• The Korean Journal of Malacology
• /
• v.28 no.4
• /
• pp.377-384
• /
• 2012

The importance of biological resources has been gradually increasing, and mollusks have been utilized as main fishery resources in terrestrial ecosystems. But little is known about genomic and transcriptional analysis in mollusks. This is the first report on the transcriptomic profile of Meretrix lusoria. In this study, we constructed cDNA library and determined 542 of distinct EST sequences composed of 284 singletons and 95 contigs. At first, we identified 180 of EST sequences that have significant hits on protein sequences of the exclusive Mollusks database through BLASTX program and 343 of EST sequences that have significant hits on NCBI NR database. We also found that 211 of putative sequences through local BLAST (blastx, E < e-10) search against KOG database were classified into 16 functional categories. Some kinds of immune response related genes encoding allograft inflammatory factor 1 (AIF-1), B-cell translocation gene 1 (BTG1), C-type lectin A, thioester-containing protein and 26S proteasome regulatory complex were identified. To determine phylogenetic relationship, we identified partial sequences of four genes (COX1, COX2, 12S rRNA and NADH dehydrogenase) that significantly matched with the mitochondrial genomes of 3 species-Ml (Meretrix lusoria), Mp (Meretrix petechialis) and Mm (Meretrix meretrix). As a result, we found that there was a little bit of a difference between sequences of Korean isolates and other known isolates. This study will be useful to develop breeding technology and might also be helpful to establish a classification system.

• Journal of Microbiology
• /
• v.45 no.2
• /
• pp.113-121
• /
• 2007

The bacterial diversity inherent to the biofilm community structure of a modified rotating biological contactor wastewater treatment process, referred to as the Rotating Activated Bacillus Contactor (RABC) process, was characterized in this study, via both culture-dependent and culture-independent methods. On the basis of culture-dependent methods, Bacillus sp. were found to exist in large numbers on the biofilm (6.5% of the heterotrophic bacteria) and the microbial composition of the biofilms was quite simple. Only three phyla were identified-namely, the Proteobacteria, the Actinobacteria (High G+C Gram-positive bacteria), and the Firmicutes (Low G+C Gram-positive bacteria). The culture-independent partial 16S rDNA sequence analysis revealed a considerably more diverse microbial composition within the biofilms. A total of eight phyla were recovered in this case, three of which were major groups: the Firmicutes (43.9%), the Proteobacteria (28.6%), and the Bacteroidetes (17.6%). The remaining five phyla were minor groups: the Planctomycetes (4.4%), the Chlorobi (2.2%), the Actinobacteria (1.1%), the Nitrospirae (1.1%), and the Verrucomicrobia (1.1%). The two most abundant genera detected were the endospore-forming bacteria (31.8%), Clostridium and Bacillus, both of which are members of the Firmicutes phylum. This finding indicates that these endospore-forming bacteria successfully colonized and dominated the RABC process biofilms. Many of the colonies or clones recovered from the biofilms evidenced significantly high homology in the 16S rDNA sequences of bacteria stored in databases associated with advanced wastewater treatment capabilities, including nitrification and denitrification, phosphorus accumulation, the removal of volatile odors, and the removal of chlorohydrocarbons or heavy metals. The microbial community structures observed in the biofilms were found to correlate nicely with the enhanced performance of advanced wastewater treatment protocols.

• Food Science of Animal Resources
• /
• v.28 no.5
• /
• pp.587-595
• /
• 2008

In order to develop a new starter for fermented milk, 1037 bacterial strains were isolated from raw milk. The strain that showed excellent acid producing and angiotensin converting enzyme (ACE) inhibitory activity (88.6%) was selected and identified as a Lactobacillus zeae based on the result of API carbohydrate fermentation pattern and 16S rDNA sequence. Lactobacillus zeae RMK354 was investigated further to study its physiological characteristics. It showed strong ACE inhibitory activity compared with commercial LAB starters tested. The optimum growth temperature of L. zeae RMK354 was $40^{\circ}C$ and it took 10 hr to reach pH 4.3 under this condition. L. zeae RMK354 showed more sensitive to penicillin-G, bacitracin, novobiocin, in a comparison of 14 different antibiotics, and showed most resistance to polymyxin B and vancomycin. It showed higher esterase and leucine arylamidase activities compared with 16 other enzymes. It was comparatively tolerant to bile juice and able to survive at pH 2 for 3 hr. It showed inhibitory activity against Salmonella Typhimurium with the rate of 60%. Based on these and previous results, L. zeae RMK354 could be an excellent starter culture for fermented milk with high level of ACE inhibitory activity.

