• 환경생물
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• 제38권2호
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• pp.289-298
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• 2020

As part of the research program "2018 Rapid screening and identification of freshwater microorganisms using MALDI-TOF/MS library" freshwater samples were collected from a branch of the Nakdong River. Almost 300 antibiotic-resistant bacterial strains were isolated from freshwater samples and subsequently identified by 16S rRNA gene sequencing. Seventeen strains among the isolates shared high 16S rRNA gene sequence similarity (>99.0%) with known species that were not previously recorded in Korea, and each of the isolates also formed a robust phylogenetic clade with the closest species. These species were phylogenetically diverse, belonging to four phyla, seven classes, 10 orders, and 13 genera. At the genus and class level, the previously unrecorded species belonged to Rhodovarius, Xanthobacter, and Shinella of the class Alphaproteobacteria; Ottowia, Simplicispira, and Zoogloea of Betaproteobacteria; Pseudomonas, Acinetobacter, and Shewanella of Gammaproteobacteria; Arcobacter of Epsilonproteobacteria; Sphingobacterium of Sphingobacteriia; Trichococcus of Bacilli; and Leucobacter of Actinobacteria. The previously unrecorded species were further characterized by examining their gram-staining, colony and cell morphology, biochemical properties, and phylogenetic position.

• Animal Systematics, Evolution and Diversity
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• 제36권4호
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• pp.347-353
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• 2020

Although sea slaters Ligia have a significant role in rocky shore habitats, their taxonomic entities have not been clearly understood. In this study, we investigated whether genetic variation inferred from a nuclear genetic marker, namely amplified fragment length polymorphism (AFLP), would conform to that of a mitochondrial DNA marker. Using both the mitochondrial DNA marker and the AFLP marker amplified by the six selective primer sets, we analyzed 95 Ligia individuals from eight locations from East Asia. The direct sequencing of mitochondrial 16S rRNA gene revealed three distinct genetic lineages, with 9.8-11.7 Kimura 2-parameter genetic distance. However, the results of AFLP genotyping analysis with 691 loci did not support those of mitochondrial DNA, and revealed an unexpectedly high proportion of shared polymorphisms among lineages. The inconsistency between the two different genetic markers may be explained by difference in DNA evolutionary history, for example inheritance patterns, effective population size, and mutation rate. The other factor is a possible genomic island of speciation, in that most of the genomic parts are shared among lineages, and only a few genomic regions have diverged.

• 한국미생물·생명공학회지
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• 제32권2호
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• pp.195-198
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• 2004

Molec-ular analysis was performed on the microflora found In the necrotic pulpal tissue collected from 5 infected root canals that were diagnosed as a periapical abscess. 16S rRNA coding gene (rDNA) library construction and sequencing were performed in order to identify the microflora, The 16S rDNA sequences from 278 clones were identified by a comparison with the database sequence in GenBank. Three phylum and 31 species, which were related to the oral microflora, were identified from the 3 samples (No. 87, 105, and 115). Dialister invisus (5.6％), Peptostreptococcus micron (18.3％), and Veillonella sp. (3.3％) were the organism present in all tee samples. Lac-tobacillusfementum (2.8％),Eubacterumsp./E. infirmum (6.7％), Shuttleworthiasatelles (3.9％), Psudorarnihacfer alactoiyticus (13.3％), Bulleidia moorei (2.8％), and Prevotella denticola (1.1％) were found in two samples. Two phylum and low species of environmental microflora were identified from 2 samples (No.95 and 101). The reason for this might be contamination of the samples with dental water. These results showed that molecular analysis could reveal more diverse microflora that are associated with endodontic infections than that revealed by conventional cultural methods. In addition, these results may of for the basic data to epidemiological studies related with endodontic infection.

• 한국어병학회지
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• 제17권3호
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• pp.159-169
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• 2004

2003년 5월과 2003년 10월동안에 제주도내 5개소의 넙치 종묘배양장에서 초기 먹이로 공급 되어지는 동물성 플랑크톤인 rotifer와 20-30일령 넙치 자어에서 장관백탁증 원인균으로 알려진 V. ichthyoenteri를 분리하기 위해 실험한 결과 총 71개의 Vibrio sp. 분리가 되었고, 생화학적 동정결과 2개의 그룹에서 24개의 V ichthyoenteri가 동정 되었다. V. ichthyoenteri의 신속한 검출을 위한 종특이적 primer를 V. ichthyoenteri(KCCM 40870)ISR의 특이적인 서열을 이용하여 제작하였다. V. ichthyoenteri를 포함한 20종의 Vibrio속 균주의 genomic DNA와 18group 분리균주 genomic DNA를 PCR한 결과 V. ichthyoenteri 만의 특이적인 band가 생성됨을 알 수가 있다. 따라서 V. ichthyoenteri(KCCM 40870) ISR의 서열로 제작한 primer가 넙치 자치어에 발병하는 장관백탁증 원인균인 Vibrio ichthyoenteri의 신속한 검출과 정확한 동정을 할 수 있는 molecular marker로 이용할 수 있음을 확인하였다.

