• Applied Biological Chemistry
• /
• v.50 no.4
• /
• pp.268-275
• /
• 2007

Diversity of the mud flat microbial population in Suncheon Bay was investigated by studying extracellular enzyme activities and 16S rDNA sequences. Four culturable bacterial strains with CMCase, xylanase and protease activities were isolated from the wetland and the mud flat. All the strains produced more xylanase activity than CMCase or protease activity, and the properties of the isolate enzymes from the wetland were similar to those from the mud flat. About 2,000 clones were obtained with the 16S rDNA amplified from the metagenomic DNA isolated from the mud samples. Based on the restriction pattern(s), seventeen clones were selected for base sequence analysis. Of the 17 clones, only 35% (6 clones) were found to be cultured strains and 65% (11 clones) to be uncultured strains. The similarities in the base sequences of the clones ranged from 91.0% to 99.9% with an average similarity of 97.3%. The clones could be divided into 7 groups, Proteobacteria (9 clones, 52.9%), Firmicutes (3 clones, 17.6%), Bacteroidetes (1 clone), Flavobacteria (1 clone), Verrucomicrobia (1 clone), Acidobacteria (1 clone), and Chloroflexi (1 clone). Most of the Proteobacteria clones were gamma Proteobacteria associated with oxidation-reduction of sulfur.

• Korean Journal of Microbiology
• /
• v.37 no.2
• /
• pp.137-144
• /
• 2001

In order to investigate the diversity of bacterial community in the mud flat of Sunchon Bay, Chunnam province, diversity of amplified 16S rDNA was examined. Total DNA was extracted from sediment soils and 16S rDNAs were amplified using PCR primers based on the universally conserved sequences in bacteria. Clonal libraries were constructed and 111 clones were examined by amplified rDNA restriction analysis (ARDRA) using HaeIII. Clones were clustered based on restriction patterns using computer program, GelCompar II. One hundred different RFLP types were detected from 111 clones. The 20 clones were selected and sequenced according to dendrograms derived from ARDRA, to cover most of the bacterial diversity in the clone libraries. None of the clones were identical to any representatives in the Ribosomal Database Project small subunit RNA databases and GenBank. All sequences showed between 77 and 96.8% similarity to the known 16s rRNA sequence from cultured organisms. The 20 clones sequenced fell into seven major lineages of the domain Bacteria: alpha-, delta-, gamma-Proteobacteria, low G+C Gram positive bacteria, high G+C Gram positive bacteria, Sphingobacteria (Cytophaga) and Cyanobacteria (chloroplast). Among the clones, the Proteobacteria were dominant.

• Korean Journal of Microbiology
• /
• v.33 no.2
• /
• pp.149-156
• /
• 1997

We have employed comparative RFL,P(Restriction Fragment Ixngth Pol~iniorphism) analysis and molecular phylogenetic techniques to investigate the diversity of uncultured microorganisms associated with the anaerobic PCP degradation in PCP-adapted enrichment cultures inoculated by samples from anaerobic cewage sludgc(Jangrim, Pusan) and leachate of landfill site(Kimhae). 16s rDNA cloncs were obtairted by PCR amplification of mixed population DNAs extracted directly from the nonactive and active stage ol each PCP-adapted culture. After three rounds of comparative RFLP analyses. two RFLP types. designated as Ala and Hld, were found prevalent and common in both active stage samples. Thc analysis of phylogenctic diversity bawd on the 5'-terminal 180 nt of sequences from whole clones of the Ala and Bld RFLP types showed close similarity among themselves. In case of Bld clones, 7XQ of them shared identical sequences. Thcse resuliq suggest that the clones of both RFLP types wcre originated from highly affiliated microorganisms which are e~iriched as a result of metabolic activity to PCP. The full-length 16s rRNA sequence of each representative clone from both RFLP types was determined. and an Ala clone w i n found to he related to Clo.strrdiurn ulfutzac~(Genk~ank No. Z69203) and a Bld clone to Thermobacteroides proteolyticus(Genbank No. X09335), with sequence similarities of 89%' and 97%. respectively.

