• Journal of Microbiology and Biotechnology
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• 제23권1호
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• pp.76-84
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• 2013

A polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) technique followed by sequencing of the 16S rDNA fragments eluted from the bands of interest on denaturing gradient gels was used to monitor changes in the bacterial microflora of two commercial kimchi, salted cabbage, and ingredient mix samples during 30 days of fermentation at $4^{\circ}C$ and $10^{\circ}C$. Leuconostoc (Lc.) was the dominant lactic acid bacteria (LAB) over Lactobacillus (Lb.) species at $4^{\circ}C$. Weissella confusa was detected in the ingredient mix and also in kimchi samples throughout fermentation in both samples at $4^{\circ}C$ and $10^{\circ}C$. Lc. gelidum was detected as the dominant LAB at $4^{\circ}C$ in both samples. The temperature affected the LAB profile of kimchi by varing the pH, which was primarily caused by the temperature-dependent competition among different LAB species in kimchi. At $4^{\circ}C$, the sample variations in pH and titratable acidity were more conspicuous owing to the delayed growth of LAB. Temperature affected only initial decreases in pH and initial increases in viable cell counts, but affected both the initial increases and final values of titratable acidity. The initial microflora in the kimchi sample was probably determined by the microflora of the ingredient mix, not by that of the salted cabbage. The microbial distributions in the samples used in this study resembled across the different kimchi samples and the different fermentation temperatures as the numbers of LAB increased and titratable acidity decreased.

• Korean Journal of Microbiology
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• 제41권4호
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• pp.281-286
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• 2005

In this study, the anaerobic enrichment cultivation was performed with the sediments and the dredged soils from the cities of Ulsan, Masan, Yeosu, Gwangyang, Ansan and Seongnam. Acetate as an electron donor and PCE (perchloroethylene) or TCE (trichloroethylene) as an electron acceptor were injected into the serum bottle with an anaerobic medium. After the incubation of 12 weeks, the removal efficiency of PCE was highest at $70\%$ in the treatment with the sediment of Ulsan. Also, the bacterial community structure was analyzed by D-DGGE (double denatured gradient gel electrophoresis) through PCR-based 16S rDNA approaches. The dominant species id the anaerobic enrichment were found to belong to the genus of Desulfovibrio.

• Korean Journal of Microbiology
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• 제49권4호
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• pp.415-418
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• 2013

Since the development of the next generation sequencing (NGS) technology, 16S rRNA gene sequencing has become a major tool for microbial community analysis. Recently, human microbiome project (HMP) has been completed to identify microbes associated with human health and diseases. HMP achieved characterization of several diseases caused by bacteria, especially the ones in human gut. While human intestinal bacteria have been well characterized, little have been studied about other animal intestinal bacteria. In this study, we surveyed diversity of livestock animal fecal microbiota and discuss importance of studying fecal microbiota. Here, we report the initiation of the fecal microbiome project in South Korea.

• The Korean Journal of Food And Nutrition
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• 제23권1호
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• pp.84-87
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• 2010

Effects of gamma irradiation on microbiological changes of Gorosoe sap were characterized during a post-irradiation storage at $4^{\circ}C$. The aseptically collected sap was irradiated and stored at $4^{\circ}C$ for 0 to 60 days and analysed for standard plate counts and 16S rDNA. There were significant differences in the total number of colony forming units(CFUs) of bacteria between irradiated and non-irradiated control sap. Bacteria of non-irradiated sap were present at levels of $1.5{\times}10^4{\sim}2.3{\times}10^8\;CFU/m{\ell}$, whereas no viable microbial cells were detected in sap after 10 kGy of irradiation during storage. According to the 16S rDNA sequence analysis, bacterial community structures decrease with time and the most abundant strain was Pseudomonas species. Our results suggested that gamma irradiation can be used to enhance the shelf-life of Gorosoe sap.

