• Mycobiology
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• 제51권6호
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• pp.401-409
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• 2023

Nigrospora (Xylariales, Apiosporaceae) consists of species of terrestrial plant endophytes and pathogens. Nigrospora has also been reported in marine environments such as mangroves, sea fans, and macroalgae. However, limited research has been conducted on Nigrospora associated with macroalgae. Here, we isolated Nigrospora species from three types of algae (brown, green, and red algae) from Korean islands (Chuja, Jeju, and Ulleung) based on phylogenetic analyses of multigenetic markers: the internal transcribed spacers (ITS), beta-tubulin (BenA), and translation elongation factor 1 (TEF1-α). A total of 17 Nigrospora strains were isolated from macroalgae and identified as nine distinct species. The majority of Nigrospora species (seven) were found on brown algae, followed by red algae (three), and then green algae (two). To our understanding, this study represents the first account of N. cooperae, N. covidalis, N. guilinensis, N. lacticolonia, N. osmanthi, N. pyriformis, and N. rubi occurring in marine environments. Additionally, this study provides the first report of the occurrence of N. cooperae, N. covidalis, N. guilinensis, N. lacticolonia, and N. osmanthi in South Korea. This study will provide valuable insights for future research exploring the functions of fungi in macroalgal communities.

• Genomics & Informatics
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• 제21권3호
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• pp.34.1-34.10
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• 2023

Nosocomial infections, commonly referred to as healthcare-associated infections, are illnesses that patients get while hospitalized and are typically either not yet manifest or may develop. One of the most prevalent nosocomial diseases in hospitalized patients is pneumonia, among the leading causes of mortality and morbidity. Viral, bacterial, and fungal pathogens cause pneumonia. More severe introductions commonly included Staphylococcus aureus, which is at the top of bacterial infections, per World Health Organization reports. The staphylococci, S. aureus, strain RMI-014804, mesophile, on-sporulating, and non-motile bacterium, was isolated from the sputum of a pulmonary patient in Pakistan. Many characteristics of S. aureus strain RMI-014804 have been revealed in this paper, with complete genome sequence and annotation. Our findings indicate that the genome is a single circular 2.82 Mbp long genome with 1,962 protein-coding genes, 15 rRNA, 49 tRNA, 62 pseudogenes, and a GC content of 28.76%. As a result of this genome sequencing analysis, researchers will fully understand the genetic and molecular basis of the virulence of the S. aureus bacteria, which could help prevent the spread of nosocomial infections like pneumonia. Genome analysis of this strain was necessary to identify the specific genes and molecular mechanisms that contribute to its pathogenicity, antibiotic resistance, and genetic diversity, allowing for a more in-depth investigation of its pathogenesis to develop new treatments and preventive measures against infections caused by this bacterium.

• 식물병연구
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• 제29권4호
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• pp.420-424
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• 2023

2020년 제주도 동백동산 내 구실잣밤나무 수피에 고약병과 관련된 Septobasidium sp.가 발견되었다. 분리한 균주는 습실 처리하여 새로 생성된 균사에 대한 genomic DNA를 추출한 뒤 internal transcribed spacer 및 small subunit rDNA 유전자에 대해 염기서열을 밝혔으며 polymerase chain reaction-based restriction fragment length polymorphism 분석을 통해 균주들간의 분자학적 특성이 조사되었다. 이 새로운 Septobasidium sp.은 기존에 알려진 고약병들과 형태학적 및 계통학적으로 다르게 나타나 새로운 종으로 보고한다. 또한 이 고약병은 관찰 당시 주변의 다른 수목들에서는 발생하지 않고 오직 구실잣밤 나무에서만 나타나는 특성으로 기주특이성이 매우 높다는 것이 확인되었다.

• Journal of Veterinary Science
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• 제25권3호
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• pp.44.1-44.13
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• 2024

Importance: The emergence and rapid increase in the incidence of multidrug-resistant (MDR) bacteria in pig farms has become a serious concern and reduced the choice of effective antibiotics. Objective: This study analyzed the phylogenetics and diversity of antibiotic resistance genes (ARGs) and molecularly identified the source of ARGs in antibiotic-resistant Escherichia coli isolated from pig farms in Banten Province, Indonesia. Methods: Forty-four antibiotic-resistant E. coli isolates from fecal samples from 44 pig farms in Banten Province, Indonesia, were used as samples. The samples were categorized into 14 clusters. Sequencing was performed using the Oxford Nanopore Technologies MinION platform, with barcoding before sequencing with Nanopore Rapid sequencing gDNA-barcoding (SQK-RBK110.96) according to manufacturing procedures. ARG detection was conducted using ResFinder, and the plasmid replicon was determined using PlasmidFinder. Results: Three phylogenetic leaves of E. coli were identified in the pig farming cluster in Banten Province. The E. coli isolates exhibited potential resistance to nine classes of antibiotics. Fifty-one ARGs were identified across all isolates, with each cluster carrying a minimum of 10 ARGs. The ant(3'')-Ia and qnrS1 genes were present in all isolates. ARGs in the E. coli pig farming cluster originated mainly from plasmids, accounting for an average of 89.4%. Conclusions and Relevance: The elevated potential for MDR events, coupled with the dominance of ARGs originating from plasmids, increases the risk of ARG spread among bacterial populations in animals, humans, and the environment.

