• Journal of Microbiology and Biotechnology
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• v.20 no.3
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• pp.643-649
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• 2010

Evaluation of the primary etiologic agents that cause aseptic meningitis outbreaks may provide valuable information regarding the prevention and management of aseptic meningitis. In Korea, an outbreak of aseptic meningitis caused by echovirus type 30 (E30) occurred from May to October in 2008. In order to determine the etiologic agent, CSF and/or stool specimens from 140 children hospitalized for aseptic meningitis at Soonchunhyang University Cheonan Hospital between June and October of 2008 were tested for virus isolation and identification. E30 accounted for 61.7% (37 cases) and echovirus 6 accounted for 21.7% (13 cases) of all the human enteroviruses (HEVs) isolates (60 cases in total). For the molecular characterization of the isolates, the VP1 gene sequence of 18 Korean E30 isolates was compared pairwise using the MegAlign with 34 reference strains from the GenBank database. The pairwise comparison of the nucleotide sequences of the VP1 genes demonstrated that the sequences of the Korean strains differed from those of lineage groups A, B, C, D, E, F, and G. Reconstruction of the phylogenetic tree based on the complete VP1 nucleotide sequences resulted in a monophyletic tree, with eight clustered lineage groups. All Korean isolates were segregated from other lineage groups, thus suggesting that the Korean strains were a distinct lineage of E30, and a probable cause of this outbreak. This manuscript is the first report, to the best of our knowledge, of the molecular characteristics of E30 strains associated with an aseptic meningitis outbreak in Korea, and their respective phylogenetic relationships.

• Parasites, Hosts and Diseases
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• v.53 no.3
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• pp.253-258
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• 2015

Toxoplasma gondii, an obligate intracellular protozoan parasite of the phylum Apicomplexa, can infect all warm-blooded vertebrates, including humans, livestock, and marine mammals. The aim of this study was to investigate whether superoxide dismutase (SOD) of T. gondii can be used as a new marker for genetic study or a potential vaccine candidate. The partial genome region of the SOD gene was amplified and sequenced from 10 different T. gondii isolates from different parts of the world, and all the sequences were examined by PCR-RFLP, sequence analysis, and phylogenetic reconstruction. The results showed that partial SOD gene sequences ranged from 1,702 bp to 1,712 bp and A + T contents varied from 50.1% to 51.1% among all examined isolates. Sequence alignment analysis identified total 43 variable nucleotide positions, and these results showed that 97.5% sequence similarity of SOD gene among all examined isolates. Phylogenetic analysis revealed that these SOD sequences were not an effective molecular marker for differential identification of T. gondii strains. The research demonstrated existence of low sequence variation in the SOD gene among T. gondii strains of different genotypes from different hosts and geographical regions.

• Mycobiology
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• v.47 no.2
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• pp.191-199
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• 2019

Most of lichens are formed by Ascomycota, less than 1% are lichenized Basidiomycota. The flora investigation of lichenized Ascomycota of South Korea has been well studied in the past three decades; however, prior to this study, none of basidiolichens was discovered. During the recent excursion, an unexpected clavarioid basidiolichen, Sulzbacheromyces sinensis was collected. Morphology and ecology has been recorded in detail. DNA was extracted, and ITS, 18S, 28S nuclear rDNA were generated. In order to further confirm the systematic position of the Korean specimens, maximum likelihood and Bayesian inference analysis including all the species of the order Lepidostromatales were conducted based on the ITS. As a result, the phylogenetic tree of the order Lepidostromatales was reconstructed, which differed from the previous studies. The inferred phylogenetic tree showed that species of Sulzbacheromyces in three different continents (Asia, South Africa and South America) were separated into three clades with support. In this study, the species worldwide distribution map of Lepidostromatales was illustrated, and S. sinensis had a widest distribution range (paleotropical extend to the Sino-Japanese) than other species (paleotropical or neotropical). Prior to this study, the range of distribution, southernmost and northernmost points and the fruiting time of S. sinensis were recorded, and the genus Sulzbacheromyces was firstly reported from Korean peninsula and Philippines.