• Proceedings of the Microbiological Society of Korea Conference
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• 한국미생물학회 2002년도 추계학술대회
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• pp.81-85
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• 2002

Oligotrophic bacteria isolated from forest soil showed a specific community consisting of various taxonomic groups compared with those in other soil or aquatic habitats. Based on the cell shape, the isolates were divided into four groups: regular rod, curved/spiral rod, irregular rod, and prosthecate bacteria. The cellular fatty acids 60 oligotrophic isolates were analyzed. At the dendrogram based on cellular fatty acid composition, four clusters(I-IV) were separated at a euclidian distance of about 50. Based on the 16S rDNA sequence analysis, the two representative strains(MH256 and MA828) of cluster 3 showed the close relation to genera, Xathomonas/Stenotrophomonas, but were not included in these genera. The isolates with Q-10 were also studied. They are corresponded to the two large groups in Proteobacteria alpha subdivision. One was incorporated in the genus Bradyrhizobium cluster, which also includes Agromonas, a genus for oligotrophic bacteria. The strains of the other group showed high similarity to the genus Agrobacterium. We attempted to screening of bioactive compounds from oligotrophs which was isolated from forest soil. The active compounds were analyzed by mass and NMR spectrum, one of them identified as crisamicin A. Another one designated as SAPH is a new compound. The results indicate that there were possibilities for finding new compounds from the rare microorganisms such as oligotrophs.

• Journal of Microbiology and Biotechnology
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• 제31권1호
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• pp.104-114
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• 2021

Petroleum-contaminated soil is considered among the most important potential anthropogenic atmospheric methane sources. Additionally, various rhizoremediation factors can affect methane emissions by altering soil ecosystem carbon cycles. Nonetheless, greenhouse gas emissions from soil have not been given due importance as a potentially relevant parameter in rhizoremediation techniques. Therefore, in this study we sought to investigate the effects of different plant and soil amendments on both remediation efficiencies and methane emission characteristics in diesel-contaminated soil. An indoor pot experiment consisting of three plant treatments (control, maize, tall fescue) and two soil amendments (chemical nutrient, compost) was performed for 95 days. Total petroleum hydrocarbon (TPH) removal efficiency, dehydrogenase activity, and alkB (i.e., an alkane compound-degrading enzyme) gene abundance were the highest in the tall fescue and maize soil system amended with compost. Compost addition enhanced both the overall remediation efficiencies, as well as pmoA (i.e., a methane-oxidizing enzyme) gene abundance in soils. Moreover, the potential methane emission of diesel-contaminated soil was relatively low when maize was introduced to the soil system. After microbial community analysis, various TPH-degrading microorganisms (Nocardioides, Marinobacter, Immitisolibacter, Acinetobacter, Kocuria, Mycobacterium, Pseudomonas, Alcanivorax) and methane-oxidizing microorganisms (Methylocapsa, Methylosarcina) were observed in the rhizosphere soil. The effects of major rhizoremediation factors on soil remediation efficiency and greenhouse gas emissions discussed herein are expected to contribute to the development of sustainable biological remediation technologies in response to global climate change.

• Journal of Korean Dental Science
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• 제16권1호
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• pp.35-46
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• 2023

Purpose: Culture-based methods for microbiological diagnosis and antibiotic susceptibility tests have limitations in the management of orofacial infections. We aimed to profile pus microbiota and identify antibiotic resistance genes (ARGs) using a culture-independent approach. Materials and Methods: Genomic DNA samples extracted from the pus specimens of two patients with orofacial abscesses were subjected to shotgun sequencing on the NovaSeq system. Taxonomic profiling and prediction of ARGs were performed directly from the metagenomic raw reads. Result: Taxonomic profiling revealed obligate anaerobic polymicrobial communities associated with infections of odontogenic origins: the microbial community of Patient 1 consisted of one predominant species (Prevotella oris 74.6%) with 27 minor species, while the sample from Patient 2 contained 3 abundant species (Porphyromonas endodontalis 33.0%; P. oris 31.6%; and Prevotella koreensis 13.4%) with five minor species. A total of 150 and 136 putative ARGs were predicted in the metagenome of each pus sample. The coverage of most predicted ARGs was less than 10%, and only the CfxA2 gene identified in Patient 1 was covered 100%. ARG analysis of the seven assembled genome/metagenome datasets of P. oris revealed that strain C735 carried the CfxA2 gene. Conclusion: A metagenomics-based approach is useful to profile predominantly anaerobic polymicrobial communities but needs further verification for reliable ARG detection.

