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REFERENCE LINKING PLATFORM OF KOREA S&T JOURNALS
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The Korean Journal of Microbiology
Journal Basic Information
Journal DOI :
The Microbiological Society of Korea
Editor in Chief :
Volume & Issues
Volume 47, Issue 4 - Dec 2011
Volume 47, Issue 3 - Sep 2011
Volume 47, Issue 2 - Jun 2011
Volume 47, Issue 1 - Mar 2011
Selecting the target year
Review and Future Development of New Culture Methods for Unculturable Soil Bacteria
Kim, Jai-Soo ;
The Korean Journal of Microbiology, volume 47, issue 3, 2011, Pages 179~187
This review describes the characteristics of various unculturable soil bacteria, successfully-cultivating examples of those bacteria, and the diverse factors to be considered for successful cultivation. Most importantly, the selection of proper media is very important because unculturable bacteria demand different types of nutrients at various concentrations of substrates, nitrogens and phosphorus. To develop a new medium to successfully culture unculturable bacteria from soil, molecular ecological studies should be combined together. The inoculum size on a plate is also important: less than 50 bacterial cells are recommended to be plated on a single culture plate. The environmental factors such as pH and salt concentration of the medium need to be adjusted as similar as possible to mimic the original soil environments, and the trial of the various temperatures and extended period of cultivation are better. Since one cannot simply tell about which one was unculturable among a great number of colonies grown on a newly developed medium, some suitable detection methods and fast identification methods are required. Many soil bacteria live with cooperation one another in their communities, so that enrichment such as coculture of using other bacterial metabolites and subsequent pure cultures can also guarantee successful cultivation of the previously uncultured bacteria in soil. Here, this review will discuss for the future perspectives to culture the unculturable soil bacteria.
Inhibition of Hepatitis C Virus (HCV) Replication by Hammerhead Ribozyme Which Activity Can Be Allosterically Regulated by HCV NS5B RNA Replicase
Lee, Chang-Ho ; Lee, Seong-Wook ;
The Korean Journal of Microbiology, volume 47, issue 3, 2011, Pages 188~193
As a specific and effective therapeutic genetic material against hepatitis C virus (HCV) multiplication, HCV internal ribosome entry site (IRES)-targeting hammerhead ribozyme which activity is allosterically regulated by HCV regulatory protein, NS5B RNA replicase, was constructed. The allosteric ribozyme was composed of sequence of RNA aptamer to HCV NS5B, communication module sequence which can transfer structural transition for inducing ribozyme activity upon binding NS5B to the aptamer, and sequence of ribozyme targeting +382 nucleotide of HCV IRES. With real-time PCR analysis, the ribozyme was found to efficiently inhibit HCV replicon replication in cells. Of note, the allosteric ribozyme was shown to inhibit HCV replicon replication more efficiently than either HCV genome-targeting ribozyme or NS5B aptamer only. This allosteric ribozyme can be used as a lead genetic agent for the specific and effective suppression of HCV replication.
Characterization of an Alkaline Protease from an Alkalophilic Bacillus pseudofirmus HS-54
Bang, Seong-Ho ; Jeong, In-Sil ;
The Korean Journal of Microbiology, volume 47, issue 3, 2011, Pages 194~199
An alkalophilic bacterium producing alkaline protease was isolated from waste water and solar saltern sample and identified as Bacillus pseudofirmus HS-54 based on morphological, biochemical characteristics as well as 16S-rRNA gene sequencing. The HS-54 protease was purified to homogeneity using ammonium sulfate precipitation, DEAE cellulose column chromatography, and sephadex G-100 gel filtration with a 4.0 purification fold. The molecular mass of the purified enzyme was estimated by SDS-PAGE to be 27 kDa. The optimal pH and temperature for the purified protease activity were 10.0 and
, respectively. The purified enzyme was relatively stable at the pH range of 6.0-11.0 and at the temperature below
. This enzyme was activated by
and inhibited by
. And this enzyme was strongly inhibited by PMSF, suggesting that it belongs to the serine protease superfamily.