• Mycobiology
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• v.46 no.2
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• pp.92-100
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• 2018

The filamentous Ascomycota Colletotrichum gloeosporioides sensu lato is a fungus that has been reported worldwide as a causal agent of anthracnose disease in avocado and other crops. In Mexico, this species affects fruits from an early stage of development in the orchard until the post-harvest stage. Although fungicides are continuously applied to control Colletotrichum species, pericarp cankers and soft rot mesocarp in fruits are still frequently observed. Considering the lack of a precise description of the causative agent, the aim of the current study was to determine the pathogens involved in this symptomatology. Twenty-four isolates were consistently obtained from the pericarp of avocado fruits cv. "Hass" collected in the central avocado-producing area of Mexico. Morphological features such as colony growth, conidia size, and mycelial appressorium were assessed. Bayesian multilocus phylogenetic analyses were performed using amplified sequences of the internal transcribed spacer region of the nuclear ribosomal DNA; actin, chitin synthase, glyceraldehyde-3-phosphate dehydrogenase partial genes; and APn2-Mat1-2 intergenic spacer and mating type Mat1-2 partial gene from the nine selected isolates. In addition, fruits were inoculated with a conidial suspension and reproducible symptoms confirmed the presence of Colletotrichum fructicola in this area. This pathogenic species can now be added to those previously reported in the country, such as C. acutatum, C. boninense, C. godetiae, C. gloeosporioides, and C. karstii. Disease management programs to reduce the incidence of anthracnose should include C. fructicola to determine its response to fungicides that are routinely applied, considering that the appearance of new species is affecting the commercial quality of the fruits and shifting the original population structure.

• Journal of Microbiology and Biotechnology
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• v.27 no.12
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• pp.2151-2155
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• 2017

Bacteriophages have gained substantial attention as biocontrol and biorecognition agents, substituting antibodies. In this study, a Salmonella Enteritidis-specific bacteriophage, KFS-SE1, was isolated, identified, and characterized. This Siphoviridae phage infects S. Enteritidis with high specificity. This phage is highly stable under various pH (5-11), temperature ($4-60^{\circ}C$), and organic solvent conditions. The KFS-SE1 genome consisted of 59,715 bp with 73 predicted open reading frames and 57.14% GC content; it had a complete set of genes required for phage reconstruction. Comparative phylogenetic analysis of KFS-SE1 revealed that it was very similar to the other Salmonella phages in the Siphoviridae family. These characteristics suggest that KFS-SE1 with its high specificity and host lysis activity toward S. Enteritidis may have various potential applications.

• Journal of Species Research
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• v.6 no.spc
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• pp.185-214
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• 2017

The genus Phyllopodopsyllus T. Scott, 1906 is nearly cosmopolitan and contains around 60 valid species, but has not been previously recorded in Korea. One of the reasons is probably the paucity of research in marginal habitats, such as marine interstitial. I describe two new species here. Numerous specimens of both sexes of P. kitazimai sp. nov. were collected from a beach near Yeongdeok, while only two females of P. busanensis sp. nov. were collected from a beach near Busan. The new species differ in numerous macro-morphological characters, such as the segmentation and armature of the antennula, armature of the mandibula, maxillula, maxilliped, and the first three swimming legs, as well as the shape of the caudal rami and the female genital field. However, they show very little difference in the number and position of cuticular organs (pores and sensilla) on all somites, which might prove these rarely used micro-characters to be useful in the reconstruction of phylogenetic relationships in this group of harpacticoids. Both species have their closest relatives in Japan. Phyllopodopsyllus kitazimai is morphologically most similar to P. punctatus Kitazima, 1981, but can be distinguished by much longer third exopodal segments of the third and fourth swimming legs. Phyllopodopsyllus busanensis shares the largest number of morphological similarities with P. setouchiensis Kitazima, 1981, but can be distinguished by shorter caudal rami. A key to species is also provided.

