• Korean Journal of Microbiology
• /
• v.42 no.4
• /
• pp.313-318
• /
• 2006

A thermophilic bacterium producing the extracellular cellulase was isolated from soybean paste, and the isolate WL-12 has been identified as Bacillus licheniformis on the basis on its 16S rRNA sequence, morphology and biochemical properties. A gene encoding the cellulase of B. licheniformis WL-12 was cloned and its nucleotide sequence was determined. This cellulase gene, designated celA, consisted of 1,551 nucleotides, encoding a polypeptide of 517 amino acid residues. The gene product contained catalytic domain and cellulose binding domain. The deduced amino acid sequence was highly homologous to those of cellulases of B. licheniformis, B. subtilis and B. amytoliquefaciens belonging to the glycosyl hydrolase family 5. When the celA gene was highly expressed using a strong B. subtilis promoter, the extracellular cellulase was produced up to 7.0 units/ml in B. subtilis WB700.

• Korean Journal of Microbiology
• /
• v.42 no.1
• /
• pp.19-25
• /
• 2006

This study was undertaken to develop PCR primers for the identification and detection of Streptococcus mutans (by)using species-specific forward and universal reverse primers. These primers targeted the variable regions of the 16S ribosomal RNA coding gene (rDNA). The primer specificity was tested against 11S. mutans strains and 10 different species (22 strains) of oral bacteria. The primer sensitivity was determined by testing serial dilutions of the purified genomic DNA of S. mutans ATCC $25175^T$. The data showed that species-specific amplicons were obtained from all the S. mutans strains tested, which was not observed in the other species. The direct and nested PCR could detect as little as 2 pg and 2 fg of the chromosomal DNA from S. mutans ATCC $25175^T$, respectively. This shows that the PCR primers are highly sensitive and applicable to the detection and identification of S. mutans.

• Journal of Microbiology and Biotechnology
• /
• v.19 no.3
• /
• pp.323-330
• /
• 2009

Nontuberculous mycobacteria (NTM) are a major cause of opportunistic infections in immunocompromised patients, making the reliable and rapid identification of NTM to the species level very important for the treatment of such patients. Therefore, this study evaluated the usefulness of the novel target genes tuf and tmRNA for the identification of NTM to the species level, using a PCRrestriction fragment length polymorphism analysis (PRA). A total of 44 reference strains and 17 clinical isolates of the genus Mycobacterium were used. The 741 bp or 744 bp tuf genes were amplified, restricted with two restriction enzymes (HaeIII/MboI), and sequenced. The tuf gene-PRA patterns were compared with those for the tmRNA (AvaII), hsp65 (HaeIII/HphI), rpoB (MspI/HaeIII), and 16S rRNA (HaeIII) genes. For the reference strains, the tuf gene-PRA yielded 43 HaeIII patterns, of which 35 (81.4%) showed unique patterns on the species level, whereas the tmRNA, hsp65, rpoB, and 16S rRNA-PRAs only showed 10 (23.3%), 32 (74.4%), 19 (44.2%), and 3 (7%) unique patterns after single digestion, respectively. The tuf gene-PRA produced a clear distinction between closely related NTM species, such as M. abscessus (557-84-58) and M. chelonae (477-84-80-58), and M. kansasii (141-136-80-63-58-54-51) and M. gastri (141-136-117-80-58-51). No difference was observed between the tuf-PRA patterns for the reference strains and clinical isolates. Thus, a diagnostic algorithm using a tuf gene-targeting PRA is a promising tool with more advantages than the previously used hsp65, rpoB, and 16S rRNA genes for the identification of NTM to the species level.

• Journal of Microbiology and Biotechnology
• /
• v.17 no.11
• /
• pp.1743-1750
• /
• 2007