Investigation on Inhibitory Effect of ErmSF N-Terminal End Region Peptide on ErmSF Methyltansferase Activity In Vivo Through Development of Co-Expression System of Two Different Proteins in One Cell
Jin, Hyung-Jong ;
The Korean Journal of Microbiology, volume 47, issue 3, 2011, Pages 200~208
Most problematic antibiotic resistance mechanism for MLS (macrolide-lincosamide-streptogramn B) antibiotics encountered in clinical practice is mono- or dimethylation of specific adenine residue at 2058 (E. coli coordinate) of 23S rRNA which is performed by Erm (erythromycin ribosome resistance) protein through which bacterial ribosomes reduce the affinity to the antibiotics and become resistant to them. ErmSF is one of the four gene products produced by Streptomyces fradiae to be resistant to its own antibiotic, tylosin. Unlike other Erm proteins, ErmSF harbors idiosyncratic long N-terminal end region (NTER) 25% of which is comprised of arginine well known to interact with RNA. Furthermore, NTER was found to be important because when it was truncated, most of the enzyme activity was lost. Based on these facts, capability of NTER peptide to inhibit the enzymatic activity of ErmSF was sought. For this, expression system for two different proteins to be expressed in one cell was developed. In this system, two plasmids, pET23b and pACYC184 have unique replication origins to be compatible with each other in a cell. And expression system harboring promoter, ribosome binding site and transcription termination signal is identical but disparate amount of protein could be expressed according to the copy number of each vector, 15 for pACYC and 40 for pET23b. Expression of NTER peptide in pET23b together with ErmSF in pACYC 184 in E. coli successfully gave more amounts of NTER than ErmSF but no inhibitory effects were observed suggesting that there should be dynamicity in interaction between ErmSF and rRNA rather than simple and fixed binding to each other in methylation of 23S rRNA by ErmSF.
Analysis of Archaeal Communities in Full-Scale Anaerobic Digesters Using 454 Pyrosequencing
Kang, Hyun-Jin ; Kim, Taek-Seung ; Lee, Young-Haeng ; Lee, Taek-June ; Han, Keum-Suk ; Choi, Young-Jun ; Park, Hee-Deung ;
The Korean Journal of Microbiology, volume 47, issue 3, 2011, Pages 209~217
Archaeal communities were investigated using 454 pyrosequencing technology based on 16S rRNA gene in 11 samples collected from six different full-scale anaerobic digesters. Observed operational taxonomic units (OTUs) estimated from the archaeal 16S rRNA gene sequences were 13-55 OTUs (3% cutoff) which was corresponded to 29-89% of Chao1 richness estimates. In the anaerobic digesters there were archaeal sequences within the orders Thermoproteales, Thermoplasmatales, Desulfurococcales as well as within the orders Methanomicrobiales, Methanobacteriales, Methanococcales, Methanosarcinales, and Methanocellales, which are known to produce methane. Among these orders, Methanococcales known to produce methane using hydrogen was the predominant taxon and constituted 51.8-99.7% of total sequences. All samples showed a very similar community structure (Pearson correlation coefficient=0.99) except for one sample based on a heat map analysis. In addition, canonical correspondence analysis correlating archaeal communities to the environmental variables demonstrated that digester temperature and total solids removal rate were the two important explanatory variables. Overall results suggested that environmental and operational variables of anaerobic digester are important factors determining archaeal diversity and community structure.
