• Journal of Microbiology
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• 제45권2호
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• pp.105-112
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• 2007

The objective of this study was to analyze the phylogenetic composition of bacterial community in the soil of an earth-cave (Niu Cave) using a culture-independent molecular approach. 16S rRNA genes were amplified directly from soil DNA with universally conserved and Bacteria-specific rRNA gene primers and cloned. The clone library was screened by restriction fragment length polymorphism (RFLP), and representative rRNA gene sequences were determined. A total of 115 bacterial sequence types were found in 190 analyzed clones. Phylogenetic sequence analyses revealed novel 16S rRNA gene sequence types and a high diversity of putative bacterial community. Members of these bacteria included Proteobacteria (42.6%), Acidobacteria (18.6%), Planctomycetes (9.0 %), Chloroflexi (Green nonsulfur bacteria, 7.5%), Bacteroidetes (2.1%), Gemmatimonadetes (2.7%), Nitrospirae (8.0%), Actinobacteria (High G+C Gram-positive bacteria, 6.4%) and candidate divisions (including the OP3, GN08, and SBR1093, 3.2%). Thirty-five clones were affiliated with bacteria that were related to nitrogen, sulfur, iron or manganese cycles. The comparison of the present data with the data obtained previously from caves based on 16S rRNA gene analysis revealed similarities in the bacterial community components, especially in the high abundance of Proteobacteria and Acidobacteria. Furthermore, this study provided the novel evidence for presence of Gemmatimonadetes, Nitrosomonadales, Oceanospirillales, and Rubrobacterales in a karstic hypogean environment.

• Journal of Periodontal and Implant Science
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• 제33권2호
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• pp.149-158
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• 2003

The purpose of this study was to isolate and characterize the Fusohacrerium nucleatum (F. nucleatum) from subgingival plaque in Korean periodontitis patients. The subgingival plaque samples of periodontitis patient were collected with sterilized paper point. The paper point was put into reduced transfer medium and then immediately transferred to laboratory. The subgingival samples were diluted by 10,000 folds and plated on F. nucleatum-selective media agar plate. The plates were incubated at 37$^{\circ}C$ in an anaerobic chamber for 3 days. The violet-colored colonies were selected and subjected to further verification whether those are F. nucleatum or not. For further confirmation, 16S rRNA genes (rDNA) were cloned from each of bacterial clones and determined sequence of 16S rDNA. In this study, we found 17 distinct clinical isolates of F. nucleatum from subgingival plaque. The clinical isolates will be a useful in various studies in periodontology.

• 미생물학회지
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• 제37권4호
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• pp.265-272
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• 2001

깨끗한 대기가 유지되는 청정지역 및 산성강하물의 영향을 받는 공단지역에서 자라는 떡갈나무(Quercus dentate Thunb.) 잎표면에서 분리한 내산성세균 배양으로부터 16S rDNA를 추출하여 모두 444개의 clone을 얻었으며, 이를 대상으로 Restriction fragment length polymorphism (RFLP)을 실시한 결과 총 17종류의 계통형 (phylotype)이 나타났다. 두 지역에서 나타난 대표적인 내산성 잎권세균 군집은 매우 단순하여 ${\gamma}$-Proteobacteria와 low-G+C gram-positive bacteria의 2개 group이었다. 식물 잎의 나이가 들수록 내산성 잎권세균 계통형의 다양성은 현저하게 증가하였다. 내산성 잎권세균 군집 구조는 $\gamma$-Proteobacteria에 속하는 Pseudomonas group과 Enterobacteriaceae, 그리고 low-G+C gram-positive bacteria 즉 Bacillus/Clostridium group에 속하는 Streptococcaceae와 Staphylococcus group이 우점하였다. 산성강하물에 따른 내산성 잎권세균 군집 구조의 변화는 상위 계통분류군(subphylum 수준)에서는 뚜렷이 볼 수 없었지만 보다 하위분류군에서 볼 때 $\gamma$-Proteobacteria의 Xanthomonadales group은 공단지역에서만, 그리고 $\alpha$-Proteobacteria의 Acetobacteraceae는 청정지역에서만 각각 검출되었으므로 이들 세균집단을 산성강서만, 그리고 $\alpha$-Proteobacteria의 Acetobacteraceae는 청정지역에서만 각각 검출되었으므로 이들 세균집단을 산성강 하물에 대한 지표세균으로서 사용할 수 있는 가능성을 남겨 놓았다.

