265 results on '"Wonyong Kim"'
Search Results
2. Clinical outcomes and predictors of response for adalimumab in patients with moderately to severely active ulcerative colitis: a KASID prospective multicenter cohort study
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Dennis Teng, Hyung Kil Kim, Hyo Jong Kim, Young-Ho Kim, Sang-Bum Kang, Jun Lee, Do Hyun Kim, Seung Yong Shin, Kang-Moon Lee, Jong-Hwa Kim, Eun Soo Kim, Dong Il Park, Tae Oh Kim, Soo Jung Park, Jong Pil Im, Eun Sun Kim, Sung-Ae Jung, Chang Hwan Choi, Young Goo Kim, You Sun Kim, Sung Jae Shin, Wonyong Kim, Hyun-Chul Kim, and Ji Won Kim
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Response rate (survey) ,medicine.medical_specialty ,business.industry ,Gastroenterology ,medicine.disease ,Ulcerative colitis ,Inflammatory bowel disease ,Internal medicine ,medicine ,Adalimumab ,Observational study ,In patient ,business ,Body mass index ,Cohort study ,medicine.drug - Abstract
Background/Aims: This study assessed the efficacy and safety of adalimumab (ADA) and explored predictors of response in Korean patients with ulcerative colitis (UC).Methods: A prospective, observational, multicenter study was conducted over 56 weeks in adult patients with moderately to severely active UC who received ADA. Clinical response, remission, and mucosal healing were assessed using the Mayo score.Results: A total of 146 patients were enrolled from 17 academic hospitals. Clinical response rates were 52.1% and 37.7% and clinical remission rates were 24.0% and 22.0% at weeks 8 and 56, respectively. Mucosal healing rates were 39.0% and 30.1% at weeks 8 and 56, respectively. Prior use of anti-tumor necrosis factor-α (anti-TNF-α) did not affect clinical and endoscopic responses. The ADA drug level was significantly higher in patients with better outcomes at week 8 (P
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- 2022
3. Genomic insight into Algoriphagus limi sp. nov. isolated from a mudflat on the Yellow Sea coast
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Soyeon Ahn, Jong-Hwa Kim, Jung-Hoon Yoon, Jung-Sook Lee, Ampaitip Sukhoom, and Wonyong Kim
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Genetics ,Molecular Biology ,Microbiology - Abstract
A Gram-negative, non-motile, and reddish-orange-colored bacterium, designated CAU 1643T, was isolated from a mudflat collected in Ganghwa Island, Republic of Korea. The bacterium was found to grow optimally at 30°C, pH 9.0–9.5, and with 0–1% (w/v) NaCl. The highest 16S rRNA gene sequence similarities to the bacterium were Algoriphagus kandeliae XY-J91T (97.9%), Algoriphagus aquimaris F21T (97.1%), Algoriphagus formosus XAY3209T (97.0%) and Algoriphagus marincola DSM 16067T (96.2%). The DNA G + C content of the type strain was 40.35 mol%. The average nucleotide identity and digital DNA–DNA hybridisation values between strain CAU 1643T and the reference strains were below the threshold value for species demarcation. The predominant cellular fatty acids were iso-C15:0, iso-C17:0 3-OH and Summed Feature 9. The major respiratory quinone was menaquinone-7. The genome showed three putative biosynthetic gene clusters (BGCs) that are responsible for different secondary metabolites. Moreover, CAU 1643T contains 72 genes that encode carbohydrate-active enzymes. Based on phenotypic, phylogenetic, and chemotaxonomic evidence, strain CAU 1643T represents novel species in the genus Algoriphagus, for which the name Algoriphagus limi sp. nov. is proposed. The type strain is CAU 1643T ( = KCTC 92080T, = MCCC 1K07150T).
