• Korean Journal of Microbiology
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• v.53 no.3
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• pp.180-192
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• 2017

The purpose of this study is to investigate the antioxidative and antimicrobial activities of sourdough fermented with the lactic acid bacteria (LAB) isolated from sliced radish kimchi. According to 16S rRNA gene sequence analysis, the isolated lactic acid bacteria were categorized as Leuconostoc dextranicum SRK03, Lactobacillus brevis SRK15, Pediococcus halophilus SRK22, Lactobacillus acidophilus SRK30, Lactobacillus plantarum SRK38, Leuconostoc citreum SRK 42, and Lactobacillus delbrueckii SRK60 with sequence similarity of 99%. After fermentation with L. dextranicum SRK03, L. acidophilus SRK30, L. plantarum SRK38 or L. delbrueckii SRK60 and Saccharomyces cerevisiae KCTC 7246 at $30^{\circ}C$ for 24 h LAB and yeast in sourdough were present at levels of $10^9$ and $10^7CFU/g$, respectively. In particular, the titratable acidity and ethanol and exopolysaccharide contents of sourdough fermented with L. dextranicum SRK03 were also significantly (P < 0.05) higher than those of sourdough fermented with L. acidophilus SRK30, L. plantarum SRK38, or L. delbrueckii SRK60. The sourdough fermented with L. dextranicum SRK03 and L. acidophilus SRK30 showed not only good DPPH radical-scavenging capacity but anti-lipid peroxidation activity. In addition, the viable counts of Bacillus cereus ATCC 11778 and Staphylococcus aureus ATCC 6538 in sourdough during storage for 5 days at $25^{\circ}C$ were significantly (P < 0.05) lower than those of pathogenic bacteria in the control group due to the organic acids and bacteriocin produced by L. acidophilus SRK30 strain.

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

• Korean Journal of Poultry Science
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• v.34 no.2
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• pp.85-90
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• 2007

The chicken liver has been involved in various biological functions including detoxification, glycogen storage and plasma protein synthesis. The aim of this study was to investigate differentially expressed genes in chicken liver in four different growing stages. Using 10 arbitrary Annealing Control Primers (ACPs), five differentially expressed genes have been identified. Based on the Basic Local Alignment Search Tool (BLAST) search results, three of them were matched with previously known genes, and the other two were matched with unknown EST sequence and a hypothetical protein, respectively. In order to confirm the expression results, quantitative real-time PCR was also performed. The high similarities between the expression data using arbitrary ACPs and quantitative real-time PCR indicate that the identified genes are the real differentially expressed genes in different growing stages. The genes identified in this study can be used as valuable biomarkers in chicken with further investigation of the functions.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.9
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• pp.1464-1473
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• 2018

Objective: To describe in-depth sequencing, the bacterial community diversity and its succession during ensiling of whole-plant maize and subsequent exposure to air. Methods: The microbial community dynamics of fermented whole-plant maize for 60 days (sampled on day 5, 10, 20, 40, 60) and subsequent aerobic exposure (sampled on day 63 after exposure to air for 3 days) were explored using Illumina Miseq sequence platform. Results: A total of 227,220 effective reads were obtained. At the genus level, there were 12 genera with relative abundance >1%, Lactobacillus, Klebsiella, Sporolactobacillus, Norank-c-cyanobacteria, Pantoea, Pediococcus, Rahnella, Sphingomonas, Serratia, Chryseobacterium, Sphingobacterium, and Lactococcus. Lactobacillus consistently dominated the bacterial communities with relative abundance from 49.56% to 64.17% during the ensiling process. Klebsiella was also an important succession bacterium with a decrease tendency from 15.20% to 6.41% during the ensiling process. The genus Sporolactobacillus appeared in late-ensiling stages with 7.70% abundance on day 40 and 5.32% on day 60. After aerobic exposure, the Lactobacillus decreased its abundance from 63.2% on day 60 to 45.03% on d 63, and Klebsiella from 5.51% to 5.64%, while Sporolactobacillus greatly increased its abundance to 28.15%. These bacterial genera belong to 5 phyla: Firmicutes (relative abundance: 56.38% to 78.43%) was dominant, others were Proteobacteria, Bacteroidetes, Cyanobacteria, and Actinobacteria. The bacterial communities clearly clustered into early-ensiling (d 5), medium-ensiling (d 10, d 20), late-ensiling (d 40, d 60), and aerobic exposure (d 63) clusters, with early- and late-ensiling communities more like each other than to the aerobic exposure communities. Conclusion: High-throughput sequencing based on 16S rRNA genes proved to be a useful method to explore bacterial communities of silage. The results indicated that the bacterial communities varied during fermentation and more dramatically during aerobic exposure. The study is valuable for understanding the mechanism of population change and the relationship between bacteria and ensilage characteristics.