Isolation, Identification, and Characterization of Ornithine-Producing Enterococcus faecalis OA18 from Kefir Grain
Yu, Jin-Ju ; Kim, Su-Gon ; Seo, Kyoung-Won ; Oh, Suk-Heung ;
The Korean Journal of Microbiology, volume 47, issue 3, 2011, Pages 218~224
Lactic acid bacteria (LAB) OA18 was isolated from yogurt prepared by using Kefir Grain as a starter. The OA18 strain was a Gram-positive, cocci-type bacterium, and able to grow anaerobically with
production. The OA18 strain grew well on MRS broth supplemented with 50 mM arginine at
and pH of 7.0-9.0. The optimum temperature and pH for growth are
and pH 7.0. The isolate fermented ribose, D-glucose, cellobiose, D-trehalose, but not L-xylose, D-melibiose, and inositol. The 16S rRNA gene sequence of the isolate showed 99.8% homology with the Enterococcus faecalis 16S rRNA gene (Access no. AB012212). Based on the biochemical characteristics and 16S rRNA gene sequence analysis data, it was identified and named as E. faecalis OA18. The E. faecalis OA18 strain showed a high ornithine-producing capacity in the presence of arginine and also showed an antimicrobial activity against Streptomyces strains such as Streptomyces coelicolor subsp. Flavus, S. coeruleorubidus, S. coeruleoaurantiacus, S. coelicolor, S. coeruleoprunus. The cell growth of E. faecalis OA18 strain was maintained in MRS broth with a NaCl concentration of 0-7%.
Production and Properties of Hemicellulases by an Isolate of Microbacterium sp.
Yoon, Ki-Hong ;
The Korean Journal of Microbiology, volume 47, issue 3, 2011, Pages 225~230
A bacterium producing the extracellular mannanase and xylanase was isolated from Korean farm soil by successive subcultures in a minimal medium supplemented with palm kernel meal (PKM) and rice bran. The isolate YB-1106 showed 98% similarity with Microbacterium arabinogalactanolyticum on the basis of 16S rRNA gene sequences. The additional carbohydrates including locust bean gum (LBG) and PKM increased the mannanase productivity of the YB-1106, while the xylanase productivity of the isolate was increased by wheat bran, oat spelt xylan, rice bran and xylose. Particularly, maximum mannanase and xylanase activities were obtained in the culture filtrate of tryptic soy broth supplemented with 1% LBG or 2% wheat bran, respectively. Both enzyme activities were produced at stationary growth phase. The mannanase of culture supernatant was the most active at
and pH 6.0, while xylanase of culture supernatant was the most active at
and pH 6.5. The predominant products resulting from the mannanase or xylanase hydrolysis were oligosaccharides for LBG or xylan, respectively.
Bile Salts Degradation and Cholesterol Assimilation Ability of Pediococcus pentosaceus MLK67 Isolated from Mustard Leaf Kimchi
Lim, Sung-Mee ;
The Korean Journal of Microbiology, volume 47, issue 3, 2011, Pages 231~240
The objective of this study was to evaluate the acid and bile tolerance, bile salt hydrolase (BSH) activity, and cholesterol assimilation ability of lactic acid bacteria isolated from mustard leaf kimchi. MLK11, MLK22, MLK27, MLK41, and MLK67 were relatively acid- and bile-tolerant strains, with more than
CFU/ml after incubation in simulated gastric juice and intestinal fluid, while MLK53 was the most sensitive strain to acid and bile. Strains MLK22 and MLK67 deconjugated the highest level of sodium glycocholate with more than 3.5 mM of cholic acid released, while deconjugation was lowest by strains MLK13 and MLK41 which released only 1.35 mM and 1.16 mM, respectively. Specially, strains MLK22 and MLK67 showed higher deconjugation of sodium glycocholate compared to sodium taurocholate and conjugated bile mixture. Although strains MLK22 and MLK67 exhibited maximal BSH activity at the stationary phase, MLK22 had somewhat higher total BSH activity compared to MLK67 towards both sodium glycocholate and sodium taurocholate. Meanwhile, cholesterol removal varied among tested strains (p<0.05) and ranged from 5.22 to 39.16
/ml. Especially, MLK67 strain assimilated the highest level of cholesterol in media supplemented with 0.3% oxgall, cholic acid, and taurocholic acid (p<0.05). According to physiological and biological characteristics, pattern of carbohydrate fermentation, and 16S rDNA sequence, strain MLK67 that may be considered as probiotic strain due to acid and bile tolerance and cholesterol-lowering effects was identified as Pediococcus pentosaceus MLK67.