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- 2023
4. Exploring the Influence of Climatic Variables on Mycobiome Composition and Community Diversity in Lichens: Insights from Structural Equation Modeling Analysis
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Ji Ho Yang, Jung-Jae Woo, Wonyong Kim, Seung-Yoon Oh, and Jae-Seoun Hur
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Background Lichens are symbiotic organisms composed of a fungus and a photosynthetic partner, which are key ecological bioindicators due to their sensitivity to environmental changes. The endolichenic fungi (ELF) living inside lichen thalli, are an important but understudied component of playing crucial ecological roles such as nutrient cycling and protection against environmental stressors. Therefore ELF community investigation is vital for fostering sustainable ecosystems and leveraging their ecological benefits. Deciphering the intricate relationships between ELF and their lichen hosts, alongside the influence of environmental factors on these communities, presents a significant challenge in pinpointing the underlying drivers of community structure and diversity.Results Our research demonstrated that locational factors were the main drivers of the ELF community structure, rather than host haplotype. Several climatic factors affected the diversity of the ELF community and contributed to the prevalence of different types of fungal residents within the ELF community. A decrease in isothermality was associated with a greater prevalence of pathotrophic and saprotrophic fungi within the ELF community, resulting in an overall increase in community diversity. By conducting a structural equation modeling analysis, we identified a robust link between climatic variables, fungal trophic mode abundance, and the species diversity of the ELF community.Conclusion This study's discoveries emphasize the significance of examining climate-related factors when investigating ELF's structure and function. The connection between fungi and climate is intricate and complex, and can be influenced by various other factors. Investigating the potential for ELF to adapt to changing climatic conditions, as well as the potential effects of changes in ELF communities on lichen function, would be valuable research areas. We anticipate that our research results will establish a basis for numerous future ELF research projects and have a significant impact on the field.
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- 2023
5. Roseobacter insulae sp. nov. and Loktanella gaetbuli sp. nov., isolated from tidal flats in the Yellow Sea in Korea
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Eun Bee Lee, Sooyeon Park, Wonyong Kim, and Jung-Hoon Yoon
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General Medicine ,Microbiology ,Ecology, Evolution, Behavior and Systematics - Abstract
Two bacterial strains (designated as YSTF-M11T and TSTF-M6T) were isolated from tidal flat sediments of the Yellow Sea, Republic of Korea, and taxonomically characterized. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain YSTF-M11T clusters with the type strains of Roseobacter species and strain TSTF-M6T clusters with the type strains of Loktanella salsilacus , Loktanella fryxellensis and Loktanella atrilutea . Strains YSTF-M11T and TSTF-M6T exhibited 16S rRNA gene sequence similarity values of 97.5–98.9 % and 94.1–97.2 % to the type strains of four Roseobacter species and to the type strains of four Loktanella species, respectively. An UBCG tree based on genomic sequences and a tree based on AAI showed that strains YSTF-M11T and TSTF-M6T form a cluster with the type strains of Roseobacter species and with the type strains of L. salsilacus , L. fryxellensis and L. atrilutea , respectively. The ANI and dDDH values between genomic sequences of strain YSTF-M11T and the type strains of four Roseobacter species and between those of strain TSTF-M6T and the type strains of the three Loktanella species were in ranges of 74.0–75.9 and 18.2–19.7 % and 74.7–75.5 and 18.8–19.3 %, respectively. The DNA G+C contents of strains YSTF-M11T and TSTF-M6T were 60.3 and 61.9 % based on their genomic sequences. Both strains contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c as the major fatty acid. Strains YSTF-M11T and TSTF-M6T were separated from recognized Roseobacter species and L. salsilacus , L. fryxellensis and L. atrilutea , respectively, by their phenotypic properties together with the phylogenetic and genetic distinctiveness. Based on data presented in this study, strains YSTF-M11T (=KACC 21642T =NBRC 115155T) and TSTF-M6T (=KACC 21643T =NBRC 115154T) are considered to represent novel species of the genera Roseobacter and Loktanella , respectively, for which the names Roseobacter insulae sp. nov. and Loktanella gaetbuli sp. nov. are proposed.
