• Journal of Species Research
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• v.11 no.4
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• pp.310-320
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• 2022

As a subset study to discover indigenous prokaryotic species in Korea, we isolated 20 bacterial strains and assigned them to the phyla Actinobacteria, Bacteroidota, Firmicutes, and Proteobacteria. From the high 16S rRNA gene sequence similarity (≥98.7%) and formation of a robust phylogenetic clades, we determined that each strain belonged to independent, predefined bacterial species. There are no official reports of these 20 species in Korea; therefore, 7 strains of the Actinobacteria, 2 strain of the Bacteroidota, 3 strains of the Firmicutes, and 8 strains of the Firmicutes are described in Korea for the first time. Gram reaction, colony and cell morphology, basic biochemical characteristics, and isolation sources are also described in the species description section.

• Korean Journal of Environmental Biology
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• v.39 no.4
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• pp.515-522
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• 2021

Jeotgal is a salty and fermented traditional Korean fish sauce. Unlike most other previous studies that investigated samples purchased from retail markets, this study focused on samples of jeotgal with traceable history to Yeonggwang, a timehonored fishing village in Korea. Three jeotgal samples, which were made from small yellow croakers, largehead hairtail, and miscellaneous fish, were selected based on information obtained from interviews with local craftsmen and literature reviews. Bacterial community profiles of the three jeotgal samples were investigated to identify indicator (and potentially core) bacteria for jeotgal ripening. The 16S rRNA gene-based metagenomic analysis revealed that the dominant phyla and classes, (Gammaproteobacteria, Betaproteobacteria, Bacilli, and Clostridia) of the three different jeotgal were identical, albeit with different composition ratios. Diversification was evident beginning at the order level. Interestingly, each dominant order was mainly comprised of single members even at the genus level. The dominant genera included Halomonas, Tetragenococcus, Halanaerobium, Pseudomonas, Massilia, and Lentibacillus. This observed genus-level heterogeneity suggests that there are diverse bacterial signatures in jeotgal and that these can be used as indicators for jeotgal ripening and/or as starters to increase its sensory quality and functionality.

• Journal of Applied Biological Chemistry
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• v.65 no.1
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• pp.63-74
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• 2022

Microbial dysbiosis in the gut is associated with human diseases, and variations in mucus alter gut microbiota. Therefore, we explored the effects of mucin on the gut microbiota using a community of 19 synthetic gut microbial species. Cultivation of these species in modified Gifu anaerobic medium (GAM) supplemented with mucin before synthetic community assembly facilitated substantial growth of the Bacteroides, Akkermansia, and Clostridium genera. The results of 16S rRNA microbial relative abundance profiling revealed more of the beneficial microbes Collinsella, Bifidobacterium, Ruminococcus, and Lactobacillus. This increased acetate levels in the community cultivated with, rather than without (control), mucin. We identified differences in predicted cell function and metabolism between microbes cultivated in GAM with and without mucin. Mucin not only changed the composition of the gut microbial community, but also modulated metabolic functions, indicating that it could help to modulate microbial changes associated with human diseases.

• Journal of Microbiology and Biotechnology
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• v.33 no.4
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• pp.471-484
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• 2023

Compost is widely used as an organic additive to improve the bioremediation of diesel-contaminated soil. In this study, the effects of compost amendment on the remediation performance, functional genes, and bacterial community are evaluated during the bioremediation of diesel-contaminated soils with various ratios of compost (0-20%, w/w). The study reveals that the diesel removal efficiency, soil enzyme (dehydrogenase and urease) activity, soil CH₄ oxidation potential, and soil N₂O reduction potential have a positive correlation with the compost amendment (p < 0.05). The ratios of denitrifying genes (nosZI, cnorB and qnorB) to 16S rRNA genes each show a positive correlation with compost amendment, whereas the ratio of the CH₄-oxidizing gene (pmoA) to the 16S rRNA genes shows a negative correlation. Interestingly, the genera Acidibacter, Blastochloris, Erythrobacter, Hyphomicrobium, Marinobacter, Parvibaculum, Pseudoxanthomonas, and Terrimonas are strongly associated with diesel degradation, and have a strong positive correlation with soil CH₄ oxidation potential. Meanwhile, the genera Atopostipes, Bacillus, Halomonas, Oblitimonas, Pusillimonas, Truepera, and Wenahouziangella are found to be strongly associated with soil N₂O reduction potential. These results provide useful data for developing technologies that improve diesel removal efficiency while minimizing greenhouse gas emissions in the bioremediation process of diesel-contaminated soil.