• Animal Bioscience
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• 제35권11호
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• pp.1808-1816
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• 2022

Objective: The study of Hanwoo (Korean native cattle) has mainly been focused on meat quality and productivity. Recently the field of microbiome research has increased dramatically. However, the information on the microbiome in Hanwoo is still insufficient, especially relationship between vagina and feces. Therefore, the purpose of this study is to examine the microbial community characteristics by analyzing the 16S rRNA sequencing data of Hanwoo vagina and feces, as well as to confirm the difference and correlation between vaginal and fecal microorganisms. As a result, the goal is to investigate if fecal microbiome can be used to predict vaginal microbiome. Methods: A total of 31 clinically healthy Hanwoo that delivered healthy calves more than once in Cheongju, South Korea were enrolled in this study. During the breeding season, we collected vaginal and fecal samples and sequenced the microbial 16S rRNA genes V3-V4 hypervariable regions from microbial DNA of samples. Results: The results revealed that the phylum-level microorganisms with the largest relative distribution were Firmicutes, Actinobacteria, Bacteroidetes, and Proteobacteria in the vagina, and Firmicutes, Bacteroidetes, and Spirochaetes in the feces, respectively. In the analysis of alpha, beta diversity, and effect size measurements (LefSe), the results showed significant differences between the vaginal and fecal samples. We also identified the function of these differentially abundant microorganisms by functional annotation analyses. But there is no significant correlation between vaginal and fecal microbiome. Conclusion: There is a significant difference between vaginal and fecal microbiome, but no significant correlation. Therefore, it is difficult to interrelate vaginal microbiome as fecal microbiome in Hanwoo. In a further study, it will be necessary to identify the genetic relationship of the entire microorganism between vagina and feces through the whole metagenome sequencing analysis and meta-transcriptome analysis to figure out their relationship.

• Annals of Clinical Microbiology
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• 제17권1호
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• pp.23-27
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• 2014

신속발육항산균은 자연환경에서 흔히 검출되는 균으로, 기회감염병원체로 인체감염의 주요 원인균으로서 인식되고 있다. M. conceptionense는 분자역학적 분석을 통해 M. fortuitum의 세번째 생체변이종에서 분리되어 새로운 종으로 명명되었다. 그러나 이 균에 의한 감염 보고는 많지 않고 특히 수술후 창상 감염에 대한 보고는 거의 없다. 이에 저자들은 16S rRNA, hsp65 및 rpoB 유전자 염기순서분석을 이용하여 동정한 M. conceptionense에 의한 수술 후 창상감염을 보고하고자 한다.

• Journal of Microbiology and Biotechnology
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• 제28권2호
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• pp.227-235
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• 2018

Foodborne illness represents a major threat to public health and is frequently attributed to pathogenic microorganisms on fresh produce. Recurrent outbreaks often come from vegetables that are grown close to or within the ground. Therefore, the first step to understanding the public health risk of microorganisms on fresh vegetables is to identify and describe microbial communities. We investigated the phyllospheres on Chinese cabbage (Brassica rapa subsp. pekinensis, N = 54). 16S rRNA gene amplicon sequencing targeting the V5-V6 region of 16S rRNA genes was conducted by employing the Illumina MiSeq system. Sequence quality was assessed, and phylogenetic assessments were performed using the RDP classifier implemented in QIIME with a bootstrap cutoff of 80%. Principal coordinate analysis was performed using a weighted Fast UniFrac matrix. The average number of sequence reads generated per sample was 34,584. At the phylum level, bacterial communities were composed primarily of Proteobacteria and Bacteroidetes. The most abundant genera on Chinese cabbages were Chryseobacterium, Aurantimonadaceae_g, Sphingomonas, and Pseudomonas. Diverse potential pathogens, such as Pantoea, Erwinia, Klebsiella, Yersinia, Bacillus, Staphylococcus, Salmonella, and Clostridium were also detected from the samples. Although further epidemiological studies will be required to determine whether the detected potential pathogens are associated with foodborne illness, our results imply that a metagenomic approach can be used to detect pathogenic bacteria on fresh vegetables.

