• Journal of Microbiology
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• v.44 no.2
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• pp.155-161
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• 2006

Comparative analysis of microbial communities in a sequencing batch reactor which performed enhanced biological phosphorus removal (EBPR) was carried out using a cultivation-based technique and 16S rRNA gene clone libraries. A standard PCR protocol and a modified PCR protocol with low PCR cycle was applied to the two clone libraries of the 16S rRNA gene sequences obtained from EBPR sludge, respectively, and the resulting 424 clones were analyzed using restriction fragment length polymorphisms (RFLPs) on 16S rRNA gene inserts. Comparison of two clone libraries showed that the modified PCR protocol decreased the incidence of distinct fragment patterns from about 63 % (137 of 217) in the standard PCR method to about 34 % (70 of 207) under the modified protocol, suggesting that just a low level of PCR cycling (5 cycles after 15 cycles) can significantly reduce the formation of chimeric DNA in the final PCR products. Phylogenetic analysis of 81 groups with distinct RFLP patterns that were obtained using the modified PCR method revealed that the clones were affiliated with at least 11 phyla or classes of the domain Bacteria. However, the analyses of 327 colonies, which were grouped into just 41 distinct types by RFLP analysis, showed that they could be classified into five major bacterial lineages: ${\alpha},\;{\beta},\;{\gamma}-$ Proteobacteria, Actinobacteria, and the phylum Bacteroidetes, which indicated that the microbial community yielded from the cultivation-based method was still much simpler than that yielded from the PCR-based molecular method. In this study, the discrepancy observed between the communities obtained from PCR-based and cultivation-based methods seems to result from low culturabilities of bacteria or PCR bias even though modified culture and PCR methods were used. Therefore, continuous development of PCR protocol and cultivation techniques is needed to reduce this discrepancy.

• Journal of the Korean Association of Oral and Maxillofacial Surgeons
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• v.29 no.1
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• pp.48-55
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• 2003

The purpose of this study was to isolate and identify the bacteria in osteomyelitis lesion of 3 patients. Two lesions were due to the post-infection after extraction. The other was resulted from mal-fixation of both sides of mandibular angles. Pus samples were collected by needle aspiration from the lesion and examined by culture method. Bacterial culture was performed in three culture systems (anaerobic, $CO_2$, and aerobic incubator). Identification of the bacteria was performed by 16S rRNA gene cloning and nucleotide sequencing method. Our results showed that Streptococci species was predominantly isolated in both lesions of extraction socket. Only one species (Proteus vulagris) was detected in lesion of mandibular angle. This study was not sufficient to identify the causative bacteria in those osteomyelitis. However, our data may be offered the clue to solve the problem.

• Food Engineering Progress
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• v.14 no.3
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• pp.263-270
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• 2010

An alkalophilic microorganism named DK-2386, which produces xylanase, was isolated from soil of Taejo-mountain, Cheonan-si, Chungnam, Korea. The isolated strain was characterized as Gram-positive, with size of 0.4${\times}$2.5 ${\mu}$m, spore forming, anaerobic, catalase positive, possessed with hydrolysis abilities of casein, starch, sodium carboxy methyl cellulose, and xylan, reduction of nitrate to nitrite, resistant against lysozyme, urease positive, and motility positive. The color of culture broth was reddish yellow. The strain DK-2386 was identified as Bacillus agaradhaerens by whole cell fatty-acid composition analysis and 16S rDNA sequence analysis. However, it was not identical to Bacillus agaradhaerens 40952 obtained from the Korean Culture Center of Microorganism in its colour of culture broth. Therefore, we have named the newly isolated strain as Bacillus agaradhaerens DK-2386.

• Korean Journal of Organic Agriculture
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• v.25 no.4
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• pp.843-859
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• 2017

The JK-1 isolate which was the best producer of indole-3-acetic acid and carotenoid among the 388 strains isolated from 28 wetlands in Jeju, was identified to be Rhodopseudomonas palustirs belongs to a typical group of non sulfur purple bacteria based on 16S sRNA sequencing. This study investigated the effect of different cultural conditions of pH, temperature, agitation, light and aeration on growth, IAA and carotenoid production of photosynthetic bacterium JK-1 for optimization of IAA and carotenoid production. It was found that growth, IAA, carotenoid, and bacteriochlorophyll production with light (3,000~3,500 Lux) and agitation (100 rpm) showed better results than those with dark/static or dark/agitation (100 rpm) in anaerobic conditions. The optimal pH, temperature and agitation speed for cell growth were 7, $30^{\circ}C$, 150 rpm, for IAA production were 9, $30^{\circ}C$, 150rpm and for carotenoid production were 6, $25^{\circ}C$, 50 rpm, cultured for 72 h under anaerobic light, respectively. The growth and IAA production were high in aerobic culture compared with anaerocic culture, whereas carotenoid and bacteriochlorophyll content were decreased extremely in aerobic condition (0.5~1 vvm). Subsequently, the optimal culture conditions for JK-1 were selected with pH 7, $30^{\circ}C$ and 100 rpm under anaerobic light and the effect on plant growth was tested by pot assay. Inoculation of JK-1 with 3% (v/v) level caused increase in shoot and root dry weigh that varied from 20%~58% to 40%~28% in young radish in camparison to uninoculated treatment at 50 days of growth. The study suggests that the JK-1 isolate may serve as efficient biofertilizer inoculants to promote plant growth.