• Journal of Dairy Science and Biotechnology
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• v.41 no.4
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• pp.211-218
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• 2023

This study aimed to identify lactic acid bacteria isolated from eight fermented milk products in Iran. We enumerated Lactobacillus species using De Man-Rogosa-Sharpe (MRS)-maltose and MRS agar with pH adjusted to 5.2, as well as assessment at 37℃ for 48 hr, studied Streptococcus spp. using M17 agar at 43℃ for 24 hr, and assessed Bifidobacterium species using nalidixic acid, paromomycin sulfate, neomycin sulfate, and lithium chloride (BL-NPNL) agar at 37℃ for 48 hr. The total viable Streptococcus spp. cell in fermented milk varied at 4.73-8.83 log CFU/mL. However, Bifidobacterium spp. were not detected in any of the tested samples. Lactobacilli were not detected in four of the eight samples, and viable Lactobacilli cells in the remaining four samples ranged 2.48-3.85 log CFU/mL. The pH of the tested samples ranged 3.53-4.19, and soluble solids (Brix measurement) ranged 7.5%-17.9%. A total of 130 isolates of gram-positive catalase-positive bacteria were characterized at the species level using 16S rRNA sequencing. Sequence analysis identified six species: Streptococcus thermophilus, Lactobacillus delbrueckii subsp. sunkii, Lactobacillus delbrueckii subsp. indicus, Lactiplantibacillus plantarum, Lacticaseibacillus rhamnosus, and Levilactobacillus brevis.

• Journal of Mushroom
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• v.22 no.2
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• pp.37-47
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• 2024

Fluorescent bacteria were isolated from sporocarps that browned into various mushrooms during survey at places of the production in Korea. We examined the pathogenicity, biodiversity, and genetic characteristics of the 19 strains identified as Pseudomonas tolaasii by sequence analysis of 16S rRNA and White Line Assay. The results emphasize the importance of rpoB gene system, fatty acid profiles, specific and sensitive PCR assays, and lipopeptide detection for the identification of P. tolaasii. As a result of these various analyses, 17 strains (CHM03~CHM19) were identified as P. tolaasii. The phylogenetic analysis based on the 16S rRNA gene showed that all strains were clustered closest to P. tolaasii lineage, two strains (CHM01, CHM02) were not identified as P. tolaasii and have completely different genetic characteristics as a result of fatty acids profile, specific and sensitive PCR, lipopetide detection, rpoB sequence and REP-PCR analysis. Pathogenicity tests showed 17 strains produce severe brown discolouration symptoms to button mushrooms and watersoaking of sporophore tissue within three days after inoculation. But two strains did not produce discolouration symptoms. Therefore, these two strains will be further investigated for correct species identification by different biological and molecular characteristics.

• Journal of Species Research
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• v.13 no.4
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• pp.353-366
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• 2024

Here we describe indigenous prokaryotic species in Korea, a total of 41 bacterial strains were isolated from freshwater from the Republic of Korea. From the high 16S rRNA gene sequence similarity (>98.7%) and formation of a robust phylogenetic clade with the closest species, it was determined that each strain belonged to predefined bacterial species. There is no official report that these 41 species belonged to 5 phyla, 10 classes, 18 orders, 23 families, and 29 genera, which were assigned to Streptomyces, Mycolicibacterium, Smaragdicoccus, Nocardiopsis, and Nocardia of the phylum Actinobacteria; Runella, Flavobacterium, Algoriphagus, Sphingobacterium, and Aequorivita of the phylum Bacteroidota; Paenibacillus, Bacillus, Metabacillus, and Fredinandcohnia of the phylum Firmicutes; Sphingobium, Erythrobacter, Duganella, Methylopila, Novosphingobium, Azospirillum, Simplicispira, Corallococcus, Pseudomonas, Devosia, Pseudorhodoferax, Pseudomonas, Prolinoborus, Pectobacterium, and Aquabacterium of the phylum Proteobacteria; Proshecobacter of the phylum Verrucomicrobia. Gram reaction, colony and cell morphology, basic biochemical characteristics, isolation source, and strain IDs are also described in the species description section.