• Journal of Life Science
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• v.25 no.6
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• pp.680-685
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• 2015

Previously, cellulase and xylanase producing microorganism, Bacillus subtilis NC1, was isolated from soil. Based on the 16S rRNA gene sequence and API 50 CHL test the strain was identified as Bacillus subtilis, and named as B. subtilis NC1. We cloned and sequenced the genes for cellulase and xylanase. Plus, the deduced amino acid sequences from the genes of cellulase and xylanase were determined and were also identified as glycosyl hydrolases family (GH) 5 and 30, respectively. In this study to optimize the medium parameters for cellulase production by B. subtilis NC1 the RSM (response surface methodology) based on CCD (central composite design) model was performed. Three factors, tryptone, yeast extract, and NaCl, for N or C source were investigated. The cellulase activity was measured with a carboxylmethyl cellulose (CMC) plate and the 3,5-dinitrosalicylic acid (DNS) methods. The coefficient of determination (R²) for the model was 0.960, and the probability value (p=0.0001) of the regression model was highly significant. Based on the RSM, the optimum conditions for cellulase production by B. subtilis NC1 were predicted to be tryptone of 2.5%, yeast extract of 0.5%, and NaCl of 1.0%. Through the model verification, cellulase activity of Bacillus subtilis NC1 increased from 0.5 to 0.62 U/ml (24%) compared to the original medium.

• Journal of Life Science
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• v.28 no.2
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• pp.223-228
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• 2018

Lactic acid bacteria were isolated from a variety of fermented seafoods and sea creatures from the East Sea Rim, Korea and were screened for ${\gamma}-amino$ butyric acid-producing (GABA) activity. Through a 16S rRNA sequence analysis, the bacteria of interest, which were GABA-positive on the thin-layer chromatography analysis, were recognized as three isolates of Lactobacillus (Lb.) brevis and one isolate of Lactococcus (Lc.) lactis. Lb. brevis FSFL0004 and FSFL0005 were isolated from fermented anglerfish and Lb. brevis FSFL0036 was derived from salted cutlass fish. The Lc. lactis strain FGL0007 was isolated from the gut of a brown sole flounder. According to HPLC analysis, the GABA contents produced by FSFL0004, FSFL0005, FSFL0036 and FGL0007 were equivalent to $10,754.37{\mu}g/ml$, $13,082.79{\mu}g/ml$, $12,290.19{\mu}g/ml$, and $45.07{\mu}g/ml$ respectively in 1% monosodium glutamate-supplemented methionyl-tRNA synthetase (MRS) broth. The four strains were inoculated in skim milk with 1% monosodium glutamate to commercialize the strains as starter cultures for GABA-enriched dairy products, and TLC results displayed the production of ${\gamma}-amino$ butyric acid by all four strains in the adaptation media. Lc. lactis FGL0007 demonstrated the greatest GABA production ($431.42{\mu}g/ml$) by HPLC analysis. The GABA production by lactic acid bacteria strains in the skim milk demonstrated in the present study may be helpful for the production of GABA-enriched dairy products.

• Journal of fish pathology
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• v.33 no.2
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• pp.111-118
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• 2020

The genus Edwardsiella belonging to the family Enterobacteriaceae is a member of Gram-negative rod-shaped bacteria that cause disease in diverse aquatic organisms such as fish, amphibians and reptiles as well as avians and mammals including human throughout the world. This genus had been composed of three species, E. hoshinae, E. ictaluri and E. tarda, but recent researches erected two novel species, E. anguillarum and E. piscicida that were conventionally identified as E. tarda. In this study, we isolated seven strains belonging to the genus Edwardsiella from freshwater fishes that had been reared at inland fish farms in South Korea and investigated their biochemical characteristics and molecular phylogenetic relationships. The seven strains showed typical characteristics of four Edwardsiella species, E. anguillarum, E. ictaluri, E. piscicida and E. tarda, by biochemical analyses of Gram staining, indole and hydrogen sulfide (H2S) production, and API (Analytic Profile Index) 20E test. Molecular phylogenetic analyses inferred from DNA sequence data of both 16S ribosomal RNA (rRNA) and DNA gyrase subunit B (gyrB) genes were congruent with the biochemical characteristics. As a result, both biochemical and molecular phylogenetic analyses identified four strains isolated from three Anguilla species as E. anguillarum, E. piscicida and E. tarda, two strains from Pelteobagrus fulvidraco and Silurus asotus as E. ictaluri, and one strain from Moroco oxycephalus as E. piscicida. In this study, we isolated and successfully identified recently newly erected species, E. anguillarum and E. piscicida in addition to historically notorious pathogenic species, E. ictaluri and E. tarda. In the future study, systematic and comprehensive monitoring of the four Edwardsiella species are required for studying differences in pathogenicity among freshwater fishes.