Two Gram-negative, nonmotile, coccobacilli, SW-$3^T$ and SW-$100^T$, were isolated from sea water of the Yellow Sea in Korea. Strains SW-$3^T$ and SW-$100^T$ contained ubiquinone-9 (Q-9) as the predominant respiratory lipoquinone and $C_{18:1}\;{\omega}9c$ and $C_{16:0}$ as the major fatty acids. The DNA G+C contents of strains SW-$3^T$ and SW- $100^T$ were 44.1 mol% and 41.9 mol%, respectively. A neighbor-joining tree based on l6S rRNA gene sequences showed that the two isolates fell within the evolutionary radiation enclosed by the genus Acinetobacter. Strains SW-$3^T$ and SW-$100^T$ exhibited a l6S rRNA gene similarity value of 95.7% and a mean DNA-DNA relatedness level of 9.2%. Strain SW-$3^T$ exhibited l6S rRNA gene sequence similarity levels of 93.5-96.9% to the validly described Acinetobacter species and fifteen Acinetobacter genomic species. Strain SW-$100^T$ exhibited l6S rRNA gene sequence similarity levels of less than 97.0% to the other Acinetobacter species except Acinetobacter towneri DSM $14962^T$ (98.0% similarity). Strains SW-$3^T$ and SW-$100^T$ exhibited mean levels of DNA-DNA relatedness of 7.3-l6.7% to the type strains of some phylogenetically related Acinetobacter species. On the basis of phenotypic, phylogenetic, and genetic data, strains SW-$3^T$ and SW-$100^T$ were classified in the genus Acinetobacter as two distinct novel species, for which the names Acinetobacter marinus sp. novo (type strain SW-$3^T$=KCTC $12259^T$=DSM $16312^T$) and Acinetobacter seohaensis sp. novo (type strain SW-$100^T$=KCTC $12260^T$=DSM $16313^T$) are proposed, respectively.

• Korean Journal of Microbiology
• /
• v.49 no.3
• /
• pp.282-285
• /
• 2013

Microbial diversities in the 300 m and 500 m deep seawaters near Goseong, Gangwon Province (South Korea), were investigated. Pyrosequencing of 16S rRNA genes of marine microbes resulted in 19,474 reads from the 300 m deep seawaters, which consisted of Alphaproteobacteria (57.41%) and Gammaproteobacteria (38.85%), and 82,806 reads from the 500 m deep seawaters, which consisted of Gammaproteobacteria (99.64%) mostly. Rhodobacterales (57.31%) were dominant in the 300 m deep seawaters, but Alteromonadales (45.65%) and Oceanospirillales (34.61%) were dominant in the 500 m deep seawaters. On the bases of operational taxonomic units and diversity indexes (Shannon and Simpson), biodiversity of marine bacteria in the 500 m deep seawaters was shown to be higher than that in the 300 m deep seawaters.

• Journal of Species Research
• /
• v.5 no.1
• /
• pp.22-26
• /
• 2016

Five bacterial strains designated DY37, BS333, JJ521, BM1, and DG13-2 were assigned to the genus Deinococcus were isolated from forest soil samples collected from Deogyusan, Busan, Changwon, and Seoul of South Korea. The isolates were Gram-staining negative or positive, and pale pink- or red-pigmented, short-rod shaped. Phylogenetic analysis based on 16S rRNA gene sequence revealed that strains DY37, BS333, JJ521, BM1, and DG13-2 were most closely related to Deinococcus aquatilis CCM $7524^T$ (with 99.0% similarity), D. ficus CC-FR2-$10^T$ (100.0%), D. grandis KS $0485^T$ (99.2%), D. roseus TDMA-$uv51^T$ (98.9%), and D. yunweiensis $YIM007^T$(100.0%), respectively. These 5 species have never been proposed in Korea; therefore 5 species of 1 genera in the family Deinococcaceae in the order Deinococcales within the class Deinococci are reported for proteobacterial species found in Korea.

• Animal cells and systems
• /
• v.16 no.5
• /
• pp.408-414
• /
• 2012

To reexamine taxonomic status of endemic Mogera wogura coreana from Korea, we first obtained partial 12S rRNA sequences (893 bp) and complete cytochrome b gene sequences (1140 bp) of this subspecies, and these sequences and partial cytochrome b sequences (402 bp) were compared to the corresponding haplotypes of M. wogura from East Asia, obtained from GenBank. The one of three 12S rRNA haplotypes in M. w. coreana was identical to one 12S rRNA haplotype of M. w. robusta from East Asia: 10 complete and 13 partial cytochrome b haplotypes of M. w. coreana formed a single clade with one complete and four partial cytochrome b haplotypes of M. w. robusta, respectively. We considered that M. w. coreana from Korea is an endemic subspecies with only morphological differences, although it is necessary to reexamine the subspecies status of M. w. coreana. Additionally, in the 12S rRNA and complete cytochrome b sequences, M. wogura from Japan was distinct from the two continental subspecies of M. w. coreana and M. w. robusta with average distances of 1.76 and 5.65%, respectively; insular M. wogura, with within-group distances of 2.09 and 4.38%, respectively, was also genetically more divergent than the mainland M. wogura, with within-group distances of 0.08 and 0.57%, respectively. Thus, we considered that insular M. wogura of Japan dispersed into neighboring East Asian continent, which is opposite to the traditional hypothesis on the origin of Japanese M. wogura.