• Journal of Microbiology and Biotechnology
• /
• v.14 no.1
• /
• pp.205-211
• /
• 2004

A 16S rDNA clone library was generated to investigate the bacterial diversity in tidal flat sediment in Ganghwa Island, Republic of Korea. A total of 103 clones were sequenced and analyzed by comprehensive phylogenetic analyses. No clones were identical to any of known 16S rRNA sequences in public databases. Sequenced clones fell into thirteen lineages of the domain Bacteria: the alpha, beta, gamma, delta, and epsilon Proteobacteria, Actinobacteria, CFB group, Chloroflexi, Acidobacteria, Planctomycetes, Verrucomicrobia, and known uncultured candidate divisions (OP11, BRC1, KSB1, and WS1). Two clones were not associated with any known bacterial divisions. The majority of clones belonged to the gamma and delta Proteobacteria (46.7%). Clones of Actinobacteria were distantly related to known taxa. It is evident from 16S rDNA-based community analysis that the bacterial community in tidal flat sediment is remarkably diverse and unique among other marine environments examined so far.

• Proceedings of the Microbiological Society of Korea Conference
• /
• 2005.05a
• /
• pp.36-39
• /
• 2005

• Microbiology and Biotechnology Letters
• /
• v.38 no.3
• /
• pp.322-328
• /
• 2010

Fermented skate is a traditional Korean food popular in Southwestern area of Korea. It has a characteristic flavor and alkaline pH. In this study we tried to determine the microbial flora in fermented skate using two different approaches. In culture-independent method, we amplified V2 region of 16S rRNA gene by PCR and cloned them into pUC18 plasmid to construct 16S rDNA fragment library. BLAST searches for the sequences obtained from this library revealed that uncultured bacterium clone 054E11.b was the most dominant flora in this fermented fish. In culture-dependent method, we diluted suspension of skate and spreaded on MRS, PCA, and MacConkey plates. We identified colonies grown on those plates by using PCR amplification of V2 region of 16S rRNA and DNA sequencing. BLAST searches of those DNA sequences resulted in totally different species with the observations from the 16S rDNA library analysis. Discrepancies of results obtained from both approaches suggest that the agar plates used in culture-dependent method may be different from the real condition of fermented skate. Therefore, results from culture-independent approach using 16S rDNA fragment library analysis may reflect real microbial flora in fermented skate.

• Journal of Korean society of Dental Hygiene
• /
• v.13 no.5
• /
• pp.889-900
• /
• 2013

Objectives : Molecular biology techniques were employed to assess diversity of bacterial in children's dental caries. Methods : DNA of germs was extracted and the diversity of the 16S rRNA clones was analyzed by amplified rDNA restriction analysis and sequencing. The experimental samples were pit and fissure caries (PC), deep dentinal caries (DC), smooth surface caries (SC), and supragingival plaque (PQ) from 50 children of age less than 12 years old. The control group was healthy teeth supragingival plaque (HT). Thirty clones from each 16S rRNA clone library of 5 samples were randomly selected, thus a total of 150 clones were analyzed. Results : Amplified rDNA restriction analysis uncovered 18, 20, 11, 17, and 22 phylotypes from healthy teeth, pit and fissure caries, deep dentinal caries, smooth surface caries, and supragingival plaque, respectively. Sequencing analysis found the dominance of Actinomycs naeslundii and Fusobacterium nucleatum in the healthy teeth; Leptotrichia sp. in the pit and fissure caries; Actinomyces sp., Streptococcus mutans, and Rahnella aquatilis in the deep dentinal caries; Streptococcus mutans and Actinomyces sp. in the smooth surface caries; Enterobacter hormaechei and Streptococcus sanguinis in the supragingival plaque. Conclusions : Clonal analysis identified 6 phyla, 20 genera, and 51 species.