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- 2023
6. Fungal community inside lichen: a curious case of sparse diversity and high modularity
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Ji Ho Yang, Jung-Jae Woo, Seung-Yoon Oh, Wonyong Kim, and Jae-Seoun Hur
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Background Lichens represent not only the mutualism of fungi and photosynthetic partners but also a compound microbial consortium harboring non-obligate fungi known as endolichenic fungi. While endolichenic fungi are known to exert a remarkable influence on lichen ecology through their crucial roles in nutrient cycling, bioprospecting and biodiversity, the enigmatic community structures of these fungal inhabitants remain shrouded in mystery, awaiting further exploration and discovery. To address this gap in knowledge, we conducted metabarcoding on two lichens, Dirinara applanta and Parmotrema tinctorum, and compared their microbial communities to those found in the pine bark to which the lichens were attached. Our hypothesis was that the endolichenic communities would exhibit distinct diversity patterns, community structures, network structures, and specialist composition compared to the surrounding epiphytic community. Results Our investigation has shed light on the clear demarcation between the endolichenic and epiphytic fungal communities, as they exhibit markedly different characteristics that set them apart from each other. This research demonstrated that the endolichenic communities contained fewer diverse fungi compared to the epiphytic communities. Through community similarity analysis, we observed that the two endolichenic communities shared more commonalities with each other than with the adjacent epiphytic communities. Moreover, we unveiled a striking contrast in the network structures between the endolichenic and epiphytic communities, as the former displayed a more modular and less nested features that is evocative of a potent host-filtration mechanism. Our statistical investigation unveiled that endolichenic communities possessed a high abundance of plant-associated fungi in their specialist category, underscoring the similarity between endolichenic fungi and the phyllosphere mycobiome. Conclusions Through our investigation, we have discovered that lichens exert a crucial "host-filtration" effect on the microorganisms within them, leading to less intricate and interconnected communities compared to the neighboring epiphytic environment. These observations provide valuable insights into the metagenomic architecture of lichens and offer a tantalizing glimpse into the unique mycobiome of these extraordinary life forms.
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- 2023
7. Potential Anti-Allergy and Immunomodulatory Properties of Lactococcus lactis LB 1022 Observed in vitro and in an Atopic Dermatitis Mouse Model
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Jihye Baek, Jong-Hwa Kim, and Wonyong Kim
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General Medicine ,Applied Microbiology and Biotechnology ,Biotechnology - Published
- 2023
8. Multifunctional Probiotic and Functional Properties of Lactiplantibacillus plantarum LRCC5314, Isolated from Kimchi
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Jong-Hwa Kim, Miri Park, Hyeokjun Cho, Wonyong Kim, Ahyoung Lim, Seokmin Yoon, Yohan Nam, and Jaewoong Park
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medicine.medical_specialty ,Bile acid ,Lipopolysaccharide ,medicine.drug_class ,Interleukin ,General Medicine ,Applied Microbiology and Biotechnology ,Nitric oxide ,law.invention ,chemistry.chemical_compound ,Probiotic ,Endocrinology ,chemistry ,In vivo ,law ,Adipogenesis ,Internal medicine ,medicine ,Tumor necrosis factor alpha ,Biotechnology - Abstract
In this study, the survival capacity (acid and bile salt tolerance, and adhesion to gut epithelial cells) and probiotic properties (enzyme activity-inhibition and anti-inflammatory activities, inhibition of adipogenesis, and stress hormone level reduction) of Lactiplantibacillus plantarum LRCC5314, isolated from kimchi (Korean traditional fermented cabbage), were investigated. LRCC5314 exhibited very stable survival at pH 2 and in 0.2% bile acid with 89.9% adhesion to Caco-2 intestinal epithelial cells after treatment for 2 h. LRCC5314 also inhibited the activities of α-amylase and α-glucosidase, which are involved in elevating postprandial blood glucose levels, by approximately 72.9% and 51.2%, respectively. Treatment of lipopolysaccharide (LPS)-stimulated RAW 264.7 cells with the LRCC5314 lysate decreased the levels of the inflammatory factors nitric oxide, tumor necrosis factor (TNF-α), interleukin (IL)-1β, and interferon-γ by 88.5%, 49.3%, 97.2%, and 99.8%, respectively, relative to those of the cells treated with LPS alone. LRCC5314 also inhibited adipogenesis in differentiating preadipocytes (3T3-L1 cells), showing a 14.7% decrease in lipid droplet levels and a 74.0% decrease in triglyceride levels, as well as distinct reductions in the mRNA expression levels of adiponectin, FAS, PPAR, C/EBPα, TNF-α, and IL-6. Moreover, LRCC5314 reduced the level of cortisol, a hormone with important effect on stress, by approximately 35.6% in H295R cells. L. plantarum LRCC5314 is identified as a new probiotic with excellent in vitro multifunctional properties. Subsequent in vivo studies may further demonstrate its potential as a functional food or pharmabiotic.
