• The Journal of the Korean Society for Microbiology
• /
• v.34 no.6
• /
• pp.519-532
• /
• 1999

Helicobacter pylori is a causative agent of type B gastritis and plays a central role in the pathogenesis of gastroduodenal ulcer and gastric cancer. To elucidate the host-parasite relationship of the H. pylori infection on the basis of molecular biology, we tried to evaluate the genomic diversity of H. pylori. An ordered overlapping bacterial artificial chromosome (BAC) library of a Korean isolate, H. pylori 51 was constructed to set up a genomic map. A circular physical map was constructed by aligning ApaI, NotI and SfiI-digested chromosomal DNA. When the physical map of H. pylori 51 was compared to that of unrelated strain, H. pylori 26695, completely different restriction patterns were shown. Fifteen known genes were mapped on the chromosome of H. pylori 51 and the genetic map was compared with those of strain 26695 and J99, of which the entire genomic sequences were reported. There were some variability in the gene location as well as gene order among three strains. For further analysis on the genomic diversity of H. pylori, when comparing the genomic structure of 150 H. pylori Korean isolates with one another, genomic macrodiversity of H. pylori was characterized by several features: whether or not susceptible to restriction digestion of the chromsome, variation in chromosomal restriction fingerprint and/or high frequency of gene rearrangement. We also examined the extent of allelic variation in nucleotide or deduced amino acid sequences at the individual gene level. fucT, cagA and vacA were confirmed to carry regions of high variation in nucleotide sequence among strains. The plasticity zone and strain-specific genes of H. pylori 51 were analyzed and compared with the former two genomic sequences. It should be noted that the H. pylori 51-specific sequences were dispersed on the chromosome, not congregated in the plasticity zone unlike J99- or 26695-specific genes, suggesting the high frequency of gene rearrangement in H. pylori genome. The genome of H. pylori 51 shows differences in the overall genomic organization, gene order, and even in the nucleotide sequences among the H. pylori strains, which are far greater than the differences reported on the genomic diversity of H. pylori.

• Korean Journal of Microbiology
• /
• v.41 no.3
• /
• pp.168-176
• /
• 2005

Vibrio vulnificus, one of the marine bacterial pathogens causing septicemia, was detected using molecular methods, namely, PCR and/or Southern hybridization, and real-time PCR. Extracted and purified total DNAs by using commercial kits were used as templates for PCR. Multiplex-PCR was conducted by employing three sets of primers for the genes, hemolysin (vvhA), phosphomannomutase (pmm), and metalloprotease (vvpE), for V vulnificus virulence. The presence of DMSO ($5\%$) and BSA ($0.1\%$) in PCR reaction mixture improved a detection efficiency by higher PCR band intensities. TaqMan real-time PCR was carried out by using gene segment of vvhA as a target. Detection limit of PCR/Southern hybridization without enrichments was to be around $10^2\;cells\;g^{-1}$ of sample. However, those three methods using the enrichment at $35^{\circ}C$ in APW showed high sensitivity ($2\~10\;cells\;g^{-1}$ of sediments). Highly sensitive detection of V vulnificus by real-time PCR was achieved within $5\~6$ hr, whereas the detection by PCR/Southern hybridization required about 36 hr. Thus, it was evident that real-time PCR is the most rapid and efficient method for detecting V vulnificus in tidal flat sediments.

• Korean Journal of Microbiology
• /
• v.41 no.3
• /
• pp.195-200
• /
• 2005

Comamonas sp. strain DJ-12 is a bacterial isolate capable of degrading of 4-chlorobiphenyl (4CB) as a carbon and energy source. The degradation pathway was characterized as being conducted by consecutive reactions of the meta-degradation of 4CB, hydrolytic dechlorination of 4-chlorobenzoate (4CBA), hydroxylation of 4-hydroxybenzoate, and meta-degradation of protocatechuate to product TCA metabolites. The 6.8 kb fragment from the chromosomal DNA of Comamonas sp. strain DJ-12 included the genes encoding for the meta-degradation of PCA; the genes of protocatechuate 4,5-dioxygenase alpha and beta subunits (pmcA and pmcB), 4-carboxy-2-hydroxymuconate-6-semialdehyde dehydrogenase (pmcC), 2-pyrone-4,6-dicarboxylate hydrolase (pmcD), 4-oxalomesaconate (OMA) hydratase(pmcE), 4-oxalocitramalate (OCM) aldolase (pmcF), and transporter gene (pmcT). They were organized in the order of pmcT-pmcE-pmcF-pmcD-pmcA-pmcB-pmcC. The amino acid sequences deduced from the nucleotide sequences of pmcABCDEFT genes from Comamonas sp. strain DJ-12 exhibited 94 to $98\%$ homologies with those of Comamonas testosteroni BR6020 and Pseudomonas ochraceae NGJ1, but only 52 to $74\%$ with homologies Sphingomonas paucimobilis SYK-6, Sphingomonas sp. LB126, and Arthrobacter keyseri 12B.

