• Journal of Microbiology and Biotechnology
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• 제29권5호
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• pp.667-686
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• 2019

Streptomyces are attractive microbial cell factories that have industrial capability to produce a wide array of bioactive secondary metabolites. However, the genetic potential of the Streptomyces species has not been fully utilized because most of their secondary metabolite biosynthetic gene clusters (SM-BGCs) are silent under laboratory culture conditions. In an effort to activate SM-BGCs encoded in Streptomyces genomes, synthetic biology has emerged as a robust strategy to understand, design, and engineer the biosynthetic capability of Streptomyces secondary metabolites. In this regard, diverse synthetic biology tools have been developed for Streptomyces species with technical advances in DNA synthesis, sequencing, and editing. Here, we review recent progress in the development of synthetic biology tools for the production of novel secondary metabolites in Streptomyces, including genomic elements and genome engineering tools for Streptomyces, the heterologous gene expression strategy of designed biosynthetic gene clusters in the Streptomyces chassis strain, and future directions to expand diversity of novel secondary metabolites.

• Journal of Species Research
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• 제7권1호
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• pp.9-12
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• 2018

In 2016, as part of a larger effort to discover indigenous prokaryotic species in Korea, we isolated the family Deinococcaceae and Planctomycetaceae as unrecorded bacterial species. From the high 16S rRNA gene sequence similarity (>98.5%) and formation of a robust phylogenetic clade with known species, it was determined that each strain was a distinct bacterial species. There are no official reports that these two species have been described in Korea; therefore, the bacterial strains of Deinococcus and Blastopirellula are described for the first time in Korea. Gram reaction, colony and cell morphology, basic biochemical characteristics, and isolation sources are also described in the species description section.

• Journal of Species Research
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• 제6권3호
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• pp.214-223
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• 2017

As part of a larger study with the aim to discover indigenous prokaryotic species in Korea, nine bacterial strains were isolated and assigned to the phylum Proteobacteria in 2016. High 16S rRNA gene sequence similarity (>98.5%) and formation of a robust phylogenetic clades with known species indicated that each strain belongs to an independent and predefined bacterial species. This is the first report of these nine species in Korea: two strains of the Methylobacterium, two strains of the Microvirga, one strain of the Pantoea, and four strains of the Psychrobacter, all within the Proteobacteria. Gram reaction, colony and cell morphology, basic biochemical characteristics, and isolation sources are also described in the species description section.

• Animal Systematics, Evolution and Diversity
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• 제38권2호
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• pp.69-82
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• 2022

The family Araneidae is a group of orb-weaving spiders and is one of the most diverse groups among the order Araneae. Eighty-one species belonging to 25 genera have been recorded in Korea to date. In this study, four araneid spiders in three genera, viz., Araneus mayumiae, Araneus ogatai, Cyclosa onoi, and Plebs baotianmanensis, were discovered for the first time in Korea. Additionally, Plebs yebongsanensis is removed from synonymy of Plebs sachalinensis, and treated as a new junior synonym of P. baotianmanensis, based on a morphological comparison of females of three Plebs species. Detailed descriptions of four species are provided with accompanying photographs.

• Journal of Ecology and Environment
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• 제48권2호
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• pp.144-151
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• 2024

Background: This study focused on the diet of Clithon retropictum, level II endangered species in Korea. Since the development of brackish water zones has led to a decline in the population of this species, to obtain information on the ecology of C. retropictum required for its conservation and restoration. To investigate the actual preys of C. retropictum in south coast of Korea, we conducted high-throughput sequencing and metabarcoding techniques to extract DNA from gut contents and periphyton in their habitats. Results: Total 118 taxonomic groups were detected from periphyton samples. 116 were Chromista and Cyanobacteria dominated in the most samples. In gut contents samples, 98 taxonomic groups were detected. Similar to the results of periphyton, 96 were Chromista and Cyanobacteria dominated in the most samples. In the principal component analysis based on the presence/absence of taxonomic groups, gut content composition showed more clustered patterns corresponding to their habitats. Bryophyta was the most crucial taxonomic group explaining the difference between periphyton and gut contents compositions of C. retropictum. Conclusions: Our finding suggests that C. retropictum may not randomly consume epilithic algae but instead, likely to supplement their diet with Bryophyta.

• Journal of Microbiology and Biotechnology
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• 제34권10호
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• pp.2005-2011
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• 2024

This study aimed to analyze bacterial communities in breast milk obtained from five breastfeeding women. Culture-dependent and culture-independent methods were used to analyze microbial communities. Total bacterial count of breast milk determined using plate count agar ranged from 3.3×10⁴±3.5×10² colony forming unit (CFU)/g to 1.7×10⁵±3.5×10³ CFU/g, with a pH between 6.4 and 6.8. Only three species, Leuconostoc citreum (17 out of 160 strains; 10.63%), Staphylococcus epidermidis (118 strains; 73.75%), and Staphylococcus lugdunensis (25 strains; 15.63%), belong to the phylum Bacillota were detected by culture-dependent analysis. Microbial communities analyzed via pyrosequencing revealed greater diversity compared to the culture-dependent analysis. At the phylum level, Bacillota accounted for 60.9% of the microbial community. At the genus level, Staphylococcus (24.57%), Streptococcus (22.93%), and Methylobacterium (8.76%) were dominant genera. While pyrosequencing demonstrated greater microbial diversity than the agar plate culture method, identified microbes might lack information or include many unculturable microbes. Most of all, considering the low total bacterial count averaging 7.2×10⁴ CFU/g, further research is needed to determine the significance of microbial presence in breast milk.

