• Journal of Species Research
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• v.12 no.spc2
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• pp.23-32
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• 2023

During screening for indigenous prokaryotic species in Republic of Korea in 2021, a total of 21 bacterial strains assigned to the phylum Bacteroidota were isolated from a variety of environmental habitats including pine cone, seaweed, soil, sea sediment, brackish water and moss. Based on the 16S rRNA gene sequence similarity value of more than 98.7% and formation of a robust phylogenetic clade with the type strain of the closest bacterial species, it was found that the 21 strains belong to independent and recognized bacterial species. There has been no official report that the identified 21 species have been isolated in Republic of Korea up to date. Therefore, 16 species in six genera of two families in the order Flavobacteriales, two species in two genera of two families in the order Cytophagales, one species in one genus of one family in the order Chitinophagales and two species in one genus of one family in the order Sphingobacteriales are proposed as unrecorded species of the phylum Bacteroidota isolated in Republic of Korea. Their Gram reaction, colony and cell morphology, basic phenotypic characteristics, isolation source, taxonomic status, strain ID and other information are described in the species descriptions.

• Journal of Species Research
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• v.12 no.4
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• pp.374-414
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• 2023

As part of a comprehensive investigation of indigenous prokaryotic species in Republic of Korea in 2022, 156 bacterial strains were isolated from diverse environmental habitats. These strains were assigned to six phyla, namely Acidobacteriota, Deinococcota, Actinomycetota, Bacillota, Bacteroidota, and Pseudomonadota. Each strain was identified based on 16S rRNA gene sequence similarity (>98.7%) and the formation of robust phylogenetic clades with their closest reported species. Among isolates, there is one species belonging to the phylum Acidobacteriota, one species belonging to the phylum Deinococcota, 28 species belonging to the phylum Actinomycetota, 19 species belonging to the phylum Bacillota, 19 species belonging to the phylum Bacteroidota, and 88 species belonging to the phylum Pseudomonadota (comprising 34 species of the class Alphaproteobacteria, 20 species of the class Betaproteobacteria, and 34 species of the class Gammaproteobacteria). Based on 16S rRNA gene sequence analysis, each strain was assigned to independent and predefined bacterial species. Since there were no published or official reports regarding these 156 isolates in Republic of Korea, they are reported as unrecorded species in Republic of Korea. The Gram stain, colony and cell morphology, basic biochemical characteristic, isolation source, and strain ID of each species are described in the species descriptions.

• Journal of Species Research
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• v.12 no.4
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• pp.415-429
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• 2023

As part of a comprehensive investigation of indigenous prokaryotic species in the Republic of Korea, 37 bacterial strains belonging to 36 species were isolated from diverse environmental habitats. These strains were assigned to five phyla, namely Deinococcota, Actinomycetota, Bacillota, Bacteroidota, and Pseudomonadota. Each strain was identified based on 16S rRNA gene sequence similarity (>98.7%) and the formation of definite phylogenetic clades with their closest reported species. Among isolates, there is one species belonging to the phylum Deinococcota, five species belonging to the phylum Actinomycetota, four species belonging to the phylum Bacillota, nine species belonging to the phylum Bacteroidota, and 17 species belonging to the phylum Pseudomonadota (comprising eight species of the class Alphaproteobacteria, one species of the class Betaproteobacteria, and eight species of the class Gammaproteobacteria). Based on 16S rRNA gene sequence analysis, each strain was assigned to independent and predefined bacterial species. Since there were no published or official reports regarding these 36 species in the Republic of Korea, they have been reported as unrecorded species in the Republic of Korea. Their Gram stain, cell morphology, colony, basic biochemical characteristics, strain ID, and isolation source of each species are described in the species descriptions.

