• Journal of Microbiology and Biotechnology
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• v.25 no.4
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• pp.431-438
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• 2015

Ever since the ban on antibiotic growth promoters (AGPs), the livestock death rate has increased owing to pathogenic bacterial infections. There is a need of developing AGP alternatives; however, the mechanisms by which AGP enhances livestock growth performance are not clearly understood. In this study, we fed 3-week-old swine for 9 weeks with and without AGPs containing chlortetracycline, sulfathiazole, and penicillin to investigate the effects of AGPs on swine gut microbiota. Microbial community analysis was done based on bacterial 16S rRNA genes using MiSeq. The use of AGP showed no growth promoting effect, but inhibited the growth of potential pathogens during the early growth stage. Our results showed the significant increase in species richness after the stabilization of gut microbiota during the post-weaning period (4-week-old). Moreover, the swine gut microbiota was divided into four clusters based on the distribution of operational taxonomic units, which was significantly correlated to the swine weight regardless of AGP treatments. Taxonomic abundance analysis indicated a negative correlation between host weight and the abundance of the family Prevotellaceae species, but showed positive correlation to the abundance of the family Spirochaetaceae, Clostridiaceae_1, and Peptostreptococcaeae species. Although no growth performance enhancement was observed, the use of AGP inhibited the potential pathogens in the early growth stage of swine. In addition, our results indicated the ecological succession of swine gut microbiota according to swine weight. Here, we present a characterization of swine gut microbiota with respect to the effects of AGPs on growth performance.

• Korean Journal of Environmental Biology
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• v.23 no.4
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• pp.335-342
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• 2005

We cloned seven genes encoding chitin synthases (CHSs) by PCR amplification from genomic DNAs of four strains of the genus Sporobolomyces and of Bensingtonia subrosea using degenerated primers based on conserved regions of the CHS genes. Though amino acid sequences of these genes were shown similar as 176 to 189 amino acids except SgCHS2, DNA sequences were different in size, which was due to various introns present in seven fragments. Alignment and phylogenetic analysis of their deduced amino acid sequences together with the reported CHS genes of basidiomycetes separated the sequences into classes I, II and III. This analysis also permitted the classification of isolated CHSs; SgCHS1 belongs to class I, BsCHS1, SaCHS1, SgCHS2, SpgCHS1, and SsCHS1 belong to class II, and BsCHS2 belongs to class III. The deduced amino acid sequences involving in class II that were discovered from five strains were also compared with those of other basidiomycetes by CLUSTAL X program. The bootstrap analysis and phylogenetic tree by neighbor-joining method revealed the taxonomic and evolutionary position for four strains of the genus Sporobolomyces and for Bensingtonia subrosea which agreed with the previous classification. The results clearly showed that CHS fragments could be used as a valuable key for the molecular taxonomic and phylogenetic studies of basidiomycetes.

• Journal of Veterinary Science
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• v.22 no.3
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• pp.37.1-37.14
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• 2021

Background: Ticks are one of the most common external parasites in dogs, and are associated with the transmission of a number of major zoonoses, which result in serious harm to human health and even death. Also, the increasing number of pet dogs and pet owners in China has caused concern regarding human tick-borne illnesses. Accordingly, studies are needed to gain a complete understanding of the bacterial composition and diversity of the ticks that parasitize dogs. Objectives: To date, there have been relatively few reports on the analysis of the bacterial community structure and diversity in ticks that parasitize dogs. The objective of this study was to investigate the microbial composition and diversity of parasitic ticks of dogs, and assessed the effect of tick sex and geographical region on the bacterial composition in two tick genera collected from dogs in China. Methods: A total of 178 whole ticks were subjected to a 16S ribosomal RNA (rRNA) next generation sequencing analysis. The Illumina MiSeq platform targeting the V3-V4 region of the 16S rRNA gene was used to characterize the bacterial communities of the collected ticks. Sequence analysis and taxonomic assignment were performed using QIIME 2 and the GreenGene database, respectively. After clustering the sequences into taxonomic units, the sequences were quality-filtered and rarefied. Results: After pooling 24 tick samples, we identified a total of 2,081 operational taxonomic units, which were assigned to 23 phyla and 328 genera, revealing a diverse bacterial community profile. The high, moderate and low prevalent taxa include 46, 101, and 182 genera, respectively. Among them, dominant taxa include environmental bacterial genera, such as Psychrobacter and Burkholderia. Additionally, some known tick-associated endosymbionts were also detected, including Coxiella, Rickettsia, and Ricketssiella. Also, the potentially pathogenic genera Staphylococcus and Pseudomonas were detected in the tick pools. Moreover, our preliminary study found that the differences in microbial communities are more dependent on the sampling location than tick sex in the tick specimens collected from dogs. Conclusions: The findings of this study support the need for future research on the microbial population present in ticks collected from dogs in China.

