• 생명과학회지
• /
• 제21권6호
• /
• pp.788-795
• /
• 2011

병원균에 대한 정확한 동정은 임상 연구실에서 필수적인 요소의 하나이다. Chyseobacterium indologenes에 대한 동정을 포함한 분자생물학적 분석과 리보솜의 16S rRNA 유전자로 한국에서 추출한 17검체와 GenBank에서 Chyseobacterium속 검색을 통해 이들과 계통관계를 평가하였다. C. indologenes의 배당 서열은 1,176 nucleotides였다. C. indologenes 내의 서열 변이는 주로 염기 치환이었다. 한국의 C. indologenes 검체는 다른 나라의 동 종과 크게 다르지 않았다. 그런데 한국의 C. indologenes의 치환율은 GenBank에 있는 동종보다 높았다. C. indologenes는 C. isbiliense, C. hominis, C. hispanicum, C. molle, C. hungaricum, and C. pallidum과 자매종을 형성하였다.

• Environmental Engineering Research
• /
• 제14권1호
• /
• pp.3-9
• /
• 2009

Microorganisms play an important role in the geochemical cycles, industry, environmental cleanup, and biotechnology among other fields. Given the high microbial diversity, identification of the microorganism is essential in understanding and managing the processes. One of the most popular and powerful method for microbial identification is comparative 16S rRNA gene analysis. Due to the highly conserved nature of this essential gene, sequencing and later comparison of it against known rRNA databases can provide assignment of the bacteria into the taxonomy, and the identity of its closest relatives. Isolation and sequencing of 16S rRNA genes directly from natural environments (either from DNA or RNA) can also be used to study the structure of the whole microbial community. Nowadays, novel sequencing technologies with massive outputs are giving researchers worldwide the chance to study the microbial world with a depth that was previously too expensive to achieve. In this article we describe commonly used research approaches for the study of individual microorganisms and microbial communities using the tools provided by Ribosomal Database Project website.

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

• 환경생물
• /
• 제21권1호
• /
• pp.77-85
• /
• 2003

본 연구는 위장관염을 일으키는 Vibrio fluvialis의 16S-23S rRNA intergenic spacer region을 분석하였다. ISR을 PCR 증폭 후 plasmid vector에 클로닝하여 염기서열을 분석하였다. 그 결과, ISR의 염기서열은 tRNA gene 조성과 크기에 따라 총 6개의 type으로 분류되었다. 각 type은 tRNA gene 조성과 수에 따라 ISR-A, ISR-E, ISR-El, ISR-lA, ISR-EKV, ISR-EKAV로 명명하였으며, ISR-A는 tRN $A^{Ala}$; ISR-lA, tRN $A^{Ile}$-tRN $A^{Ala}$; ISR-EKV, tRN $A^{Glu}$-tRN $A^{Lys}$-tRN $A^{Val}$; ISR-EKAV, tRN $A^{Glu}$-tRN $A^{Lys}$-tRN $A^{Ala}$-tRN $A^{Val}$; ISR-E와 El은 tRN $A^{Glu}$를 갖고 있었다. 이 중 ISR-EKV type은 minor type으로 존재하고 있으며, 여러 Vibrio종의 ISR-EKV type과 비교시 변이성이 높은 부위를 확인하였다. 따라서, 이 ISR-EKV의 염기서열을 여러 Vibrio종에서 V. fluuialis를 검출하기 위한 species-specific primer 제작에 이용하였다. 제작된 primer의 특이성은 여러 Vibrio 의 genomic DNA를 분리하여 PCR 반응으로 확인하였다. 그 결과, 제작된 primer는 V. fluvialis에 종 특이성이 있으며 여러 Vibrio종으로부터 빠른 검출이 가능함을 확인하였다.로부터 빠른 검출이 가능함을 확인하였다.

• Journal of Microbiology and Biotechnology
• /
• 제6권5호
• /
• pp.364-365
• /
• 1996

A region encoding the 16S rRNA was cloned by PCR from Streptomyces melanosporofaciens 7489 and sequenced by the chain-termination dideoxy sequencing method. A phylogenetic tree constructed by sequence alignment of 24 Streptomyces species suggests that there is little evolutionary distance between this strain and Streptomyces rimosus.

• 한국미생물·생명공학회지
• /
• 제42권4호
• /
• pp.377-385
• /
• 2014

본 연구에서는 고염폐수의 정화능이 우수한 미생물 기능성 커뮤니티 HWTC (Highsalt Wastewater Treatment Community)를 이용한 고염폐수 처리시스템을 개발하였으며, HWTC의 미생물 군집의 다양성을 확인해 보았다. HWTC의 고염폐수 처리능력은 HRT 2.5일만에 $COD_{cr}$ 84%의 처리효율로 확인하였다. 미생물 군집분석은 PCR-DGGE 기법과 16S rRNA gene clone library를 통하여 미생물 다양성을 확인하였다. 4%의 염농도의 폐수에서 우점하는 미생물은 Halomonas sp.와 Paenibacillus sp.로 나타났고, phylogenetic tree 분석을 통해 ${\gamma}$-proteobacteria 속하는 미생물의 다양성이 높게 나타났으며, firmicutes속 하는 미생물이 우점하고 있었다. 고염폐수를 처리할 수 있는 미생물 기능성 커뮤니티 HWTC를 이용하여, 고염의 폐수 정화를 가능하게 할 것으로 판단된다.