• Journal of Plant Biotechnology
• /
• v.47 no.2
• /
• pp.157-163
• /
• 2020

Calmodulin (CaM) mediates cellular Ca²⁺ signals in the defense responses of plants. We previously reported that GmCaM-4 and 5 are involved in salicylic acid-independent activation of disease resistance responses in soybean (Glycine max). Here, we generated a GmCaM-4 cDNA construct under the control of the cauliflower mosaic virus (CaMV) 35S promoter and transformed this construct into potato (Solanum tuberosum L.). The constitutive over-expression of GmCaM-4 in potato induced high-level expression of pathogenesis-related (PR) genes, such as PR-2, PR-3, PR-5, phenylalanine ammonia-lyase (PAL), and proteinase inhibitorII (pinII). In addition, the transgenic potato plants exhibited enhanced resistance against a bacterial pathogen, Erwinia carotovora ssp. Carotovora (ECC), that causes soft rot disease and showed spontaneous lesion phenotypes on their leaves. These results strongly suggest that a CaM protein in soybean, GmCaM-4, plays an important role in the response of potato plants to pathogen defense signaling.

• Microbiology and Biotechnology Letters
• /
• v.33 no.4
• /
• pp.295-301
• /
• 2005

About seven hundred bacterial strains were collected from Jeot-Kal, a Korean traditional fermented fishes, in various Korean districts. One of the strains designated JKK238 has its ability to antagonize in vitro the growth of a wide variety of plant pathogenic fungi responsible for diseases of economical importance. The JKK238 strain was isolated from Oh-Jeot, a kind of fermented shrimps, of Kangkyeung in Korea, and was identified as Bacillus subtilis based on its physiological characteristics, fatty acids compositions of cellular wall, and 16S rDNA sequence analysis. We isolated simply antimicrobial lipopeptides (AMLP) by $25\%$ ammonium sulfate precipitation of 3 days-old tryptic soy broth cultures of the JKK238 strain. Further analysis of AMLP revealed that B. subtilis JKK238 produces a wide variety of antifungal lipopeptide isomers from the iturin, fengycin and surfactin families simultaneously. Above results indicate that the JKK238 strain can be added to the limited number B. subtilis strains reported to co-produce the three kinds of lipopeptide families.

• Journal of Microbiology and Biotechnology
• /
• v.29 no.12
• /
• pp.1947-1956
• /
• 2019

The gut microbiome influences the health and well-being of dogs. However, little is known about the impact of breed on the fecal microbiome composition in dogs. Therefore, we aimed to investigate the differences in the fecal microbiome in three breeds of dog fed and housed under the same conditions, namely eight Maltese (8.0 ± 0.1 years), eight Miniature Schnauzer (8.0 ± 0.0 years), and nine Poodle dogs (8.0 ± 0.0 years). Fresh fecal samples were collected from the dogs and used to extract metagenomic DNA. The composition of the fecal microbiome was evaluated by 16S rRNA gene amplicon sequencing on the MiSeq platform. A total of 840,501 sequences were obtained from the 25 fecal samples and classified as Firmicutes (32.3-97.3% of the total sequences), Bacteroidetes (0.1-62.6%), Actinobacteria (0.2-14.7%), Fusobacteria (0.0-5.7%), and Proteobacteria (0.0-5.1%). The relative abundance of Firmicutes was significantly lower in the Maltese dog breed than that in the other two breeds, while that of Fusobacteria was significantly higher in the Maltese than in the Miniature Schnauzer breed. At the genus level, the relative abundance of Streptococcus, Fusobacterium, Turicibacter, Succinivibrio, and Anaerobiospirillum differed significantly among the three dog breeds. These genera had no correlation with age, diet, sex, body weight, vaccination history, or parasite protection history. Within a breed, some of these genera had a correlation with at least one blood chemistry value. This study indicates that the composition of the fecal microbiome in dogs is affected by breed.