• Genomics & Informatics
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• 제11권4호
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• pp.272-276
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• 2013

Sequence analysis of the 16S rRNA gene has been widely used for the classification of microorganisms. However, we have been unable to clearly identify five Flavobacterium species isolated from a freshwater by using the gene as a single marker, because the evolutionary history is incomplete and the pace of DNA substitutions is relatively rapid in the bacteria. In this study, we tried to classify Flavobacterium species through multilocus sequence analysis (MLSA), which is a practical and reliable technique for the identification or classification of bacteria. The five Flavobacterium species isolated from freshwater and 37 other strains were classified based on six housekeeping genes: gyrB, dnaK, tuf, murG, atpA, and glyA. The genes were amplified by PCR and subjected to DNA sequencing. Based on the combined DNA sequence (4,412 bp) of the six housekeeping genes, we analyzed the phylogenetic relationship among the Flavobacterium species. The results indicated that MLSA, based on the six housekeeping genes, is a trustworthy method for the identification of closely related Flavobacterium species.

• International Journal of Industrial Entomology and Biomaterials
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• 제2권1호
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• pp.37-53
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• 2001

Two regions of mtDNA genome, cytochrome oxidase subunit I (COI) and 165 ribosomal RNA (165 rRNA) genes, were sequenced for 15 species of the long-horned beetle belonging to four subfamilies and geographic samples of mulberry longicorn beetle, Apriona germari, from two localities in Korea. Ten samples of A. germari collected from Suwon and Busan revealed three COI haplotypes ranging in nucleotide divergence of 0.3% to 0.5%, and the two populations shared one common COI haplotype (80%). The sequence divergence among 15 species of the long-horned beetle was much higher in COI gene (12.3%∼39.4%) than 16S rRNA gene (7.2% to 23.1), and the maximum value in the COI gene is exceptional compared with other relevant studies, including that of Coleoptera. The greatly increased divergence in the COI gene, in facto was stemmed from a peculiar sequence of Prionus insularis belonging to Prioninne, divergence of which ranges from 31.2% to 39.3% from other species. We discussed possible reason of the divergence in this species. Due to the abnormality of COI gene divergence, decrease in phylogenetic signal was severe in COI nucleotide and, subsequently, the converted amino acid sequences, rendering us to put more confidence on the 16S5 rRNA gene data. Although the molecular phylogeny confidently supports the monophyletic origin of Lepturinae, the presence of discrepancy between molecular data and traditional taxonomic views also is a testable hyothesis. One such discrepancy includes taxonomic position of Sophronica obrioides and Theophilea cylindricollis belonging to Lamiinae.

• Journal of Microbiology and Biotechnology
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• 제8권2호
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• pp.146-151
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• 1998

The aminoglycoside multiple-resistance determinant from Streptoalloteichus hindustanus was cloned into Streptomyces lividans and named nbrB. The 1.2-kb ApaI- BclI fragment encompassing nbrB was located within a 2.6-kb ApaI fragment by successive subcloning experiments. The complete DNA nucleotide sequence of 1.2-kb containing nbrB was determined. The sequence contains an open reading frame that putatively encodes a polypeptide of 281 amino acids with a predicted molecular weight of 30,992. The deduced amino acid sequence of nbrB shows identities of 85.1% to kgmB of S. tenebrarius, 59.6% to sgm of Micromonospora zionensis, and 57.7% to grm of M. rosea. The similarity of nbrB to kgmB suggests that nbrB encodes a 16S rRNA methylase similar to that encoded by kgmB and that both genes might be derived from a common ancestral gene.

• The Plant Pathology Journal
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• 제37권2호
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• pp.137-151
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• 2021

The present study describes the bacterial blight of walnut, caused by Xanthomonas arboricola pv. juglandis (Xaj) in the northern Gyeongbuk province, Korea. Disease symptoms that appear very similar to anthracnose symptoms were observed in walnut trees in June 2016. Pathogens were isolated from disease infected leaves, fruits, shoots, bud, flower bud of walnut, and cultured onto yeast dextrose carbonate agar plates. Isolated bacteria with bacterial blight symptoms were characterized for their nutrient utilization profiles using Biolog GN2 and Vitek 2. In addition, isolates were subjected to physiological, biochemical, and morphological characterizations. Furthermore, isolates were identified using 16S rDNA sequence analysis, and multi-locus sequence analysis using atpD, dnaK, efp, and rpoD. To confirm pathogenicity, leaves, fruits, and stems of 3-year-old walnut plants were inoculated with bacterial pathogen suspensions as a foliar spray. One week after inoculation, the gray spots on leaves and yellow halos around the spots were developed. Fruits and stems showed browning symptoms. The pathogen Xaj was re-isolated from all symptomatic tissues to fulfill Koch's postulates, while symptoms were not appeared on control plants. On the other hand, the symptoms were very similar to the symptoms of anthracnose caused by Colletotrichum gloeosporioides. When walnut plants were inoculated with combined pathogens of Xaj and C. gloeosporioides, disease symptoms were greater in comparison with when inoculated alone. Xaj population size was more in the month of April than March due to their dormancy in March, and sensitive to antibiotics such as oxytetracycline and streptomycin, while resistant to copper sulfate.