• The Plant Pathology Journal
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• v.40 no.3
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• pp.251-260
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• 2024

Flavobacterium is a genus within the phylum Bacteroidota that remains relatively unexplored. Recent analyses of plant microbiota have identified the phylum Bacteroidota as a major bacterial group in the plant rhizosphere. While Flavobacterium species within the phylum Bacteroidota have been recognized as pathogens in the aquatic habitats, microbiome analysis and the characterization of novel Flavobacterium species have indicated the great diversity and potential of their presence in various environments. Many Flavobacterium species have positively contribute to plant health and development, including growth promotion, disease control, and tolerance to abiotic stress. Despite the well-described beneficial interactions of the Flavobacterium species with plants, the molecular mechanisms and bacterial determinants underlying these interactions remain unclear. To broaden our understanding of the genus Flavobacterium's role in plant health, we review the recent studies focusing on their ecological niche, functional roles, and determinants in plant-beneficial interactions. Additionally, this review discusses putative mechanisms explaining the interactions between plants and Flavobacterium. We have also introduced the importance of future research on Flavobacterium spp. and its potential applications in agriculture.

• 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.

• Journal of Animal Science and Technology
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• v.64 no.5
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• pp.897-910
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• 2022

Bovine fecal microbiota is important for host health and its composition can be affected by various factors, such as diet, age, species, breed, regions, and environments. The objective of this study was to evaluate the impact of diet and gender on fecal microbiota in Korean native Hanwoo cattle. The 16S rRNA gene amplicon sequencing of fecal microbiota was conducted from 44 Hanwoo cattle divided into four groups: (1) 11 heifers fed an oat hay plus total mixed ration (TMR) diet for breeding (HOTB), (2) 11 heifers fed an early fattening TMR diet (HEFT), (3) 11 steers fed the early fattening TMR diet (SEFT), and (4) 11 steers fed the late fattening TMR diet (SLFT). Firmicutes and Bacteroidota were the first and second most dominant phyla in all the samples, respectively. The Firmicutes/Bacteroidota (F/B) ratio associated with feed efficiency was significantly greater in the SLFT group than in the other groups. At the genus level, Romboutsia, Paeniclostridium, and Turicibacter were the most abundant in the SLFT while Akkermansia, Bacteroides, and Monoglobus were the most abundant in the HOTB group. Although the same early fattening TMR diet was fed to Hanwoo heifers and steers, Marvinbryantia and Coprococcus were the most abundant in the HEFT group while Alistipes and Ruminococcus were the most abundant in the SEFT group. Shannon and Simpson diversity indices were significantly lower in the SLFT group than in the other groups. Distribution of fecal microbiota and functional genetic profiles were significantly different among the four treatment groups. The present study demonstrates that different diets and genders can affect fecal microbiota and the F/B ratio may be associated with feed efficiency in Hanwoo cattle. Our results may help develop strategies to improve gut health and productivity through manipulation of fecal microbiota using the appropriate diet considering Hanwoo cattle gender.

• Journal of the Korean Applied Science and Technology
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• v.40 no.4
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• pp.881-889
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• 2023

The genus Hymenobacter, type genus of the family Hymenobacteraceae and a member of the phylum Bacteroidota includes gram-negative and red-pigmented rods. Those bacteria have been isolated from various environments of the earth. I isolated a red-pigmented, gram-negative rod from a pond in the campus of the Changwon University, Changwon, Kyeongnam and designated this bacterium as strain B2. Strain B2 was further analyzed phylogenetically and biochemically, and concluded as a member of genus Hymenobacter. BLAST search of the 16S rRNA gene sequence of strain B2 showed its homology lower than 98.7% with those sequences of the other bacteria whose 16S rRNA gene sequences have been reported. Fatty acid composition of the strain B2 was analyzed and its major fatty acids are summed feature 3(C_16:1 ω7c and/or C_16:1 ω6c, 22.8%), iso-C_15:0 (16.2%), anteiso-C_15:0(12.9%), C_16:1ω5c(12.4%) and summed feature 4 (iso-C_17:1 I/anteiso-C_17:1)(9.5%) showing significant differences in fatty acid compositions between strain B2 and the other known Hymenobacter species. DNA sequence of 16S rRNA gene of strain B2 was deposited in genbank under accession number OQ318247.