• 한국수산과학회지
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• 제42권6호
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• pp.531-536
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• 2009

A urease-positive bacterium isolated from sea water was identified as Photobacterium sp. by morphological, biochemical, and 16s rRNA gene analyses and named Photobacterium sp. strain HA-2. 2.0-fold increase enzyme activity was observed in LB medium containing 3% NaCl and 0.1% urea or not and the enzyme activity was 16.0-fold lower compared to urease-positive Vibrio parahaemolyticus AQ4673 strain when grown in the LB medium containing 3% NaCl with 0.1% urea. The cloning and sequencing of Photobacterium sp. strain HA-2 urease gene cluster is currently being analyzed in our laboratory.

• Journal of Veterinary Science
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• 제24권5호
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• pp.73.1-73.16
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• 2023

Background: Highly pathogenic avian influenza virus (HPAIV) is considered a global threat to both human health and the poultry industry. MicroRNAs (miRNA) can modulate the immune system by affecting gene expression patterns in HPAIV-infected chickens. Objectives: To gain further insights into the role of miRNAs in immune responses against H5N1 infection, as well as the development of strategies for breeding disease-resistant chickens, we characterized miRNA expression patterns in tracheal tissues from H5N1-infected Ri chickens. Methods: miRNAs expression was analyzed from two H5N1-infected Ri chicken lines using small RNA sequencing. The target genes of differentially expressed (DE) miRNAs were predicted using miRDB. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis were then conducted. Furthermore, using quantitative real-time polymerase chain reaction, we validated the expression levels of DE miRNAs (miR-22-3p, miR-146b-3p, miR27b-3p, miR-128-3p, miR-2188-5p, miR-451, miR-205a, miR-203a, miR-21-3p, and miR-200a3p) from all comparisons and their immune-related target genes. Results: A total of 53 miRNAs were significantly expressed in the infection samples of the resistant compared to the susceptible line. Network analyses between the DE miRNAs and target genes revealed that DE miRNAs may regulate the expression of target genes involved in the transforming growth factor-beta, mitogen-activated protein kinase, and Toll-like receptor signaling pathways, all of which are related to influenza A virus progression. Conclusions: Collectively, our results provided novel insights into the miRNA expression patterns of tracheal tissues from H5N1-infected Ri chickens. More importantly, our findings offer insights into the relationship between miRNA and immune-related target genes and the role of miRNA in HPAIV infections in chickens.

• 생명과학회지
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• 제22권7호
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• pp.987-990
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• 2012

녹두나물(숙주나물)은 국내뿐만 아니라 세계적으로도 널리 이용되고 있는 채소다. 그런데 녹두나물 재배를 하는 과정에서 발생되는 녹두나물 무름병은 녹두나물 생산량은 물론 품질을 심각하게 저하시킨다. 본 연구에서는 녹두나물 부패 조직으로부터 70계통의 병원균을 분리하였으며, 각 병원균의 병원성을 검정하였다. 그 가운데 강한 병원성을 가진 Pseudomonas 균류의 계통 YV-St-033를 확인하여 선발하였으며, 분리된 병원균계의 16S rRNA 유전자 염기서열을 분석하고 유전학적 유연관계를 분석하였다. YV-St-033는 P. mosselii, P. putita, P. fluorescens, P. entomophila, P. lecoglossicida 등의 종이 속한 그룹으로 확인이 되었으며, Pseudomonas mosselii R10 strain과 가장 높은 염기서열 identity (약 99%)를 보였다. 또한 YV-St-033 strain을 이용하여 영남대학교에서 보유하고 있는 녹두 유전자원들에 대해 녹두나물 무름병 저항성을 검정하였다. 3일간 배양한 녹두에 병원균을 접종하고 녹두의 생장율을 비교한 결과 YV148 line에서 높은 저항성이 확인되었으며, 그 외 녹두 계통에서도 부분적인 저항성을 나타내었다. 숙주나물 무름병에 저항성을 보인 YV 148 계통은 나물이 가늘고 연하고 생장율이 우수하여 앞으로 품종 육종의 좋은 재료로 활용될 수 있을 것으로 판단되었다.