• Environmental Engineering Research
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• 제24권2호
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• pp.181-190
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• 2019

Constructed wetlands are improvised man-made systems, designed for adopting the principle of natural wetlands for purifying wastewater - the elixir of life. They are used widely as a cost-effective and energy-efficient solution for treating greywater generated from different tertiary treatment sources. It provides an elaborate platform for research activities in an attempt to recycle earth's natural resources. Among the several organic impurities removal mechanisms existing in constructed wetland systems, the earth's active microbial population plays a vital role. This review deals with the recent advancements in constructed wetland systems from a microbiological perspective to (effect/ devise/ formulate) chemical and physical treatment for water impurities. It focuses on microbial diversity studies in constructed wetlands, influence of wetland media on microbial diversity and wetland performance, role of specific microbes in water reuse, removal of trace elements, some heavy metals and antibiotics in constructed wetlands. The impurities removal processes in constructed wetlands is achieved by combined interactive systems such as selected plant species, nature of substrate used for microbial diversity and several biogeochemical effected reaction cycles in wetland systems. Therefore, the correlation studies that have been conducted by earlier researchers in microbial diversity in wetlands are addressed herewith.

• Fisheries and Aquatic Sciences
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• 제24권9호
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• pp.297-310
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• 2021

The rockworm gut flora was identified at each growth stage to elucidate the composition of the bacterial community. The source material was Marphysa sanguinea fed regular feed and fed biofloc at the adult stage in parallel. The systematic bacterial community composition was determined based on the next-generation sequencing method, and alpha diversity and beta diversity were conducted to access the species diversity within and between the bacterial communities, respectively. The composition of the gut flora changed considerably as the rockworms developed. The shift in the gut flora was confirmed at the phylum, family, and genera level of the bacterial communities. The Vibrio species associated with high rockworm mortality occupied 7.7% of the gut flora at the larval stage; however, they disappeared in the healthy adult gut. Moreover, different gut flora was observed between adults fed regular feed and those fed biofloc. Specifically in the biofloc-fed adult gut, several immune relevant and water-purifying bacteria were detected. The biofloc-fed adult gut flora could decompose and mineralize organic sediment, and thus be effectively utilized for integrated multitrophic aquaculture. The Venn diagram revealed that only two bacterial species were shared throughout all growth stages, and the biofloc-fed adults exhibited the highest diversity within the bacterial community.

• 환경생물
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• 제42권3호
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• pp.288-300
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• 2024

Freshwater environments are rich ecosystems that support diverse microbial communities, including members of the phylum Actinomycetota critical for nutrient cycling, organic matter decomposition, and water quality maintenance. Actinomycetota known to produce numerous bioactive secondary metabolites are valuable in biotechnology, medicine, and agriculture. Despite their significance, the diversity and distribution of Actinomycetota in freshwater habitats, especially in the Republic of Korea, are underexplored. This study aimed to report the isolation and characterization of 22 previously unrecorded bacterial species of Actinomycetota from various freshwater environments in Korea. Using standard dilution plating techniques on six different culture media, 22 bacterial strains were isolated, incubated, and characterized based on colony and cellular morphologies, Gram staining, and biochemical properties. Genomic DNA was extracted and the 16S rRNA gene was sequenced to determine species identity using the EzBioCloud service with a cutoff of 98.7% sequence similarity for classification as unreported species. These strains were phylogenetically diverse, belonging to two classes, ten orders, and eighteen genera. This study enhances our understanding of bacterial diversity in freshwater ecosystems and underscores the importance of exploring microbial diversity in underexplored habitats, potentially leading to discovery of novel bioactive compounds. Findings of this study contribute valuable insights into ecological roles and biotechnological potential of Actinomycetota in freshwater environments.

• Journal of Microbiology and Biotechnology
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• 제27권10호
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• pp.1736-1743
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• 2017

Sourdough is made by fermentation of dough by lactic acid bacteria (LAB) and yeast to improve bread properties like volume, flavor, and texture. A Korean traditional sourdough was made by fermenting rice flour with rice wine (makgeolli) and used to make sponge-like bread (jeung-pyun). The aim of this study was to investigate the microbial diversity of makgeolli products and their influence on the organoleptic quality of jeung-pyun. Three commercial makgeolli were tested for jeung-pyun production, with each product exhibiting varied dough swelling rates and organoleptic qualities, and among them, J-product was ranked highest in texture and taste. Microbial analysis of the three makgeolli also showed a big difference in their population and diversity. J-product had the highest LAB and yeast counts, and the predominant species were Lactobacillus casei, Lactobacillus brevis, Leuconostoc pseudomenteroides, and Saccharomyces cerevisiae. Using J-product, sourdough was fermented at $25^{\circ}C$, $30^{\circ}C$, and $35^{\circ}C$, and the microbial growth in and textural properties of jeung-pyun were examined by instrumental and sensory tests. At high temperature ($35^{\circ}C$), the rates of dough swelling and acidification were fast due to rapid microbial growth mainly caused by LAB, resulting in a short leavening time and soft and sour jeung-pyun. Sensory tests showed consumer preference for the soft and mild-sour jeung-pyun. This study shows that LAB in makgeolli play key roles in production of jeung-pyun, influencing the textural and sensory properties. For the production of high-quality jeung-pyun, development of LAB starters with high gas productivity and low acidity and establishment of an optimal fermentation procedure for rice dough are necessary.