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- 2022
9. Endolichenic Fungal Community Analysis by Pure Culture Isolation and Metabarcoding: A Case Study of Parmotrema tinctorum
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Ji Ho Yang, Seung-Yoon Oh, Wonyong Kim, and Jae-Seoun Hur
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Infectious Diseases ,Microbiology - Published
- 2022
10. Alleviation effects of Rubus coreanus Miquel root extract on skin symptoms and inflammation in chronic atopic dermatitis
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Wonyong Kim and Jong-Hwa Kim
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General Medicine ,Food Science - Abstract
Rubus coreanus Miquel root ameliorates AD by suppression of IgE hyperproduction, inflammatory response and allergic factor with recovering skin barrier function.
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- 2022
11. Description ofDefluviimonas salinarumsp. nov. with the potential of benzene-degradation isolated from saltern in the Yellow Seacoast
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Yunjeong Lee, Jong-Hwa Kim, Jung-Hoon Yoon, Jung-Sook Lee, Ampaitip Sukhoom, and Wonyong Kim
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Genetics ,Molecular Biology ,Microbiology - Abstract
Strain CAU 1641T was isolated from saltern collected in Ganghwa Island, Republic of Korea. The bacterium was an aerobic, Gram-negative, catalase-positive, oxidase-positive, motile, and rod-shaped bacterium. Cell of strain CAU 1641T could grow at 20–40°C and pH 6.0–9.0 with 1.0–3.0% (w/v) NaCl. Stain CAU 1641T shared high 16S rRNA gene sequence similarities with Defluviimonas aquaemixtae KCTC 42108T (98.0%), Defluviimonas denitrificans DSM 18921T (97.6%), and Defluviimonas aestuarii KACC 16442T (97.5%). Phylogenetic trees based on the 16S rRNA gene and the core-genome sequences indicated that strain CAU 1641T belonged to genus Defluviimonas. Strain CAU 1641T contained ubiquinone-10 (Q-10) as the sole respiratory quinone and and summed feature 8 (C18:1ω6c and/or C18:1ω7c) as the predominant fatty acid (86.1%). The pan-genome analysis indicated that the genomes of the strain CAU 1641T and 15 reference strains contain a small core genome. The Average Nucleotide Identity and digital DNA–DNA hybridization values among strain CAU 1641T and reference strains of the genus Defluviimonas were in the range of 77.6%–78.8% and 21.1–22.1%, respectively. The genome of strain CAU 1641T has several genes of benzene degradation. The genomic G + C content was 66.6%. Based on polyphasic and genomic analyses, strain CAU 1641T represents a novel species of the genus Defluviimonas, for which the name Defluviimonas salinarum sp. nov., is proposed. The type strain is CAU 1641T ( = KCTC 92081T = MCCC 1K07180T).
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- 2023
12. Lactiplantibacillus plantarum LRCC5314 includes a gene for serotonin biosynthesis via the tryptophan metabolic pathway
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Jiseon, Jeong, Yunjeong, Lee, Seokmin, Yoon, Jong-Hwa, Kim, and Wonyong, Kim
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Serotonin ,Whole Genome Sequencing ,Probiotics ,Polysaccharides, Bacterial ,Tryptophan ,Molecular Sequence Annotation ,General Medicine ,Applied Microbiology and Biotechnology ,Microbiology ,Genes, Bacterial ,Fermentation ,Clustered Regularly Interspaced Short Palindromic Repeats ,Fermented Foods ,Genome, Bacterial ,Metabolic Networks and Pathways ,Phylogeny ,Lactobacillus plantarum - Abstract
As the functions of probiotics within the same species may not be shared, it is important to analyze the genetic characteristics of strains to determine their safety and usefulness before industrial applications. Hence the present study was undertaken to determine functional genes, and beneficial activities of strain LRCC5314, a bacterial strain isolated from kimchi through comparative genomic analysis. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain LRCC5314 was a member of the species L. plantarum. Whole genome size of strain LRCC5314 was sequence was 3.25 Mb long, with a G + C content of 44.5 mol% and 3,031 predicted genes. Strain LRCC5314 could metabolize hexoses through homofermentation, which produces only lactic acid from hexoses. According to gene annotation, strain LRCC-5314 contained genes of EPS production and CRISPR. Moreover, the strain contained genes that could encode a complete biosynthetic pathway for the production of tryptophan, which can be used as a precursor of serotonin. Notably, the tryptophan and serotonin activities strain LRCC5314 were higher than those of reference strains, L. plantarum ATCC 14917