• Korean Journal of Microbiology
• /
• v.49 no.1
• /
• pp.38-45
• /
• 2013

In this study, euryhaline marine microorganism, Bacillus sp. strain EBW4 isolated from polychaete (Perinereis aibuhitensis) of Suncheon Bay was physiologically, biochemically and genetically characterized. Based on 16S rRNA sequence, EBW14 was found to share 98.25% similarity with Bacillus hemicentroti $JSM076093^T$, 97.96% similarity with Bacillus hwajinponensis SW-$72^T$ and 96.28% similarity with B. algicoa $KMM3737^T$, respectively. The temperature range for the growth of strain EBW4 was $4-40^{\circ}C$, NaCl concentration range 0-17% and pH range pH 5-9, revealing that EBW4 was euryhaline bacterium. Major fatty acids in strain EBW4 were composed of anteiso $C_{15:0}$ (48.2%), iso $C_{16:0}$ (12.1%), anteiso $C_{17:0}$ (11.6%) and iso $C_{14:0}$ (9.4%). EBW4 was found to have DNase, amylase, protease and lipase for the degradation of macromolecules such as DNA, carbohydrates, proteins, lipids, etc. The enzyme activities of alkaline phosphatase, esterase (C4), leucine arylamidase and ${\alpha}$-chymotrypsin were also found in strain EBW4. Analysis of the biodegradation ability of EBW4 for organic hydrocarbons under different salinity conditions using synthetic water waste revealed that EBW4 exhibited the ability to degrade organic hydrocarbons very quickly, suggesting strain EBW4 may be a good candidate for the application to various industries.

• Journal of Microbiology and Biotechnology
• /
• v.28 no.1
• /
• pp.22-31
• /
• 2018

Isoflavone itself is less available in the body without the aid of intestinal bacteria. In this study, we searched for isoflavone-transforming bacteria from human fecal specimens (n = 14) using differential selection media. Isoflavone-transforming activity as the production of dihydrogenistein and dihydrodaidzein was assessed by high-performance liquid chromatography and we found Lactobacillus rhamnosus, named L. rhamnosus vitaP1, through 16S rDNA sequence analysis. Extract from Pueraria lobata (EPL) and soy hypocotyl extract were fermented with L. rhamnosus vitaP1 for 24 and 48 h at $37^{\circ}C$. Fermented EPL (FEPL) showed enhanced anti-tyrosinase activity and antioxidant capacities, important suppressors of the pigmentation process, compared with that of EPL (p < 0.05). At up to $500{\mu}g/ml$ of FEPL, there were no significant cell cytotoxicity and proliferation on B16-F10 melanoma cells. FEPL ($100{\mu}g/ml$) could highly suppress the content of melanin and melanosome formation in B16-F10 cells. In summary, Lactobacillus rhamnosus vitaP1 was found to be able to biotransform isoflavones in EPL. FEPL showed augmented anti-melanogenic potential.

• Journal of Microbiology and Biotechnology
• /
• v.19 no.10
• /
• pp.1244-1249
• /
• 2009

Endophytic fungi are known for the production of valuable metabolites, but information on the gibberellin production capacity of this group is limited. We isolated 9 endophytic fungi from the roots of salt-stressed soybean plants and screened them on waito-c rice, in order to identify plant growth promoting fungal strains. The fungal isolate TK-2-4 gave maximum plant length (20.35 cm) promotion in comparison with wild-type Gibberella fujikuroi (19.5 cm). In a separate experiment, bioassay of TK-2-4 promoted plant length and biomass of soybean cultivar Taegwangkong. The TK-2-4 culture filtrate was analyzed for the presence of gibberellins, and it was found that all physiologically active gibberellins, especially $GA_4$ and $GA_7$, were present in higher amounts ($GA_1$, 0.11 ng/ml; $GA_3$, 2.91 ng/ml; $GA_4$, 3.21 ng/ml; and $GA_7$, 1.4 ng/ml) in conjunction with physiologically inactive $GA_9$ (0.05 ng/ml), $GA_{12}$ (0.23 ng/ ml), $GA_{15}$ (0.42 ng/ml), $GA_{19}$ (0.53 ng/ml), and $GA_{20}$ (0.06 ng/ml). The fungal isolate TK-2-4 was later identified as a new strain of Phoma herbarum, through the phylogenetic analysis of 28S rDNA sequence.

• Journal of Microbiology and Biotechnology
• /
• v.28 no.9
• /
• pp.1517-1526
• /
• 2018