• Microbiology and Biotechnology Letters
• /
• v.43 no.4
• /
• pp.307-313
• /
• 2015

Unpolished rice (UR) is considered to be a healthy alternative to white rice when coping with chronic diseases. In the present study, the fermented slurry of unpolished rice (FSUR) was evaluated with respect to its antimicrobial activities and biochemical characteristics, including the quantities of sugar, total soluble sugar, organic acids, free amino acids, pH, and physiological activity. The antimicrobial efficiency of FSUR was assessed using the paper disc-agar diffusion method. FSUR exhibited strong antimicrobial activity against six pathogenic bacterial strains (Staphylococcus aureus, Escherichia coli, Listeria monocytogenes, Pseudomonas aeruginosa, Salmonella typhimurium, and Yersinia enterocolitica) and two fermentation strains (Gluconacetobacter intermedius and Lodderomyces elongisporus). The antimicrobial activity of FSUR was higher than the commercial antibiotics, carbenicillin ($50{\mu}g/ml$) and tetracycline ($50{\mu}g/ml$) against S. aureus, E. coli, L. monocytogenes, P. aeruginosa, S. typhimurium, Y. enterocolitica, and L. elongisporus. Also FSUR had a high antioxidant activity. The microorganisms were isolated from FSUR using tryptic soy broth and yeast extract-peptone-dextrose agar media. The isolated microorganisms were characterized using physiological and biochemical analyses as well as by 16S rRNA gene sequencing and phylogenic analysis. 16S rRNA gene sequence analysis showed that the isolated microorganisms had a high similarity to G. intermedius, Lactobacillus casei, Lactobacillus plantarum, and Acetobacter peroxydans.

• The Korean Journal of Food And Nutrition
• /
• v.19 no.4
• /
• pp.496-501
• /
• 2006

This study was to isolate a bacterium producing a alkaline protease from mud flats of the west seaside of Korea and to investigate the biochemical analysis of the alkaline protease producing from the isolate. The isolate was named as Gelidibacter sp. HK-1 based on 16S rRNA sequence, Gram staining and the photograph of electron microsceope. Optimum temperature for growth and pretense production of the isolate was $25^{\circ}C$. Growth of the isolate was reached at stationary phase after 10hrs followed by inoculation. Maximum activity of protease produced from the isolate was shown after 14hrs. Optimum temperature and pH for the protease activity were $45^{\circ}C$ and pH 9, respectively. Molecular weight of the pretense was about 50KD and the partial amino acid sequence of the pretense was Ala-Try-Ala-Leu-Asn-Thr-Ser-Val-Thr-Glu-Thr-Phe-Ala-Lys. The partial amino acid sequences of the protease showed significant homology with a pretense produced from Streptomyces avermitilis.

• Journal of Microbiology and Biotechnology
• /
• v.16 no.12
• /
• pp.1882-1889
• /
• 2006

A 16S rDNA clone library was generated to investigate the bacterial diversity in intertidal sediment from the coast of the Yellow Sea, P. R. China. A total of 102 clones were sequenced and grouped into 73 OTUs using a phylogenetic approach. The sequenced clones fell into 11 bacterial lineages: Proteobacteria, Bacteroidetes, Planctomycetes, Chloroflexi, Acidobacteria, Actinobacteria, Firmicutes, Spirochaetes, and candidate divisions of BRCl, OP3, and OP1l. Based on a phylogenetic analysis of these bacteria, together with the ten most closely related sequences deposited in the GenBank, it was concluded that intertidal bacteria are most likely derived from marine bacteria with a remarkable diversity, and some are particularly abundant in intertidal sediment.