The Antibacterial Effects of Oriental Medicinal Herbs on Bacteria Isolated from Contaminated Beverages
Yu, Young-Eun ; Kim, Ok-Ah ; Kim, Sang-Chan ; Park, Sung-Min ;
The Korean Journal of Microbiology, volume 47, issue 3, 2011, Pages 241~248
The use of synthetic additives for preservation and enhancement of the market quality of food products has been emerging as a societal issue in terms of safety as well as changes in consumption patterns. Various research related to natural additives is being conducted to address these issues. This study examined the antibacterial effects of 79 types of medicinal herbs used as oriental remedies on bacteria isolated from beverages of damaged marketable quality. The antibacterial effects of methanol extracts on 13 Bacillus sp. and three Paenibacillus sp. were evaluated. We found that 43 of the herbal medicines analyzed had antibacterial effects on the isolated bacteria. Of those, eight were selected, and their antibacterial effects were further examined using water, ethanol, methanol, and ethyl acetate as solvents. The results revealed that Prunus mume, Rhus javanica, and Coptis japonica had excellent antibacterial effects against the isolated bacteria. In particular, they exerted greater antibacterial effects when water and ethanol were used as solvents. This result indicates the possibility of developing natural additives using these substances. Since P. mume in particular, has not been sufficiently studied compared to other herbal medicines, it presents an opportunity for additional investigation and the possibility for development as a new product in the future.
Effects of Carbon and Nitrogen Sources on Immunosuppressant Mycophenolic Acid Fermentation by Penicillium brevi-compactum
Rho, Yong-Taek ;
The Korean Journal of Microbiology, volume 47, issue 3, 2011, Pages 249~254
Mycophenolic acid blocking the synthesis of xanthosine monophosphate is a nonnucleoside inhibitor of inosine monophosphate dehydrogenase. Therefore mycopholoic acid is a drug currently used as immunosuppressive agent in transplantation of heart, kidney and liver. Mycophenolic acid has been industrially produced through fermentation process by fungus Penicillium brevi-compactum. In this study, the profile of mycophenolic acid fermentation was observed in 5L-jar fermentor to investigate the utilization of carbon and nitrogen sources and the production of mycophenolic acid. It was investigated that what kind of carbon sources was better to cell growth and mycophenolic acid production. Fructose was the best carbon source for mycophenolic acid fermentation, but it is the most expensive one. Thereafter molasses containing sucrose as the supply source of fructose was confirmed to be the best carbon source for the industrial production. Use of molasses increased the fermentation yield of mycophenolic acid more than two times higher than glucose. It was confirmed that urea was the best inorganic nitrogen source, which did not give rise to sudden drop of culture pH. Addition of urea increased the fermentation yield of mycophenolic acid about 3.6 times higher than addition of ammonium nitrate as control. Casein, peptone and casamino acid originated from milk protein increased the fermentation yield of mycophenolic acid about 3.4 times higher than control. Peptone and casamino acid, which are casein hydrolysates, increased cell growth considerably as well.
Isolation and Characterization of Acid Protease Produced by Staphylococcus sp. CB2-3 from Digestive Organ of Harmonia axyridis
Kim, Se-Jong ; Whang, Kyung-Sook ;
The Korean Journal of Microbiology, volume 47, issue 3, 2011, Pages 255~262
Six protein-degrading bacteria were isolated from digestive organ of Harmonia axyridis. These isolates were categorized as Staphylococcus sciuri subsp. sciuri (3 strains), Bacillus subtilis (1 strain), and Bacillus thuringiensis (2 strains) by 16S rRNA gene sequence analysis. The Staphylococcus sp. CB2-3 was selected as a protease-producing bacterium which showed the highest protease activity of 58.5 U/ml at the pH 5.0 medium. The optimal pH and temperature of protease activity were pH 5.0 and
, respectively. This acid protease had a relatively high stability of 80% between
at broad temperature range. The opimal medium compositions of carbon, nitrogen and mineral source for cell growth and protease activity were investigated. When sorbitol (0.5%) was used as carbon source, enzyme activity was increased about 2 times than that of the basal medium. When skim milk (0.5%) was used as nitrogen source, activity was increased about 2.5 times than that of the control. Cell growth and enzyme activity were increased by mineral source such as KCl,
, but was completely inhibited by divalent ions such as
Analysis of Probabilistic Limits of Trait Identity in Inter-Strain Comparison of Genomic Fingerprints of Bacteria
Zo, Young-Gun ;
The Korean Journal of Microbiology, volume 47, issue 3, 2011, Pages 263~267
Genomic fingerprinting methods are useful in determining relatedness among bacterial strains. However, random coincidences in sizes of two DNA fragments in two different fingerprints may occur, resulting in erroneous interpretation of relatedness between two bacterial genomes. In this study, I estimated the probability of occurrence of DNA bands of identical size in fingerprints of two unrelated genomes, so that the significance of fingerprint-based estimation of genome relatedness could be analyzed. The probability could be estimated as outputs of a function formulated with the three parameters: the numbers of observed fragments, all possible sizes of fragments and observed fragments common in a given pair of fingerprints. The parameter most instrumental to significance of relatedness estimation was the number of all possible sizes of fragments. To keep the number of coincidentally-common size of fragments below 10, about 200 fragments should be distinguishable in the fingerprints.