• Microbiology and Biotechnology Letters
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• v.37 no.2
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• pp.176-182
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• 2009

Hydrogen producing bacterium, strain MeL 6-2 was isolated from the sludge of the factory areas in Anyang through the acclimation in basal salt medium (BSM) supplemented with 10 g/L of sucrose. Isolated strain MeL 6-2 was a facultative anaerobe which could grow in both aerobic and anaerobic environments. An aerobically grown pure culture isolated from enriched culture was analyzed by 16S rDNA sequencing and identified as Rhodopseudomonas sp. MeL 6-2. Effects of the concentrations of glucose and sucrose on the hydrogen production rate and the hydrogen production yield were investigated. When glucose in the range of 1~12 g/L was supplemented to the BSM, strain MeL 6-2 could grow without lag phase. An increased glucose concentration increased the specific hydrogen production rate linearly to $4.2\;mmol-H_2{\cdot}L^{-1}{\cdot}h^{-1}$ at 10 g/L, and $60\;mmol-H_2{\cdot}mg-DCW^{-1}{\cdot}h^{-1}$, but decreased slightly as the concentration increased to 12 g/L. The hydrogen production yield was maintained over a range from 2.6 to $3.1\;mol-H_2{\cdot}mol-glucose^{-1}$. When sucrose in the range of 1~12 g/L was supplemented to the BSM, strain MeL 6-2 could grow after ten hours. An increased sucrose concentration increased the specific hydrogen production rate and the hydrogen production yield to $163\;mmol-H_2{\cdot}mg-DCW^{-1}{\cdot}h^{-1}$ and to $4.5\;mol-H_2{\cdot}mol-sucrose^{-1}$, respectively.

• Korean Journal of Microbiology
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• v.48 no.1
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• pp.42-47
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• 2012

Hydrothermal vents (HTV) provide special environments for evolution of lives independent on solar energy. HTV samples were gained from Tofua arc trench in Tonga, South Pacific. We investigated archaeal diversity enriched using combinations of various electron donors (yeast extract and $H_2$) and electron acceptors [Iron (III), elemental sulfur ($S^0$) and nitrate. PCR amplification was performed to detect archaeal 16S rRNA genes after the cultures were incubated $65^{\circ}C$ and $80^{\circ}C$ for 2 weeks. The cultures showing archaeal growth were transferred using the dilution-to-extinction method. 16S rRNA gene PCR-Denaturing Gradient Gel Electrophoresis was used to identify the enriched archaea in the highest dilutions where archaeal growth was observed. Most of cultured archaea belonged to genus of Thermococcus (T. alcaliphilius, T. litoralis, T. celer, T. barossii, T. thoreducens, T. coalescens) with 98-99% 16S rRNA gene similarities. Interestingly, archaeal growth was observed in the cultures with Iron (III) and nitrate as an electron acceptor. It was supposed that archaea might use the elemental sulfur generated from oxidation of the reducing agent, sulfide. To cultivate diverse archaea excluding Thermococcus, it would be required to use other reducing agents instead of sulfide.

• Restorative Dentistry and Endodontics
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• v.33 no.4
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• pp.397-404
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• 2008

The purpose of this study was to evaluate the effects of MTAD, EDTA and sodium hypochlorite(NaOCl) as final irrigants on coronal leakage resistance to Enterococcus faecalis. Forty extracted human maxillary molars were used in this experiment. The teeth were randomly divided into positive control group (Group 1; n = 5), negative control group (Group 2; n = 5) and three experimental groups (n = 30). In Group 3 (n = 10), the root canals were irrigated with sodium hypochlorite. In Group 4 (n = 10) and 5 (n = 10), the root canals were irrigated with sodium hypochlorite and rinsed with EDTA and MTAD, respectively. The teeth in each group were cleaned and shaped to #40 profile with .04 taper, and obturated with gutta-percha and AH-26 root canal sealer. The coronal portion of each tooth was placed in contact with inoculum of Enterococcus faecalis in Brain Heart Infusion (BHI) culture media. Each root tip was placed in a vial containing sterile culture media. The vials were placed in anaerobic chamber and observed everyday for turbidity for 180 days. Statistical analysis was performed using Fisher's Exact Test. After 180 days, Group 3, 4, and 5 showed 7, 4 and 5 leaking samples respectively. The differences in leakage resistance were not statistically significant among Group 3, 4 and 5.