• Journal of Microbiology and Biotechnology
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• 제16권1호
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• pp.68-76
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• 2006

Despites many attempts to explore the microbial diversity in kimchi fermentation, the predominant flora remains controversial to date. In the present study, major lactic acid bacteria (LAB) were investigated in Chinese cabbage kimchi in the early phase of fermention. For the samples over pH 4.0, viable cell counts of Leuconostoc and Pediococcus were $10^6\;cfu/ml$ and below $10^2\;cfu/ml$, respectively, and 20 isolates out of 172 were subjected to a biochemical identification (API 50 CH kit) as well as molecular-typing methods including ITSPCR with a RsaI digestion and 16s rRNA gene sequence analysis for species confirmation. Seven isolates were nicely assigned to Lb. brevis, 6 to Leuconostoc spp. (2 mesenteroides, 2 citreum, I carnosum, I gasicomitatum), 4 to Weissella (3 kimchii/cibaria, 1 hanii) and 2 to other Lactobacillus spp. (1 farciminis, 1 plantarum). On the other hand, the biochemical identification data revealed 9 strains of Lb. brevis, 6 strains of Leuconostocs,2 strains of Lb. plantarum and 1 strain each of Lb. coprophilus and Lactococcus lactis. However, a single isolates, YSM 16, was not matched to the ITS-PCR database constructed in the present study. Two Lb. brevis strains by API 50 CH kit were reassigned to W kimchii/cibaria, Lb. coprophilus or W hanii, respectively, judging from the results by the above molecular typing approaches. As a whole, the identification data obtained by the biochemical test were different from those of ITS-PCR molecular method by about $63\%$ at genus-level and $42\%$ at species-level. The data by the ITS-PCR method conclusively suggest that predominant LAB species is probably heterolactic Lb. brevis, followed by W kimchii/cibaria, Leuc. mesenteroides, and Leuc. citreum, in contrast to the previous reports [3] that Leuc. mesenteroides is the only a predominant species in the early phase kimchi fermentation.

• 한국육종학회지
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• 제41권4호
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• pp.468-473
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• 2009

본 연구에서는 양파와 파간 종간교잡 F1의 불임성의 한 요인으로 여겨지는 염색체 이상과 교잡식물체의 염색체의 조성을 밝혀 향후 종간교잡을 이용한 양파의 형질개량과정에 종간교잡 육종의 효율성을 높이고자 하였다. 종간교잡식물체의 감수분열 염색체를 관찰한 결과 중기에 7쌍의 2가염색체와 2개의 1가염색체가 관찰되었다. 체세포 염색체수는 16개로 양파, 파의 염색체 수와 같았으며 GISH한 결과 파와 양파의 염색체가 각각 8개씩 확인되었다. 5S, 45S, TSD DNA를 probe로 하여 양파, 파, 종간잡종의 염색체의 signal을 관찰한 결과 5S와 45S rDNA는 는 3종 모두에서 1쌍의 염색체에서 나타났는데 5S의 경우 염색체의 subcentromeric 에서 45S는 부수체 염색체에서 관찰되었다. TSD DNA는 염색체의 telomeric 부위에서 관찰되었으나 양파의 경우 2쌍은 염색체의 말단부와 중심체 부분에서 signal이 관찰되었고 종간교잡 세포에서도 2쌍이 관찰되어 양파에서 유래된 염색체임이 확인되었다.

• Journal of Microbiology
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• 제45권1호
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• pp.1-5
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• 2007

The bacterial compositions between the dental unit water system and human saliva were characterized and compared by direct sequence analysis of 16S rDNA clone libraries. Based on the species richness estimation, bacterial diversity in the dental unit water system (DUW) was more diverse than that of the human saliva (HS). The Chaol estimates of species richness in HS and DUW samples were 12.0 and 72.4, respectively. The total numbers of OTUs observed in the combined libraries accounted for 83% (HS) and 59% (DUW) of the Chaol diversity estimate as defined at the 80% similarity threshold. Based on the sequence analysis, the phylum Proteobacteria was the major group in both clone libraries at phylum level. DUW clone library contained 80.0% Proteobacteria, 8.0% Bacteroides, 4.0% Nitrospira, 4.0% Firmicutes, 2.0% Planctomycetes and 2.0% Acidobacteria. On the other hand, human saliva (HS) clone library contained 55.5% Proteobacteria, 36.1% Firmicutes and 8.4% Bacteroides. The majority of bacteria identified belonged to phylum Proteobacteria in both samples. In dental unit water system (DUW), Alphaproteobacteria was detected as the major group. There was no evidence of the bacterial contamination due to a dental treatment. Most sequences were related to microorganisms derived from biofilm in oligotrophic environments.