• Journal of Species Research
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• 제10권3호
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• pp.276-286
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• 2021

We performed a taxonomic study on Korean Pacificincolidae (Bryozoa: Cheilostomata) with the materials collected from 39 localities(ports, intertidal and subtidal zones) in the coastal seas of South Korea from 1981 to 2020. Korean Mucronella perforata reported by Rho and Seo (1985) turned out to be not Pacificincola perforata, but Primavelans glabricollaris n. sp. based on morphological data. Pacificincola perforata, which was transferred from Mucronella perforata (Okada and Mawatari, 1937), is also added to the Korean fauna. This study is the first to use mitochondrial 16S rRNA gene sequences to study the family Paficincolidae. The NJ analysis also reconfirmed the validity of the genus Primavelans, established on the basis of the early astogeny by De Blauwe in 2006, with the mitochondrial 16S rRNA sequences. The inter-genetic distance among two species belong to the Pacificincolidae was in the range of 13.39±1.83 mm. Primavelans glabricollaris n. sp. is thus distinguished from Pacificincola perforata with both morphological and molecular data. A new species, Primavelans glabricollaris, and a new record, Pacificincola perforata from Korea are herein described in detail and illustrated by scanning electron microscopy.

• Journal of Species Research
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• 제13권1호
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• pp.10-31
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• 2024

In this study, 11 strains of epilithic cyanobacteria belonging to six unrecorded species in Korea were isolated from gravel submerged in freshwater of seven collection sites in Korea. The morphological characteristics of the six species isolated in this study were consistent with the type strain of each species, and the similarity of the 16S rRNA gene sequences with the type strain of each species were 98.8-100%. In the phylogenetic tree using the 16S rRNA gene sequences, the 11 strains of these six species formed the same cluster as the strains of each species. The habitat of each previously reported species is mainly the soil surface, but all Korean strains appeared from the gravel submerged in freshwater. As a result of the morphological, ecological, and molecular analyses, these six species of cyanobacteria were identified as Geminocystis papuanica, Allocoleopsis franciscana, Ancylothrix terrestris, Klisinema persicum, Scytolyngbya timoleontis, and Shackletoniella antarctica, which were added as newly recorded species in Korea.

• 운동영양학회지
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• 제25권4호
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• pp.24-37
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• 2021

[Purpose] To determine whether physical activity (PA), primarily the recommended 60 minutes of moderate-to-vigorous PA, is associated with gut bacterial microbiota in 10-year-old children. [Methods] The Block Physical Activity Screener, which provides minutes/day PA variables, was used to determine whether the child met the PA recommendations. 16S rRNA sequencing was performed on stool samples from the children to profile the composition of their gut bacterial microbiota. Differences in alpha diversity metrics (richness, Pielou's evenness, and Faith's phylogenetic diversity) by PA were determined using linear regression, whereas beta diversity (unweighted and weighted UniFrac) relationships were assessed using PERMANOVA. Taxon relative abundance differentials were determined using DESeq2. [Results] The analytic sample included 321 children with both PA and 16S rRNA sequencing data (mean age [SD] =10.2 [0.8] years; 54.2% male; 62.9% African American), where 189 (58.9%) met the PA recommendations. After adjusting for covariates, meeting the PA recommendations as well as minutes/day PA variables were not significantly associated with gut richness, evenness, or diversity (p ≥ 0.19). However, meeting the PA recommendations (weighted UniFrac R² = 0.014, p = 0.001) was significantly associated with distinct gut bacterial composition. These compositional differences were partly characterized by increased abundance of Megamonas and Anaerovorax as well as specific Christensenellaceae_R-7_group taxa in children with higher PA. [Conclusion] Children who met the recommendations of PA had altered gut microbiota compositions. Whether this translates to a reduced risk of obesity or associated metabolic diseases is still unclear.

• Journal of Animal Science and Technology
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• 제47권3호
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• pp.465-474
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• 2005

A two-step broad-range PCR method detecting gram-negative bacteria at the level as low as 2 CFU was developed by using primers of GNFI and GNRI and then semi-nested primer of GNF2 and GNRI. The nucleotide sequences of the primers were determined based on l6S rRNA gene. The DNA fragments of 1173 bp and 169 bp were amplified in one-step PCRs with primer sets of GNFI-GNRI and GNF2-GNRl, respectively, using template DNA from seven strains of gram-negative bacteria including Escherichia coli, Enterobacter aerogenes, Klebsiella pneumoniae, Pseudomonas spp., and Acinetobacter baumaii but not from Achromobacter lyticus, Alca/igens faecalis, and five strains of gram-positive bacteria. DNA fragments of 180 bp were amplified from LTLT-pasteurized milk and UHf-pasteurized milk in the two-step PCR. The DNA fragments were amplified from LTLT-pasteurized milk which was added with Pseudomonas j/uorescens and subsequently heated at 65 $^{\circ}C$, 80 $^{\circ}C$, and 100 $^{\circ}C$ for 30 min but they were not amplified from the milk autoclaved at 121$^{\circ}C$ for 15 min. It was suggested in PCR that Pseudomonas fluorescens heated at 65 $^{\circ}C$ for 30 min in milk was more sensitive to DNase treatment than viable bacteria.