• The Journal of Engineering Geology
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• v.23 no.1
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• pp.37-46
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• 2013

Leakage of leachate from animal carcass disposal is a significant issue because disease can easily spread to humans and other livestock. In this study, we analyzed the physicochemical properties of leachate and tested for the presence of aerobic bacteria in leachate using molecular biology methods, for 16 animal carcass disposals in the first stage (after burial for 5 months). Leachate physicochemical analysis revealed higher total coliforms, TOC, $NH^{4+}$, and $NO^{3-}$ concentrations compared with previously published data. In most leachate samples, the concentrations of $NH^{4+}$ and $NO^{3-}$ exceeded the Korean guideline values for drinking water. In 16S rRNA sequence analysis of the distribution of leachate under aerobic conditions, Bacillus pumilus, Lysinibacillus sphaericus, and B. sphaericus were observed with high frequency, whereas no food-poisoning-related bacteria such as B. cereus or Salmonella were detected. The present findings improve our knowledge of the transport of leachate from animal carcass disposal sites through geologic media, and are useful in risk analysis and for subsequent studies.

• Journal of Microbiology and Biotechnology
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• v.21 no.1
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• pp.55-61
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• 2011

Forty yeast strains isolated from soils taken from different locations in Egypt were tested for their P-solubilizing activities on the basis of analyzing the clear zone around colonies growing on a tricalcium phosphate medium after incubation for 5 days at $25^{\circ}C$, denoted as the solubilization index (SI). Nine isolates that exhibited P-solubilization potential with an SI ranging from 1.19 to 2.76 were genetically characterized as five yeasts belonging to the genus Saccharomyces cerevisiae and four non-Saccharomyces, based on a PCR analysis of the ITS1-26S region amplied by SC1/SC2 species-specific primers. The highest P-solubilization efficiency was demonstrated by isolate PSY- 4, which was identified as Saccharomyces cerevisiae by a sequence analysis of the variable D1/D2 domain of the 26S rDNA. The effects of single and mixed inoculations with yeast PSY-4 and Bacillus polymyxa on the P-uptake and growth of corn were tested in a greenhouse experiment using different levels of a phosphorus chemical fertilizer (50, 100, and 200 kg/ha super phosphate 15.5% $P_2O_5$). The results showed that inoculating the corn with yeast PSY-4 or B. polymyxa caused significant increases in the shoot and root dry weights and P-uptake in the shoots and roots. The P-fertilization level also had a significant influence on the shoot and root dry weights and P-uptake in the shoots and roots when increasing the P-level from 50 up to 200 kg/ha. Dual inoculation with yeast strain PSY-4 and B. polymyxa at a P-fertilization level of 200 kg/ha gave higher values for the shoot and root dry weights and P-uptake in the shoots and roots, yet these increases were nonsignificant when compared with dual inoculation with yeast strain PSY-4 and B. polymyxa at a P-fertilization level of 100 kg/ha. The best increases were obtained from dual inoculation with yeast strain PSY-4 and B. polymyxa at a P-fertilization level of 100 kg/ha, which induced the following percentage increases in the shoot and root dry weights, and P-uptake in the shoots and roots; 16.22%, 46.92%, 10.09%, and 31.07%, respectively, when compared with the uninoculated control (fertilized with 100 kg/ha).

• Microbiology and Biotechnology Letters
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• v.44 no.2
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• pp.156-162
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• 2016

In this study, we isolated a new agar-degrading marine bacterium and characterized its agarase. An agardegrading marine bacterium SH-1 was isolated from seawater, collected from the seashore of Namhae in Gyeongnam province, Korea, and cultured in marine agar 2216 media. It was identified as Maribacter. sp. SH-1 by phylogenetic analyses, based on 16S rRNA gene sequence. The extracellular agarase was extracted from culture media of Maribacter sp. SH-1 and characterized. Its relative activities were 56, 62, 94, 100, and 8% at 20, 30, 40, 50, and 60℃, respectively, whereas 15, 100, 60, and 21% relative activities were observed at pH 5, 6, 7, and 8, respectively. Its extracellular agarase exhibited maximum activity (231 units/l) at pH 6.0 and 50℃, in 20 mM Tris-HCl buffer. Therefore, this agarase would be applicable as it showed the maximum activity at the temperature at which the agar is in a sol state. Furthermore, the agarase activities remained over 90% at 20, 30, and 40℃ after 0.5 h exposure at these temperatures. Thin layer chromatography analysis suggested that Maribacter sp. SH-1 produces extracellular β-agarase, as it hydrolyzes agarose to produce neoagarooligosaccharides, such as neoagarohexaose (34.8%), neoagarotetraose (52.2%), and neoagarobiose (13.0%). Maribacter sp. SH-1 and its β-agarase would be useful for the production of neoagarooligosaccharides, which shows functional properties, like skin moisturizing, skin whitening, inhibition of bacterial growth, and delay in starch degradation.