• Genomics & Informatics
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• v.21 no.3
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• pp.40.1-40.11
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• 2023

Microbial community profiling using 16S rRNA amplicon sequencing allows for taxonomic characterization of diverse microorganisms. While amplicon sequence variant (ASV) methods are increasingly favored for their fine-grained resolution of sequence variants, they often discard substantial portions of sequencing reads during quality control, particularly in datasets with large number samples. We present a streamlined pipeline that integrates FastP for read trimming, HmmUFOtu for operational taxonomic units (OTU) clustering, Vsearch for chimera checking, and Kraken2 for taxonomic assignment. To assess the pipeline's performance, we reprocessed two published stool datasets of normal Korean populations: one with 890 and the other with 1,462 independent samples. In the first dataset, HmmUFOtu retained 93.2% of over 104 million read pairs after quality trimming, discarding chimeric or unclassifiable reads, while DADA2, a commonly used ASV method, retained only 44.6% of the reads. Nonetheless, both methods yielded qualitatively similar β-diversity plots. For the second dataset, HmmUFOtu retained 89.2% of read pairs, while DADA2 retained a mere 18.4% of the reads. HmmUFOtu, being a closed-reference clustering method, facilitates merging separately processed datasets, with shared OTUs between the two datasets exhibiting a correlation coefficient of 0.92 in total abundance (log scale). While the first two dimensions of the β-diversity plot exhibited a cohesive mixture of the two datasets, the third dimension revealed the presence of a batch effect. Our comparative evaluation of ASV and OTU methods within this streamlined pipeline provides valuable insights into their performance when processing large-scale microbial 16S rRNA amplicon sequencing data. The strengths of HmmUFOtu and its potential for dataset merging are highlighted.

• Microbiology and Biotechnology Letters
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• v.24 no.1
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• pp.1-8
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• 1996

Characterization and numerical identification were carried out for an actinomycetes SL20209. Morphological, cultural and physiological perperties of SL20209 which porduced valistatin and des-$asp^4$-amastatin as inhibitors of aminopeptidase M were evaluated. The isolate was identified to be the genus of Streptomyces. Fourty-three taxonomic units were analysed by using a TAXON program. The isolate was classified into the major cluster 29 of Streptomyces and best-matched to Streptomyces griseoplanus.

• Journal of Microbiology and Biotechnology
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• v.8 no.6
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• pp.645-649
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• 1998

A glycolipid type of biosurfactants was obtained from a strain which had been isolated from soil. The cell was identified as Pseudomonas aeruginosa from taxonomic characteristics and was designated as YPJ80. Thin layer chromatography and deoxyhexose detection tests were done to verify the type of biosurfactant. Critical micelle concentration (CMC) of the surfactant was observed to be 50 ppm and the minimum surface tension was 30.1 mN/m. As an emulsifier, YPJ80 biosurfactant was superior to emulsan in the emulsification of crude Arabian light oil.