• Parasites, Hosts and Diseases
• /
• v.35 no.3
• /
• pp.203-210
• /
• 1997

The difrrrenlial display reverse transcription polymerase chain reaction (DDRT-PCR) aniilysis roils performed to identify the pathogellir strain specific amplicons. mRNAs were purified from the trophozoites of the pathogenif strain YS-27 and the non-pathogenic strain S 16. respectively. Three kinds of rirsl stranded rDNAs were reverse transcribed from the mRNAs by one base anchored oligo-dT 11M (M: A. C, or G) primers. Each cDNA lemplatr was used for DDRT-PCK analysis. A total of 144 pathogenic strain specific amplicons was observed in DDRT-PCR analysis using primer combinations of the 11 arbitrary primers and the 3 one base anchored oli해-dT11M primers. Of these 31 amplit'tons were verified as the amplirons amplified only from the mRNAs of the pathogenic strain by DNA slots biol llybridizatioil. Furthel cklaracleization of the 31 pathogenic strain sprcifil amplicons by DNA slot blot hybridlnation analysis using biotin labeled Probes or the PCR amplified DNA of rysteine proteinase genes revealed that 21 of them were amplliried from the maNAs of the cysteine proteinase genes. Four randomly selected amplirons out of the rest 10 amplirons were used fur screening of cDNA library followed by immunoscreening and all of them were turned outs to be amplified from the mRNA.

• Korean Journal of Microbiology
• /
• v.34 no.4
• /
• pp.194-199
• /
• 1998

Bacterial diversity was determined by amplification and sequencing of 16S rDNA at Tancheon and Jungrang in Han river. Twenty-seven clones constructed were divided 7 groups using RFLP. Fifteen clones were classified 4 groups in Tancheon and the group (HT-1 clone) including many clones was affiliated a high similarity with Aerobacter cryaerophilus (the class Proteobacteria including members of the delta subdivisions). The other two groups (HT-6 and HT-9 clone) including several clones were classified with the class Cytophagales in Tancheon. Twelve clones were classified 3 groups in Jungrang and the group (HJ-1 clone) including many clones was affiliated a high similarity with Sphingomonas sp. (the class Proteobacteria including members of the alpha subdivisions). As a whole results, the class Proteobacteria (alpha, beta and delta subdivision), the order Cytophagales, and the order Actinomycetales were detected.

• Korean Journal of Microbiology
• /
• v.44 no.3
• /
• pp.237-243
• /
• 2008

Chemical and microbial characteristics of bacterial populations were investigated in a quercus and pine humus forest soil. Soil pH was $5.3\pm0.4$ and $4.1\pm0.9$ from each sample of a quercus and pine humus forest soil; C/N ratio of humus forest soil was $17.84\pm4.6%$ and $21.76\pm8%$, respectively. Total organic acid was investigated as 69.57 mM/g dry soil and 53.72 mM/g dry soil in each humus forest soil. Glutamine, pyruvate, succinate, lactic acid and acetic acid of pine humus forest soil were $1.5\sim4.5$ times higher than those of quercus humus forest soil. As we evaluated phylogenetic characteristics of bacterial populations by 16S rRNA-ARDRA analysis with DNA extracted from each humus forest soil. Based on the 16S rRNA sequences, 44 clone from ARDRA groups of quercus humus forest soil were classified into 7 phyla: ${\alpha},{\beta},{\gamma},{\delta}$-Proteobacteria, Acidobacteria, Actinobacteria, and Firmicutes. Thirty-two clone from ARDRA groups of pine humus forest soil were classified into 8 phyla: ${\alpha},{\beta},{\gamma}$-Proteobacteria, Acidobacteria, Bacteroides, Verrucomicrobia, Planctomycetes, and Gemmatomonadetes. According to PCA (Principal Component Analysis) based on 16S rRNA base sequence, there were three main groups of bacteria. All clone of Cluster I were originated from quercus humus forest soil, while 67% clone of Cluster II and 63% clone of Clusters III were separated from pine humus forest soil.