• Journal of the Korea Organic Resources Recycling Association
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• 제25권1호
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• pp.57-65
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• 2017

In a column experiment with low rank coal, rice straw was additionally supplied to induce methane gas generation by microorganisms in the state of supplying microorganisms and nutrients, and long-term biogas production characteristics were observed. When the weight ratio of the rice straw to coal was 0.04 or less, there was no significant gas generation. At 0.08, the biogas was generated for about 90 days. However, the methane gas generation was only 5% compared with the vial test result at optimum condition. Therefore, in order to produce biogas in the coal deposit in situ, a reactor that operates at COD concentration of 2000 mg/L or more at a ratio of 1:3 or more of rice straw to coal should be installed on the ground or under the ground. Liquid from the column filled with coal and rice straw and a liquid from vial containing rice straw were analyzed by microbial community analysis using pyrosequencing method, and compared the dominant microbial species among the two samples. In terms of the uniformity and diversity of the bacteria, the coal-filled column showed various species distribution, which has shown to be a disadvantageous microbial distribution to methane production.

• Asian-Australasian Journal of Animal Sciences
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• 제20권4호
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• pp.543-549
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• 2007

Two experiments were conducted to investigate the effects of disodium fumarate on the in vitro rumen fermentation profiles of different substrates and microbial communities. In experiment 1, nine diets (high-forage diet (forage:concentrate, e.g. F:C = 7:3, DM basis), medium-forage diet (F:C = 5:5, DM basis), low-forage diet(F:C = 1:9, DM basis), cracked corn, cracked wheat, soluble starch, tall elata (Festuca elata), perennial ryegrass and rice straw) were fermented in vitro by rumen microorganisms from local goats. The results showed that during 24 h incubations, for all substrates, disodium fumarate increased (p<0.05) the gas production, and tended to increase (p<0.10) the acetate, propionate and total VFA concentration and decrease the ratio of acetate to propionate, whereas no treatment effect was observed for the lactate concentration. The apparent DM loss for tall elata, perennial ryegrass and rice straw increased (p<0.05) with the addition of disodium fumarate. With the exception of tall elata, perennial ryegrass and rice straw, disodium fumarate addition increased the final pH (p<0.05) for all substrates. In experiment 2, three substrates (a high-forage diet, a medium-forage diet and a high concentrate diet) were fermented by mixed rumen microbes in vitro. A polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) technique was applied to compare microbial DNA fingerprints between substrates at the end of 24 h incubation. The results showed that when Festuca elata was used as substrate, the control and disodium fumarate treatments had similar DGGE profiles, with their similarities higher than 96%. As the ratio of concentrate increased, however, the similarities in DGGE profiles decreased between the control and disodium fumarate treatment. Overall, these results suggest that disodium fumarate is effective in increasing the pH and gas production for the diets differing in forage: concentrate ratio, grain cereals and soluble starch, and in increasing dry matter loss for the forages (tall elata, perennial ryegrass and rice straw) in vitro, whereas its effect on changes of ruminal microbial community may largely depend on the general nature of the substrate.

• Clean Technology
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• 제18권2호
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• pp.209-215
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• 2012

The performance and removal efficiencies of a pilot scale biofilter were estimated by using ammonia and hydrogen sulfide as the odorous gases. Expanded polyurethane foam coated with powdered activated carbon and zeolite was used as a biofilm supporting medium in the biofilter. Odorous gases from the sludge thickener of a municipal wastewater treatment plant were treated in the biofilter for 10 months and the inlet ammonia and hydrogen sulfide concentrations were 0.1-1.5 and 2-20 ppmv, respectively. The removal efficiencies reached about 100% at the empty bed retention time (EBRT) of 3.6-5 seconds except for the adaptation periods. The pressure drop of the biofilter caused by the gas flow was also low that the maximum attained was 31 mm $H_2O$ during the operation. Its stability was confirmed in the long term due to the fact that the biofilter and the polyurethane medium had a minimum plugging and compression. The microbial community on the medium is critical for the performance of the biofilter especially the distribution of ammonia oxidizing bacteria (AOB) and sulfur oxidizing bacteria (SOB). The distribution of Nitrosomonas sp. (AOB) and Thiobacillus ferroxidans (SOB) was confirmed by FISH (fluorescence in situ hybridization) analysis. The longer the operation time, the more microbial population observed. Also, the medium close to the gas inlet had more microbial population than the medium at the gas outlet of the biofilter.