• Journal of Microbiology and Biotechnology
• /
• v.17 no.6
• /
• pp.913-918
• /
• 2007

A Gram-positive, aerobic, rod-shaped, nonmotile, endospore-forming bacterium, designated Gsoil $349^T$, was isolated from soil of a ginseng field and characterized using a polyphasic approach. Comparative analysis of 16S rRNA gene sequences revealed that the strain Gsoil $349^T$ belongs to the family Paenibacillaceae, and the sequence showed closest similarity with Cohnella thermotolerans DSM $17683^T$ (94.1%) and Cohnella hongkongensis DSM $17642^T$ (93.6%). The strain showed less than 91.3% 16S rRNA gene sequence similarity with Paenibacillus species. In addition, the presence of MK-7 as the major menaquinone and $anteiso-C_{15:0},\;iso-C_{16:0},\;and\;C_{16:0}$ as major fatty acids suggested its affiliation to the genus Cohnella. The G+C content of the genomic DNA was 53.4 mol%. On the basis of its phenotypic characteristics and phylogenetic distinctiveness, strain Gsoil $349^T$ should be treated as a novel species within the genus Cohnella for which the name Cohnella panacarvi sp. nov. is proposed. The type strain is Gsoil $349^T\;(=KCTC\;13060^T=\;DSM\;18696^T)$.

• Journal of Veterinary Science
• /
• v.24 no.5
• /
• pp.73.1-73.16
• /
• 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.

• Journal of Microbiology and Biotechnology
• /
• v.27 no.4
• /
• pp.825-833
• /
• 2017

Strain IMCC26207 was isolated from the surface layer of Lake Soyang in Korea by the dilutionto-extinction culturing method, using a liquid medium prepared with filtered and autoclaved lake water. The strain could neither be maintained in a synthetic medium other than natural freshwater medium nor grown on solid agar plates. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain IMCC26207 formed a distinct lineage in the order Acidimicrobiales of the phylum Actinobacteria. The closest relative among the previously identified bacterial taxa was "Candidatus Microthrix parvicella" with 16S rRNA gene sequence similarity of 91.7%. Here, the draft genome sequence of strain IMCC26207, a freshwater actinobacterium, is reported with the description of the genome properties and annotation summary. The draft genome consisted of 10 contigs with a total size of 3,316,799 bp and an average G+C content of 57.3%. The IMCC26207 genome was predicted to contain 2,975 protein-coding genes and 51 non-coding RNA genes, including 45 tRNA genes. Approximately 76.8% of the protein coding genes could be assigned with a specific function. Annotation of the IMCC26207 genome showed several traits of adaptation to living in oligotrophic freshwater environments, such as phosphorus-limited condition. Comparative genomic analysis revealed that the genome of strain IMCC26207 was distinct from that of "Candidatus Microthrix" strains; therefore, we propose the name "Candidatus Limnosphaera aquatica" for this bacterium.

• Proceedings of the Zoological Society Korea Conference
• /
• 2000.10a
• /
• pp.135.2-135
• /
• 2000

No Abstract, See Full Text

• Proceedings of the Korean Society for Food Science of Animal Resources Conference
• /
• 1996.11a
• /
• pp.101-101
• /
• 1996

• Proceedings of the Zoological Society Korea Conference
• /
• 1997.10b
• /
• pp.141.1-141
• /
• 1997

No Abstract, See Full Text

• Journal of Microbiology and Biotechnology
• /
• v.28 no.2
• /
• pp.227-235
• /
• 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.

• Journal of fish pathology
• /
• v.20 no.1
• /
• pp.25-31
• /
• 2007

Vibriosis is one of the most important diseases affecting marin fish. In this study, a bacterium belonging to the Vibrio were isolated from maroon clownfish (Premnas biaculeatus) larvae (3～7 days after hatching). The bacterium was identified as Vibrio ponticus KJS1 by 16S rRNA gene sequence analysis. The result of biochemical test using the GN2 microplate (BioLog Inc, USA) showed that it has the ability to use 35 substrates including dextrin and sucrose was detected, could not degrade 52 substrates including α-cyclodextrin, and showed the weak ability to use 7 substrates including glycogen. It was sensitive to oxolinic acid, flumequine, ciprofloxacine, ofloxacin, norfloxacin, nalidixic acid, pefloxacin, and doxycycline hydrochloride.

• Korean Journal of Ichthyology
• /
• v.22 no.3
• /
• pp.201-205
• /
• 2010

One specimen of a natural hybrid of an Oplegnathus (Oplegnathus fasciatus $\times$ Oplegnathus punctatus) was found in Tongyeong, Korea in August 2008. We, herein, describe its morphological and genetic characteristics and compare them with those of O. fasciatus and O. punctatus. In morphology, the hybrid showed many distinctive black rounded blotches on body sides and four faint vertical bars, being in those features similar to O. punctatus. Although the counts and measurements of the hybrid mostly overlapped between O. fasciatus and O. punctatus, the Oplegnathus hybrid resembled O. punctatus in the ratio of pelvic-fin length in standard length: Oplegnathus hybrid (26.7%) was closer to O. punctatus (26.4%) than to O. fasciatus (17.2~23.6%). In genetics, as a result of analysis of 510 base pair sequences of mitochondrial DNA 16S rRNA, the hybrid was closer to O. fasciatus (d=0.000~0.010) than to O. punctatus (d=0.020). Our results suggest that the natural hybridization represented by the subject specimen occurred between an O. fasciatus female and an O. punctatus male.

• Asian-Australasian Journal of Animal Sciences
• /
• v.28 no.4
• /
• pp.568-572
• /
• 2015

Acetes chinensis is an economically important shrimp that belongs to the Sergestidae family; following fermentation, A. chinensis' economic value, however, is low in China, and much of the catch in China is exported to Korea at a low price, thus leading to potential false labeling. For this reason, we developed a simple method to identify A. chinensis' origin using allele-specific polymerase chain reaction (PCR). Ten single nucleotide polymorphisms (SNPs) were identified from partial (i.e., 570 bp) DNA sequence analysis of the mitochondrial 16s rRNA gene in 96 Korean and 96 Chinese individual shrimp. Among 10 SNP sites, four sites were observed in populations from both countries, and two sites located in the middle with SNP sites at their 3'-ends were used to design allele-specific primers. Among the eight internal primers, the C220F primer specific to the Chinese A. chinensis population amplified a DNA fragment of 364 bp only from that population. We were able to identify the A. chinensis population origin with 100% accuracy using multiplex PCR performed with two external primers and C220F primers. These results show that the 16S rRNA gene that is generally used for the identification of species can be used for the identification of the origin within species of A. chinensis, which is an important finding for the fair trade of the species between Korea and China.