• Korean Journal of Agricultural Science
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• v.4 no.2
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• pp.167-172
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• 1977

Colony morphology, growth responses on some simple carbon sources and taxonomic position were established for three stock cultures of National Collection of Industrial Bacteria, Scotland. It was confirmed that NCIB 8077 belonged to the Cellulomonas species and that NCIB 8633 and NCIB 8634 belonged to the Pseudomonas species. Taxonomy of other cellulolytic bacteria published on various journals was also discussed.

• The Korean Journal of Mycology
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• v.50 no.3
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• pp.243-248
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• 2022

In Japan and China, Podosphaera pseudofusca causes powdery mildew in Fatoua villosa. During a taxonomic revision of Korean powdery mildew fungi, isolates newly collected from F. villosa were studied. Through morphological examination and molecular phylogenetic analyses of the internal transcribed spacer region and large subunit gene of rDNA, the powdery mildew fungus was identified as Podosphaera xanthii. In this study, we propose the merging of P. pseudofusca sensu Braun into the P. xanthii complex. To the best of our knowledge, this is the first report of Podosphaera powdery mildew on F. villosa in Korea.

• Fisheries and Aquatic Sciences
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• v.14 no.1
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• pp.43-54
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• 2011

Gene structure of copper/zinc-superoxide dismutase (Cu/Zn-SOD; sod1) was characterized in Hemibarbus mylodon (Teleostei; Cypriniformes), an endangered freshwater fish species in Korean peninsula. Full-length cDNA of H. mylodon SOD1 consisted of a 796-bp open reading frame sequence encoding 154 amino acids, and the deduced polypeptide sequence shared high sequence homology with other orthologs, particularly with regard to metal-coordinating ligands. Genomic structure of the H. mylodon sod1 gene (hmsod1; 1,911 bp from the ATG start codon to the stop codon) was typical quinquepartite (i.e., five exons interrupted by four introns); the lengths of the exons were similar among species belonging to various taxonomic positions. The molecular phylogeny inferred from sod1 genes in the teleost lineage was in accordance with the conventional taxonomic assumptions. 5'-flanking upstream region of hmsod1, obtained using the genome walking method, contained typical TATA and CAAT boxes. It also showed various transcription factor binding motifs that may be potentially involved in stress/immune response (e.g., sites for activating proteins or nuclear factor kappa B) or metabolism of xenobiotic compounds (e.g., xenobiotic response element; XRE). The hmsod1 transcripts were ubiquitously detected among tissues, with the liver and spleen showing the highest and lowest expression, respectively. An experimental challenge with Edwardsiella tarda revealed significant upregulation of the hmsod1 in kidney (4.3-fold) and spleen (3.1-fold), based on a real-time RT-PCR assay. Information on the molecular characteristics of this key antioxidant enzyme gene could be a useful basis for a biomarker-based assay to understand cellular stresses in this endangered fish species.

• The Bulletin of The Korean Astronomical Society
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• v.41 no.2
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• pp.48.2-48.2
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• 2016

The wide-field and the round-the clock operation capabilities of the KMTNet enables the discovery, astrometry and follow-up physical characterization of asteroids and comets in a most efficient way. We collectively refer to the team members, partner organizations, the dedicated software subsystem, the computing facility and research activities as Deep Ecliptic Patrol of the Southern Sky (DEEP-South). Most of the telescope time for DEEP-South is devoted to targeted photometry of Near Earth Asteroids (NEAs) to push up the number of the population with known physical properties from several percent to several dozens of percent, in the long run. We primarily adopt Johnson R-band for lightcurve study, while we employ BVI filters for taxonomic classification and detection of any possible color variations of an object at the same time. In this presentation, the progress and new findings since the last KAS meeting will be outlined. We report DEEP-South preliminary lightcurves of several dozens of NEAs obtained at three KMTNet stations during the first year runs. We also present a physical model of asteroid (5247) Krylov, the very first Non principal Axis (NPA) rotator that has been confirmed in the main belt (MB). A new asteroid taxonomic classification scheme will be introduced with an emphasis on its utility in the LSST era. The progress on the current version of automated mover detection software will also be summarized.