Investigating bacterial diversity and its metabolic capabilities is crucial for interpreting the ecological patterns in a desert environment and assessing the presence of exploitable microbial resources. In this study, we evaluated the spatial heterogeneity of physicochemical parameters, soil bacterial diversity and metabolic adaptation at meter scale. Soil samples were collected from two quadrats of a desert (Thar Desert, India) with a hot, arid climate, very little rainfall and extreme temperatures. Analysis of physico-chemical parameters and subsequent variance analysis (p-values < 0.05) revealed that sulfate, potassium and magnesium ions were the most variable between the quadrats. Microbial diversity of the two quadrats was studied using Illumina bar-coded sequencing by targeting V3-V4 regions of 16S rDNA. As for the results, 702504 high-quality sequence reads, assigned to 173 operational taxonomic units (OTUs) at species level, were examined. The most abundant phyla in both quadrats were Actinobacteria (38.72%), Proteobacteria (32.94%), and Acidobacteria (9.24%). At genus level, Gaiella represented highest prevalence, followed by Streptomyces, Solirubrobacter, Aciditerrimonas, Geminicoccus, Geodermatophilus, Microvirga, and Rubrobacter. Between the quadrats, significant difference (p-values < 0.05) was found in the abundance of Aciditerrimonas, Geodermatophilus, Geminicoccus, Ilumatobacter, Marmoricola, Nakamurella, and Solirubrobacter. Metabolic functional mapping revealed diverse biological activities, and was significantly correlated with physicochemical parameters. The results revealed spatial variation of ions, microbial abundance and functional attributes in the studied quadrats, and patchy nature in local scale. Interestingly, abundance of the biotechnologically important phylum Actinobacteria, with large proposition of unclassified species in the desert, suggested that this arid environment is a promising site for bioprospection.

• Journal of Applied Biological Chemistry
• /
• v.52 no.4
• /
• pp.163-169
• /
• 2009

A total of 155 microbial strains were isolated from the Korean traditional soybean paste based on their morphological features on the growth of agar plate. Among the isolated strains, a total of 28 strains were capable of hydrolyzing isoflavone glycoside to isoflavone aglycone efficiently in the soybean paste. Finally, two strains, K123-1 and SI, were selected because of their resistance to 15% NaCl and ability to convert isoflavone glycoside to isoflavone aglycone efficiently during the fermentation of soybean paste. The isolated strains K123-1 and SI were identified to be Pichia guilliermondii and Candida fermentati, respectively, using the partial 26S rDNA sequence analysis and phylogenic analysis. Pichia guilliermondii K123-1 and Candida fermentati SI converted daidzin to daidzein up to 96% and 95%, respectively, and genistin to genistein up to 92% when soybean pastes were fermented at $30^{\circ}C$ for 20 days with a single isolated strain. Pichia guilliermondii K123-1 and Candida fermentati SI were able to grow in the presence of 15% NaCl on both liquid medium and agar plate. We think that Pichia guilliermondii K123-1 and Candida fermentati SI might be one of good candidates for making functional soybean paste because they are isolated from the Korean traditional soybean paste and have a good ability to convert isoflavone glycosides to isoflavone aglycones and a high salt tolerance.

• Microbiology and Biotechnology Letters
• /
• v.33 no.2
• /
• pp.90-95
• /
• 2005

An Actinomycetes producing an anti-VRSA (vancomycin-resistant Staphylococcus aureus) substance was isolated from soil. The cultural, morphological, physiological and phylogenetic analyses of an isolated strain were investigated for identification. Cultural characteristics based on ISP (International Streptomyces Project) were as follows: white aerial mycelium, yellow reverse side, and good growth on various medium. Also, the isolate did not produce the soluble pigment. Morphological characteristics were showed cylindrical spore chain and smooth spore surface by SEM (Scanning Electron Microscope). Physiological characteristics were showed LL-type by DAP isomer analysis and detected glycine, glutamic acid and alanine. A phylogenetic analysis of the 16S rDNA provided a clue that the isolated strain was actually a member of the genus Streptomyces, because the determined sequence exhibited a higher homology with Streptomyces echinatus. The isolate was identified to be a genus of Streptomyces sp.. The optimal culture conditions for the maximum production of anti-VRSA substance by Streptomyces sp. were attained in a culture medium composed of $2.0\%$ (w/v) glucose, and $0.4\%$ (w/v) yeast extract. The anti-VRSA substance was highly produced after 5 days of culture. Optimal pH and temperature conditions for the production of anti-VRSA substance were pH 7.0 and $28^{\circ}C$, respectively.

• Mycobiology
• /
• v.39 no.3
• /
• pp.200-205
• /
• 2011

Marssonina coronaria associated with apple blotch disease causes severe premature defoliation, and is widely distributed in Korea. Thirteen isolates were collected from orchards located in Gyeongbuk Province from 2005~2007. All isolates displayed over 99.6% and 99.2% sequence similarity to each other in internal transcribed spacer regions and partial sequences of 28S rDNA, respectively. The isolates were phylogenetically closely related to Chinese isolates. Selected isolates did not differ in their pathogenicity. The optimum conditions for fungal growth were $20^{\circ}C$ and pH 6 on peptone potato dextrose agar (PPDA). Peptone and mannose were the best nitrogen and carbon source, respectively. Fungal growth was better on PPDA than on common potato dextrose agar. This study provides valuable information for integrated disease management program and facilitates the routine culturing of M. coronaria.