• International Journal of Oral Biology
• /
• 제38권1호
• /
• pp.29-36
• /
• 2013

Mitis group streptococci (MGS) were classified based on the nucleotide sequences 16S rRNA gene (16S rDNA) and comprised 13 Streptococcus species. However, 16S rDNA homogeneity among MGS was too high to discriminate between clinical strains at the species level, notably between Streptococcus mitis, Streptococcus oralis, Streptococcus pneumoniae, and Streptococcus pseudopneumoniae. The purpose of this study was to discriminate between 37 strains of MGS isolated from Korean oral cavities using phylogenetic analysis of the DNA-dependant RNA polymerase beta-subunit gene (rpoB). 16S rDNA and rpoB from clinical strains of MGS were sequenced using the dideoxy chain termination method and analyzed using MEGA version 5 software. The resulting phylogenetic data showed that the rpoB sequences could delineate clinical strains of MGS at the species level. Phylogenetic analysis of rpoB is therefore a useful approach for identifying MGS at the species level.

• 환경생물
• /
• 제30권1호
• /
• pp.54-63
• /
• 2012

This study characterizes three $Anabaena$ strains and 5 $Trichormus$ strains isolated from Korean waters and 3 $Anabaena$ $flos-aquae$ strains procured from the UTEX based on morphological features and molecular analyses. The $Anabaena$ and $Trichormus$ isolates were morphologically assigned to $A.$ $variabilis$ K$\ddot{u}$tzing and $T.$ $variabilis$(K$\ddot{u}$tzing ex Bornet et Flahault) Kom$\acute{a}$rek et Anagnostidis, respectively. The $Anabaena$ and $Trichormus$ strains differed significantly in the mean length of their vegetative cells. The 16S rRNA genes from the $Anabaena$ strains showed a 100% identity to that from $A.$ $variabilis$ ATCC 29413, while the 16S rRNA genes from the $Trichormus$ strains showed a 99.9% identity to that from $T.$ $variabilis$ GREIFSWALD. The overall topology was in agreement for the 16S rRNA gene and $cpcBA$-IGS trees in the both tree-constructing methods. In a neighbor-joining tree based on the 16S rRNA gene, the 3 $Anabaena$ strains were asso-ciated with $A.$ $variabilis$, the 5 $Trichormus$ strains with $T.$ $variabilis$, and the 3 $Anabaena$ (UTEX) strains were with $Nostoc$. To date, this is the first report on $A.$ $variabilis$ and $T.$ $variabilis$ strains originating from Korea.

• 미생물학회지
• /
• 제39권3호
• /
• pp.192-196
• /
• 2003

다양한 유산균 자원을 확보하기 위한 일환으로, 동치미에서 유산균을 분리하였다. 동치미에서 분리된 균주는, 당이용성과 16S rRNA 유전자분석을 통하여,Lactobacillus plantarum HB1으로 밝혀졌다. 이 균주는 Gram 양성균이었으며, catalase를 갖고 있지 않았다. 16S rRNA유전자의 염기배열 120 bp을 분석해 본 결과,1～88 bp 영역에서는 기존의 것과 거의 100%의 상동성을 보여 주었고,나머지 32 bp의 영역에서는 상당한 변이를 보여 주었다. 따라서 본 균주는 기존의 L. plantarum과는 다른 균주임을 확인할 수 있었다. 동치미의 무에 포함되어 있는 질산염은 체내에서 아질산염으로 바뀐다. 아질산염은 아민과 반응을 일으켜 니트로사민이 되는데, 이 성분은 위암 발생을 일으키는 주요인자중의 하나이다. 동치미에서 분리된 본 균주의 배양액에 400 ${\mu}M$의 아질산염을 첨가한 경우 1시간30분 후에 거의 소거되었다. 아질산염 소거작용에 관여하는 본 균주 배양액 중의 특정성분의 분리, 소거작용 기작 등에 관한 보다 깊이 있는 연구가 앞으로 필요하다.

• Journal of Microbiology and Biotechnology
• /
• 제27권7호
• /
• pp.1288-1299
• /
• 2017

Composting is widely used to transform waste into valuable agricultural organic fertilizer. Anaerobic ammonium-oxidizing (anammox) bacteria play an important role in the global nitrogen cycle, but their role in composting remains poorly understood. In the present study, the community structure, diversity, and abundance of anammox bacteria were analyzed using cloning and sequencing methods by targeting the 16S rRNA gene and the hydrazine oxidase gene (hzo) in samples isolated from compost produced from cow manure and rice straw. A total of 25 operational taxonomic units were classified based on 16S rRNA gene clone libraries, and 14 operational taxonomic units were classified based on hzo gene clone libraries. The phylogenetic tree analysis of the 16S rRNA gene and deduced HZO protein sequences from the corresponding encoding genes indicated that the majority of the obtained clones were related to the known anammox bacteria Candidatus "Brocadia," Candidatus "Kuenenia," and Candidatus "Scalindua." The abundances of anammox bacteria were determined by quantitative PCR, and between $2.13{\times}10^5$ and $1.15{\times}10^6$ 16S rRNA gene copies per gram of compost were found. This study provides the first demonstration of the existence of anammox bacteria with limited diversity in cow manure composting.