• 미생물학회지
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• 제47권1호
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• pp.66-73
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• 2011

각 지역에서 수집한 무당벌레(JK, CK, CJ)의 소화기관을 채취하여 장내세균의 밀도를 조사한 결과, 호기배양의 경우 $6.0{\times}10^4$ CFU/gut, 혐기배양 결과 $8.0{\times}10^6$ CFU/gut로 계수되었다. 호기적 조건에서 배양된 세균 집락은 총 7가지 형태로 분류되었으며, 혐기적 조건에서 배양된 집락은 총 3가지 형태로 유사한 특징을 나타내었다. 무당벌레 각 소화기관으로부터 호기성세균 34균주와 혐기성세균 82균주, 총 116균주의 장내세균을 순수분리하였다. 호기성 세균 34균주를 대상으로 16S rRNA 유전자 염기서열을 해석한 결과, ${\alpha}$-Proteobacteria (3균주), ${\gamma}$-Proteobacteria (2 균주), Firmicutes (24 균주), Actinobacteria (4 균주) 그리고 Deinococcus-Thermus (1균주) 계통군으로 분류되었다. Firmicutes 계통군의 Bacillus thuringiensis와 Staphylococcus 속의 다양한 종은 JK, CK 및 CI 무당벌레 소화기관에서 모두 공통적으로 분리되었다. 형태적으로 유사한 혐기세균의 16S rRNA-ARDRA 패턴양상을 분석하여 유사도 70%에서 비교한 결과, 17개 ARDRA group으로 분류되었다. 각 ARDRA group에 속하는 대표 혐기성세균의 16S rRNA 유전자 염기서열을 해석한 결과, 무당벌레 소화기관에서 분리된 모든 혐기성 장내세균은 ${\gamma}$-Proteobacteria 계통군에 속하는 것으로 나타났으며 Hafnia alvei, Enterobacter ludwigii, Enterobacter kobei, Pseudomonas oryzihabitans 그리고 Pseudomonas koreensis와 높은 유연관계를 갖는 것으로 확인되었다. 무당벌레 소화기관으로부터 분리된 전체 장내세균의 약 70%가 ${\gamma}$-Proteobacteria 계통군에 속하였으며, 23%가 Firmicutes 계통군으로 무당벌레 소화기관 내 주요 계통군임이 확인되었다.

• International Journal of Oral Biology
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• 제45권2호
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• pp.70-75
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• 2020

The aim of this study was to identify strain KCOM 1265 isolated from subgingival plaque at the species level by comparing 16S ribosomal RNA gene (16S rDNA) and genome sequences. The whole genome of strain KCOM 1265 was extracted using the phenol-chloroform extraction method. 16S rDNA was amplified using polymerase chain reaction and sequenced using the dideoxy chain termination method. Pairwise genome comparison was performed using average nucleotide identity (ANI) and genome-to-genome distance (GGD) analyses. The data showed that the percent similarity of 16S rDNA sequence of strain KCOM 1265 was 99.6% as compared with those of Fusobacterium polymorphum ATCC 10953^T and Fusobacterium hwasookii KCOM 1249^T. The ANI values of strain KCOM 1265 with F. polymorphum ATCC 10953^T and F. hwasookii KCOM 1249^T were 95.8% and 93.0%, respectively. The GGD values of strain KCOM 1265 with F. polymorphum ATCC 10953^T and F. hwasookii KCOM 1249^T were 63.9% and 49.6%, respectively. These results indicate that strain KCOM 1265 belongs to F. polymorphum.

• 대한수의학회지
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• 제42권2호
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• pp.225-229
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• 2002

We report that mycoplasma organisms from lung tissues of slaughter pigs were identified to genes fragments with references use of nested-PCR technique(nPCR). Seven strains of mycoplasma species were isolated from 70 lung tissues. The organisms were detected by in vitro amplification of 16S rRNA and 23S rRNA genes. Nucleotide sequences of the spacer between 16S and 23S in the ribosomal RNA operons of mycoplasma were identified by the analysis of products from the nested PCR. Four common PCR primers, MhF1, MhF2 MhR1 and MhR2, were designed by analysis between these sequences by first amplified with F1, R1 and second with F2, R2, respectively. Specific amplification of the spacer region for reference strains of M. hyopneumoniae, M. hyorhinis, M. flocculare were confirmed by first round of PCR in which the traduced fragments of 690bp, 460bp, 630bp. But amplications of second round was changed to 240bp, 210bp, 230bp, respectively. Three different strains (M. hyopneumoniae:4, M. hyorhinis:2, M. flocculare:1) were detected by the nested-PCR technique. The results suggest that the detection of swine mycoplasma by n-PCR can be analyzed the nucleotide sequences between rRNA operons and homology study.