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- 2021
13. Pseudoalteromonas insulae sp. nov., isolated from a tidal flat
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Ji Hyeon Song, Eun Bee Lee, Jun Hyeong Cho, Wonyong Kim, and Jung-Hoon Yoon
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A Gram-stain-negative, aerobic, non-spore-forming, motile by single polar flagellum and ovoid or rod-shaped bacterial strain, designated BDTF-M6T, was isolated from tidal flat sediment collected from the Yellow Sea, Republic of Korea. Neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain BDTF-M6T fell within the clade comprising the type strains of Pseudoalteromonas species. Strain BDTF-M6T exhibited the highest 16S rRNA gene sequence similarity value (98.3%) to the type strain of P. caenipelagi and sequence similarities of less than 97.9% to the type strains of the other Pseudoalteromonas species. The DNA G+C content of strain BDTF-M6T from genomic sequence data was 50.0%. The ANI and dDDH values between strain BDTF-M6T and the type strains of forty-four Pseudoalteromonas species were less than 70.3 and 22.6%, respectively. Strain BDTF-M6T contained Q-8 as the predominant ubiquinone and C16:0, summed feature 3 (C16:1 ω7c and/or C16:1 ω6c) and C18:1 ω7c as the major fatty acids. The major polar lipids of strain BDTF-M6T were phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminolipid and one unidentified glycolipid. Distinguished phenotypic properties, along with the phylogenetic and genetic distinctiveness, revealed that strain BDTF-M6T is separated from recognized Pseudoalteromonas species. On the basis of the data presented, strain BDTF-M6T is considered to represent a novel species of the genus Pseudoalteromonas, for which the name Pseudoalteromonas insulae sp. nov. is proposed. The type strain is BDTF-M6T (= KACC 22179T = NBRC 115118T).
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- 2022
14. Echinicola arenosa sp. nov., isolated from marine sand
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Ampaitip Sukhoom, Jung-Hoon Yoon, Jong-Hwa Kim, Veeraya Weerawongwiwat, Jung-Sook Lee, Wonyong Kim, and Jihye Baek
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DNA, Bacterial ,Biochemistry ,Microbiology ,Genome ,Sand ,Genus ,RNA, Ribosomal, 16S ,Botany ,Genetics ,Molecular Biology ,Gene ,Phospholipids ,Phylogeny ,Base Composition ,Strain (chemistry) ,biology ,Phylogenetic tree ,Bacteroidetes ,Fatty Acids ,Nucleic Acid Hybridization ,Sequence Analysis, DNA ,General Medicine ,16S ribosomal RNA ,biology.organism_classification ,Terpenoid ,Bacterial Typing Techniques ,Bacteria - Abstract
A novel bacterium, designated CAU 1574T, was isolated from marine sand. Cells were Gram stain negative, aerobic, gliding and rod shaped. Growth was observed at 20–37 °C (optimum, 30 °C), a pH of 5.5–10.0 (optimum, 8.0), and 0–3.0% (w/v) NaCl concentrations (optimum, 1%). Based on the results of 16S rRNA gene sequence analyses, strain CAU 1574T belonged to the genus Echinicola, and showed the highest similarity to Echinicola shivajiensis JCM 17847T (97.5%). Phylogenomic analysis based on consisting of 92 core genes extracted from the genome sequences showed that strain CAU 1574T was affiliated with species in the genus Echinicola. The average nucleotide identity (ANI), average amino acid identity (AAI), and digital DNA–DNA hybridization (dDDH) values between strain CAU 1574T and the closely related species were below the cut-off values of 95–96, 90, and 70%, respectively used for species demarcation. The chemotaxonomic data of CAU 1574T were as follows: major isoprenoid quinone, MK-7; predominant polar lipids, phosphatidylethanolamine, two unidentified aminophospholipids and two unidentified lipids; major fatty acids, iso-C15:0, summed feature 3 (C16:1 ω6c/C16:1 ω7c). The 5.4 Mb genome included 20 contigs and 4237 protein-coding genes with a 39.8 mol% G + C content. Based on the phylogenetic, phenotypic, and physiological result, strain CAU 1574T represents a novel species of this genus Echinicola, for which the name Echinicola arenosa sp. nov. is proposed. The type strain is CAU 1574T (= KCTC 82410T = MCCC 1K05669T).
