• Animal cells and systems
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• v.15 no.1
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• pp.45-51
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• 2011

To clarify the taxonomic status of five specimens of Albula collected from Korea and Taiwan (Albula sp.), genetic differences among them and other congeneric species were investigated based on mitochondrial DNA cytochrome b sequences. All five specimens of Albula sp. showed identical haplotypes and strongly supported a monophyletic group on phylogenetic analysis. The genetic differences between Albula sp. and ten other species of Albula ranged from 0.100 to 0.164. These values were almost equal to or exceeded the interspecific differences among the latter ten species (0.038-0.206). Morphological comparisons of Albula sp. and another four Indo-Pacific species, A. argentea, A. glossodonta, A. oligolepis and A. virgata, are also presented. Albula sp. could be distinguished from the latter four species in their numbers of pored lateral-line scales, anal fin rays and vertebrae, as well as in several proportional measurements.

• Journal of Environmental Science International
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• v.25 no.5
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• pp.615-623
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• 2016

Bird species (BS) of the Nakdong River estuary (NRE) were selected to suggest conservation and management strategies, taking habitats and major threats into consideration. Five BS (Cygnus spp., Calidris alpina, Sterna albifrons, Fulica atra, and Anser fabalis) were selected following analysis of their dominance, national importance, seasonality, taxonomic group, and distribution within the NRE. The BS comprise two winter birds, one summer, one passage bird, and one resident bird. They can also be classified into four taxonomic groups: two under ducks and geese (Anatidae), and one each under gulls (Laridae), shorebirds (Scolopacidae), and diving birds (Rallidae). The results show that BS could be a useful tool in guiding estuary management because their habitats are clearly distinct, and include important areas of the NRE. A reduction of feeding and resting places-such as tidal flats, Scirpus planiculmis habitat, and agricultural farmland-and climate change are major threats to BS, therefore countermeasures to such threats should be considered in future estuary management plans.

• Mycobiology
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• v.49 no.4
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• pp.308-345
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• 2021

Lactifluus (Pers.) Roussel is an ectomycorrhizal genus that was recently recognized to be distinct from the genus Lactarius. To date, 226 Lactifluus species have been reported worldwide. Misidentification of Lactifluus species is common because of intraspecific morphological variation, cryptic diversity, and the limited number of taxonomic keys available. Molecular data are indispensable for species delimitation; a multilocus phylogenetic analysis showed that most Asian Lactifluus species are not conspecific with morphologically similar species present on other continents. In particular, Korea has misused European and North American Lactifluus names. In this study, we evaluated the taxonomy of Lactifluus in Korea using both morphological and multilocus molecular (ITS, nrLSU, rpb1, and rpb2) data. We examined 199 Lactifluus specimens collected between 1980 and 2016, and a total of 24 species across the four Lactifluus subgenera were identified. All Korean species are distinct and clearly separated from European and North American species. Five taxa corresponded to previously described species from Asia and the remaining 19 taxa are confirmed as new species. Herein, we provide keys to the Korean Lactifluus species within their subgenera, molecular phylogenies, a summary of diversity, and detailed description of the new species.

• Journal of Korean Dental Science
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• v.16 no.1
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• pp.35-46
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• 2023

Purpose: Culture-based methods for microbiological diagnosis and antibiotic susceptibility tests have limitations in the management of orofacial infections. We aimed to profile pus microbiota and identify antibiotic resistance genes (ARGs) using a culture-independent approach. Materials and Methods: Genomic DNA samples extracted from the pus specimens of two patients with orofacial abscesses were subjected to shotgun sequencing on the NovaSeq system. Taxonomic profiling and prediction of ARGs were performed directly from the metagenomic raw reads. Result: Taxonomic profiling revealed obligate anaerobic polymicrobial communities associated with infections of odontogenic origins: the microbial community of Patient 1 consisted of one predominant species (Prevotella oris 74.6%) with 27 minor species, while the sample from Patient 2 contained 3 abundant species (Porphyromonas endodontalis 33.0%; P. oris 31.6%; and Prevotella koreensis 13.4%) with five minor species. A total of 150 and 136 putative ARGs were predicted in the metagenome of each pus sample. The coverage of most predicted ARGs was less than 10%, and only the CfxA2 gene identified in Patient 1 was covered 100%. ARG analysis of the seven assembled genome/metagenome datasets of P. oris revealed that strain C735 carried the CfxA2 gene. Conclusion: A metagenomics-based approach is useful to profile predominantly anaerobic polymicrobial communities but needs further verification for reliable ARG detection.