• 대한환경공학회지
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• 제22권5호
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• pp.939-947
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• 2000

연속 회분식 반응기를 이용하여 생물학적 인 제거에 관한 미생물 분포 연구를 수행하였다. 탄소원으로 초산을 넣은 합성 폐수를 사용하였고 미생물 체류 시간과 수리학적 체류 시간은 각각 10일과 16시간으로 유지하였다. 인 방출과 흡수가 운전 시간이 경과됨에 따라 점점 빠르게 일어났으며 약 200일 경과 후 안정적인 인 제거가 유지되었다. 안정적인 생물학적 인 제거가 유지될 때의 미생물 분포를 조사하기 위하여 17개의 ribosomal RNA (rRNA) signature probe를 합성하여 슬러지로부터 분리한 전체 rRNA에 대하여 slot hybridization을 실시하였다. 분리한 전체 RNA에는 proteobacteria의 베타군 (beta subclass)에 속하는 rRNA가 가장 많이 함유되어 있음을 확인하였고 CTE probe와 관계된 rRNA가 다음으로 많이 분포하였다. 전통적으로 생물학적 인 제거를 담당하는 미생물로 여겨져 왔던 Acinetobacter, Aeromonas, Pseudomonas의 rRNA는 10% 미만으로 존재하고 있음이 확인되었다. 이러한 결과로부터 Rhodocyclus 그룹같은 proteobacteria의 베타군과 CTE에 속하는 미생물이 인 제거에 중요한 역할을 수행할 것으로 생각되었고 Acinetobacter, Aeromonas, Pseudomonas 등은 생물학적 인 제거에 있어서 과평가된 것으로 판단되었다.

• 한국응용곤충학회지
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• 제49권3호
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• pp.251-259
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• 2010

톱다리개미허리노린재(Riptortus clavatus)의 장내세균이 분리되었다. 형태학적 분석과 생화학적 분석을 통하여 세균이 Staphylococcus succinus와 가장 유사한 것으로 동정되었다. 16S rRNA 유전자의 염기서열은 이러한 동정 결과를 뒷받침했다. 페니실린G를 톱다리개미허리노린재 성충에게 경구투여 하였을 때 장내세균 밀도 감소와 치사 효과를 유발하였다. 동일한 방법으로 곤충병원세균(Xenorhabdus nematophila)의 세 가지 대사물질(benzylideneacetone, proline-tyrosine, and acetylated phenylalanine-glycine-valine)을 처리하였을 때, 톱다리개미허리노린재 장내세균의 밀도감소와 치사효과를 확인하였다. 이러한 결과는 톱다리개미허리노린재의 장내세균이 Staphylococcus sp.이며, 곤충병원세균 대사물질의 항균 활성이 장내세균과 궁극적으로 톱다리개미허리노린재의 생존에 영향을 미친다는 것을 제시하였다.

• The Plant Pathology Journal
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• 제40권2호
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• pp.171-191
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• 2024

Identification of Helicotylenchus species is very challenging due to phenotypic plasticity and existence of cryptic species complexes. Recently, the use of rDNA barcodes has proven to be useful for identification of Helicotylenchus. Molecular markers are a quick diagnostic tool and are crucial for discriminating related species and resolving cryptic species complexes within this speciose genus. However, DNA barcoding is not an error-free approach. The public databases appear to be marred by incorrect sequences, arising from sequencing errors, mislabeling, and misidentifications. Herein, we provide a comprehensive analysis of the newly obtained, and published DNA sequences of Helicotylenchus, revealing the potential faults in the available DNA barcodes. A total of 97 sequences (25 nearly full-length 18S-rRNA, 12 partial 28S-rRNA, 16 partial internal transcribed spacer [ITS]-rRNA, and 44 partial cytochrome c oxidase subunit I [COI] gene sequences) were newly obtained in the present study. Phylogenetic relationships between species are given as inferred from the analyses of 103 sequences of 18S-rRNA, 469 sequences of 28S-rRNA, 183 sequences of ITS-rRNA, and 63 sequences of COI. Remarks on suggested corrections of published accessions in GenBank database are given. Additionally, COI gene sequences of H. dihystera, H. asiaticus and the contentious H. microlobus are provided herein for the first time. Similar to rDNA gene analyses, the COI sequences support the genetic distinctness and validity of H. microlobus. DNA barcodes from type material are needed for resolving the taxonomic status of the unresolved taxonomic groups within the genus.