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- 2021
15. Snuella sedimenti sp. nov., isolated from marine sediment
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Ampaitip Sukhoom, Jong-Hwa Kim, Wonyong Kim, Veeraya Weerawongwiwat, Jung-Sook Lee, and Jung-Hoon Yoon
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DNA, Bacterial ,Geologic Sediments ,Biochemistry ,Microbiology ,RNA, Ribosomal, 16S ,Genetics ,Seawater ,Molecular Biology ,Phylogeny ,Gram ,Base Composition ,biology ,Phylogenetic tree ,Strain (chemistry) ,Chemistry ,Fatty Acids ,Sediment ,Vitamin K 2 ,Sequence Analysis, DNA ,General Medicine ,biology.organism_classification ,16S ribosomal RNA ,Flavobacteriaceae ,Terpenoid ,Bacterial Typing Techniques ,Yeosuana - Abstract
A Gram stain-negative, aerobic, motile by gliding, rod-shaped bacterial strain CAU 1569T was isolated from marine sediment on Shido Island in Incheon. It grew at 20–37 °C (optimum, 30 °C), pH 6.0–9.0 (optimum, 7.0), 2–6% NaCl (w/v) (optimum, 2%). Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain CAU 1569T formed a distinct lineage with only the type strain of Snuella. Strain CAU 1569T showed high similarity to S. lapsa KACC 14152T (95.8%), Mariniflexile gromovii KMM KCTC 12570T, Aestuariibaculum marinum KCTC 52521T (95.4%), A. suncheonense KACC 16186T (94.6%) and Yeosuana aromativorans KCCM 42019T (94.4%). The genome contained 57 contigs, 3,437 protein-coding gene, 3 rRNAs (5, 16, and 23S), 43 tRNAs, and with a 35.7 mol% G + C content. The DDH value between strain CAU 1569T and S. lapsa KACC 14152T was 39.4 ± 0.6%. The only isoprenoid quinone was menaquinone 6 (MK-6). The major fatty acids were iso-C15:0, C15:1-iso G, and C17:0 iso 3-OH. Strain CAU 1569T contained diphosphatidylglycerol, aminoglycolipid, unidentified aminolipid, and three unidentified lipids. Based on phylogenetic, genomic, physiologic, and chemotaxonomic characterizations, strain CAU 1569T represents a novel Snuella species, which the name Snuella sedimenti sp. nov. is proposed. The type of strain is CAU 1569T (= KCTC 82409T = MCCC 1K05670T).
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- 2021
16. Zhongshania aquimaris sp. nov., isolated from seawater
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Veeraya Weerawongwiwat, Jong-Hwa Kim, Jung-Sook Lee, Jung-Hoon Yoon, Ampaitip Sukhoom, and Wonyong Kim
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DNA, Bacterial ,RNA, Ribosomal, 16S ,Fatty Acids ,Genetics ,Seawater ,Sequence Analysis, DNA ,General Medicine ,Molecular Biology ,Biochemistry ,Microbiology ,Phospholipids ,Phylogeny ,Bacterial Typing Techniques - Abstract
A Gram-negative, motile, rod-shaped, aerobic bacterial strain CAU 1632
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- 2022
17. Mesonia aestuariivivens sp. nov., isolated from a tidal flat
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Sooyeon Park, Jung-Sook Lee, Wonyong Kim, and Jung-Hoon Yoon
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DNA, Bacterial ,Fatty Acids ,Sequence Analysis, DNA ,General Medicine ,Biochemistry ,Microbiology ,Bacterial Typing Techniques ,RNA, Ribosomal, 16S ,Republic of Korea ,Genetics ,Seawater ,Flavobacteriaceae ,Molecular Biology ,Phylogeny - Abstract
A Gram-negative, aerobic, non-flagellated and ovoid or rod-shaped bacterial strain (JHPTF-M18T), which was isolated from a tidal flat sediment in Republic of Korea, was taxonomically characterized. 16S rRNA gene sequence analysis showed that strain JHPTF-M18T forms phylogenetic lineage within the radiation comprising type strains of Mesonia species. The 16S rRNA gene of strain JHPTF-M18T shared sequence similarities of 97.7% with that of type strain of M. mobilis and 92.9-96.8% with those of type strains of eight other Mesonia species. The DNA G+C content was 33.1% based on its genomic sequence. ANI and dDDH values between strain JHPTF-M18T and the type strains of M. mobilis, M. oceanica, M. phycicola and M. algae were 73.1-79.7% and 18.5-22.8%, respectively. Strain JHPTF-M18T contained MK-6 as the predominant menaquinone and iso-C15:0, iso-C17:0 3-OH and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c) as its major fatty acids. Major polar lipids of strain JHPTF-M18T were phosphatidylethanolamine and two unidentified lipids. Strain JHPTF-M18T was separated from recognized Mesonia species by its phenotypic properties together with the phylogenetic and genetic distinctiveness. Based on data presented in this study, strain JHPTF-M18T is considered to represent a novel species of the genus Mesonia. The name Mesonia aestuariivivens sp. nov. is proposed for JHPTF-M18T (= KACC 22185T = NBRC 115119T).