• Journal of Korean society of Dental Hygiene
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• v.5 no.2
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• pp.131-145
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• 2005

There are normal inhabitants doing medically useful functions in the body. There are many kinds of bacteria performing specific functions in the oral cavity. Two strains of lactic add bacteria were isolated from normal inhabitants of children's oral cavity, which inhibited the production of volatile sulfur compounds by anaerobic bacteria. The authors identified the isolates by 16S rDNA partial sequencing. 1. Two isolates were Gram-positive bacilli and produced hydrogen peroxide. 2. When Streptococcus mutans was cultured in the media, the mean weight of formed artificial plaque on the orthodontic wires was $124.4{\pm}30.4$ mg, whereas being reduced to $5.2{\pm}2.0$ mg and $10.6{\pm}6.6$ mg in the media cultured with Streptococcus mutans and each isolate, respectively(p<0.05). 3. The number of viable cells of Streptococcus mutans was $3.4{\times}10^9$ per ml in the cultured solution, whereas those of Streptococcus mutans in the combined culture with each of isolates were $4.6{\times}10^8$ and $2.4{\times}10^8$ per ml. 4. The optical density was 1.286 in the supernatant of Fusoacterium nucleatum after vortexing for 30 minutes, whereas in the supernatant of combined Fusoacterium nucleatum and each isolate, they were reduced to 0.628 and 00497, which the percentages of coaggregation between them were 2904% and 57.8%, respectively. 5. The optical density of Fusoacterium nucleatum precipitate was 1.794 in the culture media containing cysteine and $FeSO_4$ being reduced to 1.144 and 0.915 in the coaggregated precipitates of Fusoacterium nucleatum and each isolate. 6. The similarity values of 16S rDNA sequence between each of isolates and Lactobacillus salivarius subsp. salicinius were 99.60% and 99.73%, respectively, meaning that isolates were Lactobacillus salivarius subsp. salicinius. These results indicated that two strains isolated from children's saliva, which inhibited the formation of plaque and the production of volatile sulfur compounds, were identified as Lactobacillus salivarius subsp. salicinius.

• Korean Journal of Soil Science and Fertilizer
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• v.45 no.4
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• pp.515-523
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• 2012

The study investigated the biochemical methane potential (BMP) assay of cellulose supplementing with mixed methanogens and cellulolytic bacteria to improve anaerobic digestion for methane production. For the BMP assay, 7 different microbial supplementation groups were consisted of the cultures of mixed methanogens (M), Fibrobacter succinogenes (FS), Ruminococcus flavefaciensn (RF), R. albus (RA), RA+FS and M+RA+FS including control. The cultures were added in the batch reactors with the increasing dose levels of 1% (0.5 mL), 3% (1.5 mL) and 5% (2.5 mL). Incubation for the BMP assay was carried out for 40 days at $38^{\circ}C$ and anaerobic digestate obtained from an anaerobic digester with pig slurry as inoculum was used. In results, 5% FS increased total biogas and methane production up to 10.4~22.7% and 17.4~27.5%, respectively, compared to other groups (p<0.05). Total solid (TS) digestion efficiency showed a similar trend to the total biogas and methane productions. Generally the TS digestion efficiency of the FS group was higher than that of other groups showing at the highest value of 64.2% in the 5% FS group. Volatile solid (VS) digestion efficiencies of 68.4 and 71.0% in the 5% FS and the 5% RF were higher than other groups. After incubation, pH values in all treatment groups were over 6.4 indicating that methanogensis was not inhibited during the incubation. In conclusion, the results indicated that the hydrolysis stage for methane production in anaerobic batch reactors was the late-limiting stage compared with the methanogenesis stage, and especially, as the supplementation levels of F. succinogenes supplementation increased, the methane production was increased in the BMP assay compared with other microbial culture addition.

• Korean Journal of Agricultural Science
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• v.43 no.3
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• pp.387-393
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• 2016

This study was conducted to determine the fermentative characteristics of wheat bran inoculated with a starter culture of direct-fed microbes as a microbial wheat bran (DMWB) feed additive. Wheat bran was prepared with 1% (w/w, 0.5% Lactobacillus plantarum and 0.5% of Saccharomyces cerevisiae) starter culture treatment (TW) or without starter culture as a control (CW). Those were fermented under anaerobic conditions at $30^{\circ}C$ incubation for 3 days. Samples were taken at 0, 1, 2, and 3 days to analyze chemical composition, microbial growth, pH, and organic acid content. Chemical composition was not significantly different between CW and TW (p > 0.05). In TW, the number of lactic acid bacteria and yeast increased during the 3 days of fermentation (p < 0.05) and the population of lactic acid bacteria was significantly higher than in CW (p < 0.05). After 3 days, the number of yeast in TW was $7.50{\pm}0.07log\;CFU/g$, however, no yeast was detected in CW (p < 0.05). The pH values of both wheat bran samples decreased during the 3 days of fermentation (p < 0.05), and TW showed significantly lower pH than CW after 3 days of fermentation (p < 0.05). Contents of lactic acid and acetic acid increased significantly at 3rd day of fermentation in TW. However, no organic acids were generated in CW during testing period. These results suggest that 3 days of fermentation at $37^{\circ}C$ incubation after the inoculation wheat bran with starter culture makes it possible to produce a direct-feed with a high population of lactic acid bacteria at more than $10^{11}CFU/g$.