Analysis of RNA Polymerase Beta Subunit (rpoB) Gene Sequences for the Discrimination of Cyanobacteria Anabaena Species
Cheon, Ju-Yong ; Lee, Min-Ah ; Ki, Jang-Seu ;
The Korean Journal of Microbiology, volume 47, issue 3, 2011, Pages 268~274
Anabaena (Cyanobacteria, Nostocales) are important for water quality controls, because they are often responsible for freshwater green tides; moreover, some species are reported to produce hepatotoxin. In this study, we sequenced RNA polymerase beta subunit (rpoB) gene of Anabaena, and evaluated their sequences for the potential use of a molecular taxonomic marker in this taxon. Anabaena rpoB showed low DNA similarity and high genetic divergences when compared those of 16S rRNA, and the molecular differences were statistically significant (Student t-test, p<0.01). Parsimony analyses showed the rpoB gene evolves 4.8-fold faster than 16S rRNA. In addition, phylogeny of the rpoB gene separated each Anabaena strain more clearly compared with a 16S rRNA tree. These results suggest that the rpoB gene is a useful marker for the molecular phylogenetics and the species discrimination of Anabaena.
Bacterial Community Profiling during the Manufacturing Process of Traditional Soybean Paste by Pyrosequencing Method
Kim, Yong-Sang ; Jeong, Do-Yeon ; Hwang, Young-Tae ; Uhm, Tai-Boong ;
The Korean Journal of Microbiology, volume 47, issue 3, 2011, Pages 275~280
In order to evaluate the diversity and change of bacterial population during the manufacturing process of traditional soybean paste (doenjang), bacterial communities were analyzed using 16S rRNA gene-based pyrosequencing. In rice straw, the most important inoculum source for fermentation, the bacterial sequences with a relative abundance greater than 1% were assigned to four phyla, Proteobacteria (71%), Actinobacteria (20.6%), Bacteroidetes (4.2%), and Firmicutes (1.3%). Unlike bacterial community composition of rice straw, a different pattern of bacterial population in meju was observed with predominantly high abundance (99.1%) of Firmicutes. Phylum composition in young doenjang was almost same as that of meju. Major genera in young doenjang were Bacillus (81.3%), Clostridium (6.9%) and Enterococcus (6.3%) and the predominant species among bacterial population was B. amyloliquefaciens (63.6%). Abundance of the phylum Firmicutes in mature doenjang was 99.98%, which was even higher value than those in meju and young doenjang. Predominant species in mature doenjang were B. amyloliquefaciens (67.3%), B. atrophaeus (12.7%), B. methylotrophicus (6.5%), B. mojavensis (3.2%), and B. subtilis. (2.5%), which were also identified as major species of the microbial flora in meju. These results suggested that rice straw was a primary source for supplement of Bacillus species in manufacturing the traditional doenjang and that some species of Bacillus strains were mainly involved in the fermentation process of traditional doenjang.