• 한국균학회지
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• 제51권3호
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• pp.179-190
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• 2023

Grapevine downy mildew, caused by Plasmopara viticola, significantly damages vineyards and is one of the most devastating diseases affecting cultivated grapes worldwide. In this study, we characterized the phenotypic and molecular traits of 11 P. viticola isolates from four grape-growing regions in South Korea. Additionally, we investigated the diversity of pathogenicity among these isolates and conducted an assay to evaluate the response of grape cultivars to P. viticola infection. Lemon-shaped sporangia were identified in the collected isolates, which released zoospores into the suspension at room temperature. Within a few hours of inoculation, the zoospores developed germ tubes. We tested 11 P. viticola isolates for pathogenicity in 845 grape cultivars to screen for grape host resistance to downy mildew infection. Among the tested isolates, JN-9 showed the highest virulence. Grape cultivars displayed varying phenotypic reactions to P. viticola infection: approximately 7% were highly susceptible, 41% were susceptible, 20% were moderately susceptible, 8% were resistant, and 24% exhibited extreme resistance. Phylogenetic analysis based on four genomic regions (internal transcribed spacer 1 [ITS1], actin, beta-tubulin, and cytochrome c oxidase II) revealed a close evolutionary relationship among all the Korean isolates, forming a single monophyletic lineage. Notably, these isolates showed greater similarity to European isolates than to American isolates. This comprehensive study contributes to a deeper understanding of the identity and behavior of P. viticola, which is crucial for developing effective resistance strategies against this pathogen in grape cultivars cultivated in South Korea.

• 생명과학회지
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• 제24권4호
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• pp.461-466
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• 2014

본 연구에서는 독도에 자생하는 3종의 해안식물 해국(Aster sphathulifolius), 땅채송화(Sedum oryzifolium), 갯까치수영(Lysimachia mauritiana)을 연구 재료로 사용하였다. 각 식물에서 근권세균을 각 9주씩 분리하고, 동정하여 이들 세균의 다양성을 조사하고 근권 토양의 세균 집단 조성을 분석하였다. 16S rDNA의 염기서열 분석 결과, 계통학적으로 총 4문 19종의 근권세균이 분리, 동정, 확인되었다. 또한 본 실험을 통하여 독도 자생식물 근권 균주의 최적 생육 환경이 확인되었다. S. oryzifolium는 Rhodobacterales목, Micrococcales목, Corynebacteriales목, Flavobacteriales목, Oceanospirillales목, Bacillales목의 세균 균주가 확인되었으며, 자생식물 L. mauritiana에서는 Micrococcales목, Flavobacteriales목, Rhizobiales목, Oceanospirillales목, Rhodobacterales목, Bacillales목의 세균균주가 확인되었다. 자생식물 A. sphathulifolius에서는 Flavobacteriales목, Rhizobiales목, Corynebacteriales목, Micrococcales목, Alteromonadales목 및 Bacillales목의 균주가 분리, 동정, 확인되었다. 본 연구를 바탕으로 3종의 자생식물에서 방선균문(Actinobacteria)과 프로테오박테리아문(Proteobacteria)에 속하는 근권세균이 많이 존재함을 확인할 수 있었다.

• Asian-Australasian Journal of Animal Sciences
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• 제27권7호
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• pp.926-931
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• 2014

Pork from Jeju black pig (population J) and Berkshire (population B) has a unique market share in Korea because of their high meat quality. Due to the high demand of this pork, traceability of the pork to its origin is becoming an important part of the consumer demand. To examine the feasibility of such a system, we aim to provide basic genetic information of the two black pig populations and assess the possibility of genetically distinguishing between the two breeds. Muscle samples were collected from slaughter houses in Jeju Island and Namwon, Chonbuk province, Korea, for populations J and B, respectively. In total 800 Jeju black pigs and 351 Berkshires were genotyped at thirteen microsatellite (MS) markers. Analyses on the genetic diversity of the two populations were carried out in the programs MS toolkit and FSTAT. The population structure of the two breeds was determined by a Bayesian clustering method implemented in structure and by a phylogenetic analysis in Phylip. Population J exhibited higher mean number of alleles, expected heterozygosity and observed heterozygosity value, and polymorphism information content, compared to population B. The $F_{IS}$ values of population J and population B were 0.03 and -0.005, respectively, indicating that little or no inbreeding has occurred. In addition, genetic structure analysis revealed the possibility of gene flow from population B to population J. The expected probability of identify value of the 13 MS markers was $9.87{\times}10^{-14}$ in population J, $3.17{\times}10^{-9}$ in population B, and $1.03{\times}10^{-12}$ in the two populations. The results of this study are useful in distinguishing between the two black pig breeds and can be used as a foundation for further development of DNA markers.