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- 2022
18. Halomarinibacterium sedimenti gen. nov., sp. nov., a carotenoid pigment-producing bacterium isolated from marine sediment
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Jiseon Jeong, Veeraya Weerawongwiwat, Yunjeong Lee, Jong-Hwa Kim, Ampaitip Sukhoom, Kijeong Kim, and Wonyong Kim
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DNA, Bacterial ,Geologic Sediments ,Fatty Acids ,Vitamin K 2 ,Sequence Analysis, DNA ,General Medicine ,Carotenoids ,Biochemistry ,Microbiology ,Bacterial Typing Techniques ,RNA, Ribosomal, 16S ,Genetics ,Seawater ,Molecular Biology ,Phylogeny - Abstract
A Gram-negative, strictly aerobic, non-motile, rod-shaped bacterial strain CAU 1614
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- 2022
19. Transcriptional Divergence Underpinning Sexual Development in the Fungal Class Sordariomycetes
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Wonyong Kim, Zheng Wang, Hyeonjae Kim, Kasey Pham, Yujia Tu, Jeffrey P. Townsend, and Frances Trail
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Fungal Proteins ,Neurospora crassa ,Virology ,Gene Expression Regulation, Fungal ,Sexual Development ,Fruiting Bodies, Fungal ,Transcriptome ,Microbiology - Abstract
Gene expression divergence through evolutionary processes is thought to be important for achieving programmed development in multicellular organisms. To test this premise in filamentous fungi, we investigated transcriptional profiles of 3,942 single-copy orthologous genes (SCOGs) in five related sordariomycete species that have morphologically diverged in the formation of their flask-shaped perithecia. We compared expression of the SCOGs to inferred gene expression levels of the most recent common ancestor of the five species, ranking genes from their largest increases to smallest increases in expression during perithecial development in each of the five species. We found that a large proportion of the genes that exhibited evolved increases in gene expression were important for normal perithecial development in Fusarium graminearum. Many of these genes were previously uncharacterized, encoding hypothetical proteins without any known functional protein domains. Interestingly, the developmental stages during which aberrant knockout phenotypes appeared largely coincided with the elevated expression of the deleted genes. In addition, we identified novel genes that affected normal perithecial development in Magnaporthe oryzae and Neurospora crassa, which were functionally and transcriptionally diverged from the orthologous counterparts in F. graminearum. Furthermore, comparative analysis of developmental transcriptomes and phylostratigraphic analysis suggested that genes encoding hypothetical proteins are generally young and transcriptionally divergent between related species. This study provides tangible evidence of shifts in gene expression that led to acquisition of novel function of orthologous genes in each lineage and demonstrates that several genes with hypothetical function are crucial for shaping multicellular fruiting bodies.