• The Korean Journal of Mycology
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• v.51 no.1
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• pp.7-24
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• 2023

More than five hundreds of yeast species (including 9 variants) encompassing 142 genera and 48 classes of 2 phyla exist in Korea. However, only 173 species have been cataloged in the National Species List of Korea (NSLK), the backbone reference to claim sovereign rights over biological resources, as of December 2021, due to the lack of taxonomic descriptions, although some of these species are extensively used in industry. The present pilot study investigated the taxonomy of strains belonging to the six most widely used or frequently isolated yeast species (Meyeromyma guilliermondii, Saccharomyces cerevisiae, Saccharomycopsis fibuligera, Wickerhamomyces anomalus, Candida tropicalis, and Papiliotrema flavescens) to include these species in the NSLK. Strains with diverse habitats and geographic origins were retrieved from the National Institute of Biological Resources culture collection. These strains clustered in the same clade as the type strains of the designated species according to phylogenetic analysis of the D1/D2 sequences. Moreover, we described the cell morphology and physiological characteristics of representative strains of each species. This study suggests that these six species are indigenous to Korea and can be accordingly listed in the NSLK.

• The Korean Journal of Mycology
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• v.51 no.4
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• pp.287-306
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• 2023

According to our previous study, 500 species of yeast exist in Korea, including nine variants comprising 142 genera and 48 classes in two phyla. Additionally, 4,483 fungal species have been documented at the National Institute of Biological Resources (NIBR). However, despite the industrial use of several yeasts, only 173 species formed part of the National Species List of Korea (NSLK) as of December 2021, mainly due to the lack of taxonomic descriptions. This study aimed to investigate the taxonomy of seven newly isolated yeast species (Hyphopichia burtonii, Starmerella sorbosivorans, Cyberlindnera mycetangii, Cutaneotrichosporon oleaginosum, Nakazawaea ernobii, Pichia kudriavzevii, and Schizosaccharomyces japonicus) for inclusion in the NSLK. The strains were clustered for the phylogenetic analysis of fungal rDNA (D1/D2-26S) sequences. This study provides descriptions of their cell morphology and physiological characteristics, the results of which confirm the indigenous origin of these seven species in Korea and recommend their inclusion in the NSLK.

• Genomics & Informatics
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• v.21 no.4
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• pp.49.1-49.11
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• 2023

Recent advances in sequencing technologies and platforms have enabled to generate metagenomics sequences using different sequencing platforms. In this study, we analyzed and compared shotgun metagenomic sequences generated by HiSeq3000 and BGISEQ-500 platforms from 12 sediment samples collected across the Norwegian coast. Metagenomics DNA sequences were normalized to an equal number of bases for both platforms and further evaluated by using different taxonomic classifiers, reference databases, and assemblers. Normalized BGISEQ-500 sequences retained more reads and base counts after preprocessing, while a slightly higher fraction of HiSeq3000 sequences were taxonomically classified. Kaiju classified a higher percentage of reads relative to Kraken2 for both platforms, and comparison of reference database for taxonomic classification showed that MAR database outperformed RefSeq. Assembly using MEGAHIT produced longer assemblies and higher total contigs count in majority of HiSeq3000 samples than using metaSPAdes, but the assembly statistics notably improved with unprocessed or normalized reads. Our results indicate that both platforms perform comparably in terms of the percentage of taxonomically classified reads and assembled contig statistics for metagenomics samples. This study provides valuable insights for researchers in selecting an appropriate sequencing platform and bioinformatics pipeline for their metagenomics studies.