• 미생물학회지
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• 제49권4호
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• pp.328-335
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• 2013

케라틴 단백질 분해 세균 Chryseobacterium sp. FBF-7(KACC 91463P)을 이용하여 대량생산한 닭우모 단백질 가수분해물(CPH)을 토마토에 처리한 결과, 토마토 줄기와 뿌리의 생장이 현저하게 증가되었다. 닭우모 가수분해물을 처리한 토마토 근권토양 내 세균군집 변동에 대한 계통학적 해석을 위하여 16S rRNA 유전자 서열을 기반으로 454 pyrosequencing을 수행하였다. 가수분해물을 처리하지 않은 토마토 근권토양(NCPH)의 16S rRNA 유전자 염기서열(3,281 reads)과 가수분해물을 처리한 토마토 근권토양(TCPH)의 16S rRNA 유전자 염기서열(2,167 reads)은 각각 6.33과 6.54의 다양성 지수를 나타내어 세균군집의 다양성에는 영향을 미치지 않는 것으로 확인되었다. 각 토마토 근권토양에는 총 19개의 문(phyla)의 세균이 존재하였고, 이중의 약 40%가 Proteobacteria이었다. Proteobacteria의 Bradyrhizobiaceae에 속하는 Bradyrhizobium, Agromonas, Nitrobacter 그리고 Afipia (BANA group)는 NCPH와 TCPH의 모든 근권토양에서 우점을 이루어 닭우모 가수분해믈 처리에 의해 토양 토착세균 군집에 영향을 미치지 않는 것으로 확인되었다.

• Asian-Australasian Journal of Animal Sciences
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• 제33권6호
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• pp.888-901
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• 2020

Objective: A set of microsatellite markers with high polymorphism from Tsaiya duck were used for the genetic monitoring and genetic structure analysis of Brown and White Tsaiya duck populations in Taiwan. Methods: The synthetic short tandem repeated probes were used to isolate new microsatellite markers from the genomic DNA of Tsaiya ducks. Eight populations, a total of 566 samples, sourced from Ilan Branch, Livestock Research Institute were genotyped through novel and known markers. The population genetic variables were calculated using optional programs in order to describe and monitor the genetic variability and the genetic structures of these Tsaiya duck populations. Results: In total 24 primer pairs, including 17 novel microsatellite loci from this study and seven previously known loci, were constructed for the detection of genetic variations in duck populations. The average values for the allele number, the effective number of alleles, the observed heterozygosity, the expected heterozygosity, and the polymorphism information content were 11.29, 5.370, 0.591, 0.746, and 0.708, respectively. The results of analysis of molecular variance and principal component analysis indicated a contracting Brown Tsaiya duck cluster and a spreading White Tsaiya duck cluster. The Brown Tsaiya ducks and the White Tsaiya ducks with Pekin ducks were just split to six clusters and three clusters when K was set equal to 6 and 3 in the Bayesian cluster analysis. The individual phylogenetic tree revealed eight taxa, and each individual was assigned to its own population. Conclusion: According to our study, the 24 novel microsatellite markers exhibited a high capacity to analyze relationships of inter- and intra-population in those populations with a relatively limited degree of genetic diversity. We suggest that duck farms in Taiwan could use the new (novel) microsatellite set to monitor the genetic characteristics and structures of their Tsaiya duck populations at various intervals in order to ensure quality breeding and conservation strategies.

• 한국버섯학회지
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• 제15권2호
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• pp.78-83
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• 2017

버섯과에서 한국, 중국, 일본에서 재배 또는 수집하여 농촌진흥청에 보관 중인 32개의 팽이버섯 계통에 대하여 조사하였다. 팽이버섯의 미소반복서열(microsatellite)을 포함하고 있는 490개의 DNA 단편을 얻었다. 다양한 팽이버섯 균들의 PCR을 통한 DNA 프로파일링을 수행함으로써 다형성 변이가 많이 검출되었다. 총 34개의 대립 유전자가 12개의 다형성 SSR 마커 중에서 검출되었고, 평균 3.42개의 대립 유전자와 대립 유전자의 수는 유전자좌당 2개에서 7개까지 분포하였다. 대립 형질 빈도는 0.42(GB-FV-127)에서 0.98(GB-FV-166)이었으며 이형접합체 관측치($H_O$)와 기대치($H_E$)는 각각 0.00에서 0.94(평균 = 0.18)와 0.03에서 0.67(평균 = 0.32)이었다. 다형성 지수는 (PIC) GB-FV-127 마커에서 가장 높은 0.61, 평균대립 유전자 수는 5를 나타내었고, GB-FV-166마커에서 0.03과 2로 가장 낮았다. 본 연구에서 평균 PIC 값(0.29)은 대립 유전자의 평균 수(3.42)로 관찰되었다. 결론적으로 우리는 풍부한 SSR 라이브러리에서 12 개의 다형성 SSR 마커를 개발하는데 성공했다. 이러한 SSR은 계통 발생 분석, 유전적 변이 평가에 중요하게 사용될 것이다.