirocin, and ceftizoxime. Especially, S. saprophyticus strains showed more multidrug resistance to oxacillin, vancomycin, clindamycin, erythromycin, lincomycin, ceftizoxime, mupirocin, and tetracycline than did other species. Conclusion: The results of this study showed that a monitoring system for multidrug-resistant bacteria is needed in facilities for children, as the community-associated infections of these bacteria are increasing.

• Journal of Microbiology and Biotechnology
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• v.15 no.4
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• pp.772-779
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• 2005

Ammonia-oxidizing bacteria (AOB) were enriched by repeating fed-batch cultivations in an AOB-selective medium of activated sludges from a domestic wastewater treatment plant. Enriched culture showed strong capabilities of ammonia oxidation [0.810 mg $NH_4^+$-N/mg mixed liquor suspended solids (MLSS)$\cdot$day] as well as $NO_x^-$-N production (0.617 mg $NO_x^-$-N/ mg MLSS$\cdot$day). Degree of enrichment was examined through fluorescent in situ hybridization (FISH) analyses using an AOB-specific Cy3-labeled oligonucleotide probe (NSOl90) and terminal-restriction fragment length polymorphism (T-RFLP) analyses. FISH analyses confirmed that the fraction of AOB among 4',6-diamidino-2-phenylindole (DAPI)-stained cells increased from about less than $0.001\%$ to approximately $42\%$ after enrichment of AOB, and T-RFLP analyses showed that bacterial community became simpler as enrichment was continued. When the enriched culture of AOB was added (150 mg/l as dry suspended solid) to the normal activated sludge (3,000 mg/l as dry suspended solid), nitrification efficiencies were improved from 0.020 mg $NO_x^-$-N/mg MLSS$\cdot$day to 0.041 mg $NO_x^-$-N/mg MLSS$\cdot$day in a synthetic wastewater and also from 0.0007 mg $NO_x^-$-N/mg MLSS$\cdot$day to 0.0918 mg $NO_x^-$-N/mg MLSS$\cdot$day in a real domestic wastewater. Therefore, it is expected that this enrichment method could be used for improving efficiency of nitrification in wastewater treatment plants.