• Korean Journal of Environmental Biology
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• v.41 no.3
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• pp.308-324
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• 2023

This study investigated unrecorded freshwater bacterial species in Korea. Water and sediment samples were collected from the Nakdong River basin from 2020-2022. Bacterial isolates obtained through the conventional culture method with commercial media were subjected to 16S rRNA gene sequencing to identify unrecorded bacterial species. Results of 16S rRNA gene sequencing of the bacterial isolates revealed that a total of 44 bacterial isolates shared 16S rRNA gene sequence similarities of more than 98.65%, with validly published bacterial species not reported in Korea yet. These isolates were phylogenetically assigned to 4 phyla, 7 classes, 21 orders, 33 families, and 42 genera. A total of 2, 6, 12, and 24 species belonged to phyla Bacillota, Bacteroidota, Actinomycetota, and Pseudomonadota, respectively. Here, we provide details of these 44 unrecorded bacterial species, including Gram staining, colony and cellular morphologies, biochemical properties, and phylogenetic position.

• Journal of Soil and Groundwater Environment
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• v.28 no.5
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• pp.12-24
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• 2023

The Songji lagoon is brackish environment with a mixture of saline and fresh water, and the interaction of groundwater-lagoon water creates a physicochemical gradient. Although some studies have been conducted on the hydrological and geochemical characteristics of the Songji lagoon, microbial ecological studies have not yet been conducted. In this study, we investigated the effect of groundwater and surface water interaction on water quality as well as microbial community changes in the Songji Lagoon using 16S rRNA gene sequencing. Hydrochemical analyses show that samples were classified as 5 hydrochemical facies (HF) and hydrochemical facies evolution (HFE) revealed the intrusion phase was more dominant (57.9%) than the freshening phase (42.1%). Higher microbial diversity was found in freshwater in comparison to saline water samples. The microbial community at the phylum level shows the most dominance of Proteobacteria with an average of 37.3%, followed by Bacteroidota, Actinobacteria, and Patescibacteria. Heat map analyses of the top 18 genera showed that samples were clustered into 5 groups based on type, and Pseudoalteromonas could be used potential indicator for seawater intrusion.

• Journal of Ginseng Research
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• v.47 no.5
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• pp.627-637
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• 2023

Background: Damage to the healthy intestinal epithelial layer and regulation of the intestinal immune system, closely interrelated, are considered pivotal parts of the curative treatment for inflammatory bowel disease (IBD). Plant-based diets and phytochemicals can support the immune microenvironment in the intestinal epithelial barrier for a balanced immune system by improving the intestinal microecological balance and may have therapeutic potential in colitis. However, there have been only a few reports on the therapeutic potential of plant-derived exosome-like nanoparticles (PENs) and the underlying mechanism in colitis. This study aimed to assess the therapeutic effect of PENs from Panax ginseng, ginseng-derived exosome-like nanoparticles (GENs), in a mouse model of IBD, with a focus on the intestinal immune microenvironment. Method: To evaluate the anti-inflammatory effect of GENs on acute colitis, we treated GENs in Caco2 and lipopolysaccharide (LPS) -induced RAW 264.7 macrophages and analyzed the gene expression of proinflammatory cytokines and anti-inflammatory cytokines such as TNF-α, IL-6, and IL-10 by real-time PCR (RT-PCR). Furthermore, we further examined bacterial DNA from feces and determined the alteration of gut microbiota composition in DSS-induced colitis mice after administration of GENs through 16S rRNA gene sequencing analysis. Result: GENs with low toxicity showed a long-lasting intestinal retention effect for 48 h, which could lead to effective suppression of pro-inflammatory cytokines such as TNF-α and IL-6 production through inhibition of NF-κB in DSS-induced colitis. As a result, it showed longer colon length and suppressed thickening of the colon wall in the mice treated with GENs. Due to the amelioration of the progression of DSS-induced colitis with GENs treatment, the prolonged survival rate was observed for 17 days compared to 9 days in the PBS-treated group. In the gut microbiota analysis, the ratio of Firmicutes/Bacteroidota was decreased, which means GENs have therapeutic effectiveness against IBD. Ingesting GENs would be expected to slow colitis progression, strengthen the gut microbiota, and maintain gut homeostasis by preventing bacterial dysbiosis. Conclusion: GENs have a therapeutic effect on colitis through modulation of the intestinal microbiota and immune microenvironment. GENs not only ameliorate the inflammation in the damaged intestine by downregulating pro-inflammatory cytokines but also help balance the microbiota on the intestinal barrier and thereby improve the digestive system.