• Microbiology and Biotechnology Letters
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• v.39 no.3
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• pp.287-293
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• 2011

The purpose of this study was to isolate and characterize fungal deteriogens, which induce discoloration of the cement tunnel, and calcite forming bacteria (CFBs), which have antifungal activity against fungal deteriogens. Isolation of mold, bacteria and yeast was performed using several solid media and partially identified using internal transcribed spacer (ITS); 5.8S rRNA gene sequencing and 16s rDNA sequencing. A total of 19 microbial strains were identified with the most widely distributed fungal strain being Cladospirum sphaerospermum. In addition, five bacteria derived from the tunnel were identified as CFBs. Amongst the latter, Bacillus aryabhatti KNUC205 exhibited antifungal activity against Cladospirum sphaerospermum KNUC253 and Aspergillus niger KCTC6906 as concentrated filtered supernatants.

• Korean Journal of Microbiology
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• v.45 no.2
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• pp.193-199
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• 2009

A bacterium producing the halotolerant extracellular protease was isolated from squid jeotgal, and was identified as Bacillus sp. SJ-10 based on morphological, physiological and biochemical characteristics, as well as phylogenetic analysis using 16S rRNA gene sequence. The strain grew at $20^{\circ}C\sim55^{\circ}C$, pH 5~8, and 0%~14% NaCl and optimal growth conditions were $35{\pm}5^{\circ}C$, pH 7, and 5% NaCl. The major cellular fatty acids were anteiso-$C_{15:0}$, anteiso-$C_{17:0}$, and $C_{16:0}$ DNA G+C content was 50.58 mol% and menaquinone consisted of MK-7 Phylogenic analysis based on the 16S rRNA gene sequence indicated that SJ-10T belongs to the genus Bacillus. About 40 kDa of the salt-tolerant protease was purified by 40% ammonium sulfate saturation and Mono Q column chromatography. The optimal activity of the protease was pH 8 and stable at pH 5~10. The optimum temperature and NaCl concentration were $35{\pm}5^{\circ}C$ and $5{\pm}1%$, respectively.

• Korean Journal of Microbiology
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• v.48 no.3
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• pp.192-199
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• 2012

Microalgal biotechnology has gained prominence because of the ability of microalgae to produce value-added products including biodiesel through photosynthesis. However, carbon and nutrient source is often a limiting factor for microalgal growth leading to higher input costs for sufficient biomass production. Use of municipal wastewater as a low cost alternative to grow microalgae as well as to treat the same has been demonstrated in this study using mini raceway open ponds. Municipal wastewater was collected after primary treatment and microalgae indigenous in the wastewater were encouraged to grow in open raceways under optimum conditions. The mean removal efficiencies of TN, TP, COD-$_{Mn}$, $NH_3$-N after 6 days of retention time was 80.18%, 63.56%, 76.34%, and 96.74% respectively. The 18S rRNA gene analysis of the community revealed the presence of Chlorella vulgaris and Scenedesmus obliquus as the dominant microalgae. In addition, 16S rRNA gene analysis demonstrated that Rhodobacter, Luteimonas, Porphyrobacter, Agrobacterium, and Thauera were present along with the microalgae. From these results, it is concluded that microalgae could be used to effectively treat municipal wastewater without aerobic treatment, which incurs additional energy costs. In addition, municipal wastewater shall also serve as an excellent carbon and nitrogen source for microalgal growth. Moreover, the microalgal biomass shall be utilized for commercial purposes.