• Journal of Life Science
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• v.32 no.12
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• pp.1005-1012
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• 2022

This study was conducted to investigate the taxonomic composition and diversity of fecal microbiota between birth and weaning stages of Halla horses using 16S rRNA gene amplicon sequencing analysis. Proteobacteria (35.7%) and Firmicutes (45.6%) were identified as the most common phylum in birth and weaning, respectively. Escherichia (19.7%) and Clostridium (14.0%) were observed as the most dominant genus in birth, and Fibrobacter (6.6%) was the highest in weaning. The results of α-diversity showed that the richness and evenness in microbial communities were statistically significant (p<0.001) in birth and weaning. The results of β-diversity indicated that the birth and weaning stages were clearly divided into two groups at the genus and species levels. Permutational multivariate analysis of variance (PERMANOVA) showed that the microbiota composition differences between birth and weaning were statistically significant (q<0.001). A linear discriminant analysis effect (LEfSe) was performed to select taxonomic makers between the birth and weaning stages. On the genus level, Escherichia, Bacteroides, Clostridium, and Methylobacterium were relatively abundant at birth, whereas Fibrobacter was more abundant at weaning. We expect that this research can be utilized as basic data in the identification of microbial communities involved in disease prevention and nutrient absorption in Halla horses.

• Hwankyungkyoyuk
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• v.14 no.2
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• pp.15-27
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• 2001

The purpose of this study is to understand and compare the characteristics of the content organization system of three Environment textbooks currently used, and to examine its connectivity with the teaching & teaming methods included in the Environment subject part of the 7th Korean National Curriculum. For the analysis three Environment textbooks for middle school and their teacher's guide books by three companies. published(A, B, and C) The result of the taxonomic analysis showed that three Environment books had different steps to get to the lesson class unit in the way that A of six steps, B of five steps and C of seven steps. The amount of main text was different In the domains of'Human and Environment','Environmental Problems and its Counter-plan'and'Environmental Conservation'of three textbooks each. All of three textbooks had the biggest percentage in sub-domains of'Living Environment to Keep'and'Global Environmental Problem'in 'Environmental Problems and its Counter-plan'domain. Considering teaching & loaming methods all of three textbooks contained many activities as 55 in A, 66 in H and 91 in C. Among 9 teaching 8E teaming methods and others listed in the Environment subject part of the 7th Korean National Curriculum, the investigation method is most frequently used in all of three textbooks. The drama, the paly and the case study were used rarely as teaching & teaming methods in activities In the consideration of the content amount regarding academic fields, it was revealed that three textbooks overemphasized the aspect of natural sciences comparing the aspect of human & social sciences aspect as a whole. Generally the appendix section of all three textbooks were well organized to support the teaching and teaming activities in main text.

• Clinics in Shoulder and Elbow
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• v.19 no.2
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• pp.67-72
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• 2016

Background: The aim of this study was to analyze the questions in the shoulder and elbow section of the Korean Orthopaedic In-Training Examination (KOITE) and compare them with those of the US Orthopaedic In-Training Examination (US OITE). Methods: Twenty-nine questions in the shoulder and elbow section of the KOITE from 2010 to 2014 were analyzed and compared with those of the US OITE (80 questions) by literature review. A thorough analysis of the contents was performed after categorizing as topics, diagnostic tools, treatment modalities, taxonomic classification, and references. Results: The shoulder and elbow section of the KOITE was 5.8% weight which was similar to the US OITE (5.9%). The most commonly appearing topic was anterior labral injury (17.2%) on the KOITE compared to instability and arthritis (21.3%, each) on the US OITE. Magnetic resonance imaging was most frequently appeared imaging modality on the KOITE (41.0%) compared to the radiograph on the US OITE (43.0%). The Latarjet procedure was the most commonly asked treatment modality (22.2%) on the KOITE, whereas arthroplasty (33.3%) on the US OITE. The KOITE showed an even taxonomic classification distribution compared to the US OITE. Campbell's operative orthopaedics covered 96.6% questions as a reference on the KOITE compared to the Journal of Bone and Joint Surgery, American Volume on the US OITE, which covered 45.0%. Conclusions: This specific analysis shows us current trends of the shoulder and elbow section of the KOITE and it might be developed for use in the educational curricula for the trainee.