• Microbiology and Biotechnology Letters
• /
• v.47 no.4
• /
• pp.596-602
• /
• 2019

In September 2017, the rhizospheric soil of Tetragonia tetragonoides (Pall.) Kuntze was further sampled. One hundred and thirty eight species of microorganisms were isolated from the soil. Indole-3-acetic acid (IAA) production, siderophore production, and phosphate degradation were examined in order to confirm bacterial growth from isolated microorganisms. As a result, most strains were able to produce auxins or siderophores and to solubilize phosphate. In addition, 138 isolated strains were treated with tobacco extract and conferred pathogen resistance to host plants upon treatment. As a result, 35 strains that were able to reduce pathophysiology by more the 60% were selected. Among them, 6 strains with high induced systemic resistance (ISR) activity were found. All of these strains belong to the genus Bacillus according to the 16S rDNA sequence analysis. Bacillus aryabhattai KUDC6619 showed outstanding effects with reduced infection in tobacco and pepper plants. Probably, these Bacillus species play a beneficial role by association with T. tetragonoides for its survival in the harsh conditions found on the island of Dokdo.

• Applied Biological Chemistry
• /
• v.48 no.3
• /
• pp.201-206
• /
• 2005

The development of microbial inoculant was conducted using a by-product of oriental herbal medicine. The constituent of the by-product, which was high in organic matter, was 11.3% of crude protein, 5.1% of crude lipid, 49.7% of NDF (neutral detergent fiber), and 33.8% of ADF (acid detergent fiber). Microorganisms isolated from the by-product of oriental herbal medicine were 35 species. Among them, 6 bacterial species, 4 fungal species, 2 actnomycetes species, and 1 yeast species were effective in the utilization of the by-products. The 13 strains screened were tested for the plant growth-promoting effect in soybean seedling. BL-333 strain was found to increase the soybean yield by about 23% as compared with control. The strain BL-333 was identified as Paenibacillus marcerans. P. marcerans BL-333 showed high anti-fungal activities against virulent fungi, especially Fusarium sp. and Collectotrichum sp. Yields of plants which were inoculated with microbial inoculant prepared with P. marcerans BL-333 and by-product of oriental herbal medicine were found to be higher than control by $3{\sim}24%$. The yield was especially promoted in lettuce, radish, chinese cabbage and cucumber plants.

• Korean Journal of Food Science and Technology
• /
• v.46 no.1
• /
• pp.115-120
• /
• 2014

The purpose of this study was to develop a rice straw-derived Bacillus cereus (B. cereus)-free starter culture for traditional soybean fermented products using a B. cereus-specific bacteriophage, BCP8-2. To determine the optimal medium that supports the growth of rice straw-derived microorganisms and BCP8-2 activity, 5 different culture media were tested. The 5% ground bean (GB) medium was selected for further study. No B. cereus was detected in the BCP8-2-treated rice straw in GB medium, whereas B. cereus at a level of $10^7$ CFU/mL was recovered in the no-phage control. The total bacterial count reached approximately $10^9$ CFU/mL regardless of phage addition. When the 16S rRNA sequence-based microbial community was monitored using denaturing gradient gel electrophoresis (DGGE) and pyrosequencing, a similar microbial community was observed in the phage-treated and control samples. In conclusion, we demonstrate that phage can be used to prepare a rice straw-derived B. cereus-free starter culture with minimal effect on natural microflora.

• Microbiology and Biotechnology Letters
• /
• v.35 no.1
• /
• pp.1-10
• /
• 2007

The 44 endophytic bacterial strains were isolated from surface-sterilized root of rice cultivated in seven different locations of Chungcheong province, Korea. Each isolate was introduced into rice seedlings grown gnotobiotically by inoculating scissor-cut first true leaf with cell suspensions, and the colonization capacity of each isolate in root tissue was analyzed at 7 days after inoculation. Sixteen out of 44 isolates were re-isolated from root successfully with the frequency of $10^{3-5}$ CFU/g tissue. Interestingly, seven out of 16 isolates were identified as Burkholderia species. The identity between inoculated strains and re-isolates was confirmed by genomic finger-printing and 16S rDNA sequence analysis. By a confocal laser scanning microscopic observation it was revealed that KJ001 strain, one of the sixteen isolates tagged with gfp colonized in root tissue especially around xylem. Six out of seven Burkholderia strains obtained in this study showed antagonizing activities against seven different fungal pathogens, contain nifH gene, and five of them enhanced growth of cucumber over 30%. The isolates showed no hypersensitive response on tobacco leaves and no pathogenecity in rice. From these results it was found that the endophytic Burkholderia strains will be useful in agriculture to develop a biocontrol agent or a bio-fertilizer.