• ALGAE
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• v.23 no.3
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• pp.209-217
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• 2008

Two different molecular markers, the plastid rbcL and mitochondrial cox1 genes, were used to define the taxonomic position of the northwest Pacific Ocean species currently named Gracilaria chorda. We analyzed both genes (1,222 bp for rbcL and 1,245 bp for cox1) from 18 specimens collected in Korea, Japan, and China. Phylogenetic reconstruction revealed that this organism should be classified in the genus Gracilariopsis, rather than in the Gracilaria. Thus, Gracilariopsis chorda (Holmes) Ohmi is the legitimate name for Gracilaria chorda Holmes. Within the species, the sequences differed by 8 bp (0.7%) in rbcL and 5 bp (0.4%) in cox1. Six haplotypes of cox1 tended to be geographically organized. Gp. chorda is characterized by coarse, elongate terete axes, short filiform branchlets usually at irregular intervals, an abrupt transition in cell size from medulla to cortex, cystocarps without tubular nutritive cells connecting the gonimoblast to the upper pericarp, and relatively large gonimoblast cells of the cystocarp in the specimens collected from Wando in southern Korea.

• Journal of Veterinary Science
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• v.19 no.6
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• pp.798-807
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• 2018

Several studies have reported the effect of absorption of procyanidins and their contribution to the small intestine. However, differences between dietary interventions of procyanidins and interventions via antibiotic feeding in pigs are rarely reported. Following 16S rRNA gene Illumina MiSeq sequencing, we observed that both procyanidin administration for 2 months (procyanidin-1 group) and continuous antibiotic feeding for 1 month followed by procyanidin for 1 month (procyanidin-2 group) increased the number of operational taxonomic units, as well as the Chao 1 and ACE indices, compared to those in pigs undergoing antibiotic administration for 2 months (antibiotic group). The genera Fibrobacter and Spirochaete were more abundant in the antibiotic group than in the procyanidin-1 and procyanidin-2 groups. Principal component analysis revealed clear separations among the three groups. Additionally, using the online Molecular Ecological Network Analyses pipeline, three co-occurrence networks were constructed; Lactobacillus was in a co-occurrence relationship with Trichococcus and Desulfovibrio and a co-exclusion relationship with Bacillus and Spharerochaeta. Furthermore, metabolic function analysis by phylogenetic investigation of communities by reconstruction of unobserved states demonstrated modulation of pathways involved in the metabolism of carbohydrates, amino acids, energy, and nucleotides. These data suggest that procyanidin influences the gut microbiota and the intestinal metabolic function to produce beneficial effects on metabolic homeostasis.

• Fisheries and Aquatic Sciences
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• v.24 no.5
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• pp.181-190
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• 2021

Grouper is one of the most economically important fishes with various morphological forms and characteristics, meaning it is often difficult to identify species and distinguish between life stages, sometimes leading to morphological misidentification. Therefore, identification using a molecular deoxyribose nucleic acid (DNA) approach was needed as an alternative means to identify closely related species. This study aims to determine the molecular phylogeny of grouper from the northern part of the Bird's Head Seascape of Papua. The DNA sequence of each cytochrome oxidase I (COI) gene was used to study the molecular relationship among closely related species of grouper. The results showed that there were 16 Epinephelinae that have been compared to a gene bank (National Centre for Biotechnology Information, NCBI) in the sequence length of 623 base pairs. The closest genetic distance was found between Cephalopholis miniata and Cephalopholis sexmaculata (0.036), while the furthest genetic distance was observed between Plectropomus laevis and Cephalopholis spiloparaea (0.247). This finding was further reinforced by the morphological characters of each species. This finding highlighted that five genera were represented as a monophyletic group (clade), i.e., Epinephelus, Cephalopholis, Plectropomus, Saloptia and Variola.