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- 2022
20. Gut microbiota restoration through fecal microbiota transplantation: a new atopic dermatitis therapy
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Ki Young Kim, Wonyong Kim, and Jong-Hwa Kim
- Subjects
0301 basic medicine ,Clinical Biochemistry ,Basophil ,Gut flora ,Immunoglobulin E ,Biochemistry ,Feces ,Mice ,fluids and secretions ,0302 clinical medicine ,T-Lymphocyte Subsets ,Biological therapy ,biology ,digestive, oral, and skin physiology ,Disease Management ,Atopic dermatitis ,Fecal Microbiota Transplantation ,Experimental models of disease ,Treatment Outcome ,medicine.anatomical_structure ,Molecular Medicine ,Female ,030211 gastroenterology & hepatology ,Disease Susceptibility ,Ileum ,digestive system ,Antibodies ,Article ,Dermatitis, Atopic ,Immunomodulation ,03 medical and health sciences ,medicine ,Animals ,Lymphocyte Count ,Molecular Biology ,Eosinophil ,Fatty Acids, Volatile ,medicine.disease ,biology.organism_classification ,Gastrointestinal Microbiome ,Disease Models, Animal ,030104 developmental biology ,Immunology ,biology.protein ,Metagenome ,Metagenomics ,Calprotectin ,Biomarkers - Abstract
The pathogenesis of atopic dermatitis (AD) involves complex factors, including gut microbiota and immune modulation, which remain poorly understood. The aim of this study was to restore gut microbiota via fecal microbiota transplantation (FMT) to ameliorate AD in mice. FMT was performed using stool from donor mice. The gut microbiota was characterized via 16S rRNA sequencing and analyzed using Quantitative Insights into Microbial Ecology 2 with the DADA2 plugin. Gut metabolite levels were determined by measuring fecal short-chain fatty acid (SCFA) contents. AD-induced allergic responses were evaluated by analyzing blood parameters (IgE levels and eosinophil percentage, eosinophil count, basophil percentage, and monocyte percentage), the levels of Th1 and Th2 cytokines, dermatitis score, and the number of mast cells in the ileum and skin tissues. Calprotectin level was measured to assess gut inflammation after FMT. FMT resulted in the restoration of gut microbiota to the donor state and increases in the levels of SCFAs as gut metabolites. In addition, FMT restored the Th1/Th2 balance, modulated Tregs through gut microbiota, and reduced IgE levels and the numbers of mast cells, eosinophils, and basophils. FMT is associated with restoration of gut microbiota and immunologic balance (Th1/Th2) along with suppression of AD-induced allergic responses and is thus a potential new therapy for AD., Eczema: Fecal transplant reduces inflammation in mice Fecal transplants that restore a healthy gut microbiome could help quell the immune processes responsible for eczema, an itchy skin condition also known as atopic dermatitis. Wonyong Kim and colleagues from Chung-Ang University College of Medicine in Seoul, South Korea, transplanted fecal samples from healthy mice to mice with experimentally induced eczema. After the transplant, the mice showed signs of a healthier gut ecosystem, as evidenced by the presence of certain favorable bacterial metabolites. The treatment also restored a more favorable immune balance and lowered the blood levels of certain inflammatory cells and signaling molecules associated with allergic responses. The mice exhibited fewer signs of skin irritation. The findings suggest that human testing of the intervention is warranted and some small trials have already begun.
- Published
- 2021
21. Arenibacterium halophilum gen. nov., sp. nov., a halotolerant bacterium in the family Rhodobacteraceae isolated from a coastal sand dune
- Author
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Jung-Sook Lee, Jong-Hwa Kim, Jihye Baek, Ampaitip Sukhoom, Wonyong Kim, and Jung-Hoon Yoon
- Subjects
food.ingredient ,Sulfitobacter ,biology ,Roseovarius ,General Medicine ,biology.organism_classification ,16S ribosomal RNA ,Microbiology ,Aestuariihabitans ,food ,Marinovum ,RRNA Operon ,Phaeobacter ,Rhodobacteraceae ,Ecology, Evolution, Behavior and Systematics - Abstract
A Gram-stain-negative, non-pigmented, non-spore-forming, motile, strictly aerobic bacterial strain, designated CAU 1492T, was isolated from a coastal sand dune and its taxonomic position was examined using a polyphasic approach. Cells of strain CAU 1492T grew optimally at 30 °C, pH 7.0 and in 3 % (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence of CAU 1492T showed that it formed a distinct lineage within the family Rhodobacteraceae as a separate deep branch, with 96.8 % or lower sequence similarity values to representatives of the genera Marivita , Donghicola , Sulfitobacter , Marinovum , Phaeobacter , Primorskyibacter , Roseovarius and Aestuariihabitans . Strain CAU 1492T was closely related to Marivita geojedonensis DPG-138T (96.8 %), Donghicola eburneus SW-277T (96.7 %), Sulfitobacter porphyrae SCM-1T (96.7 %), Marinovum algicola FF3T (96.6 %) and Aestuariihabitans beolgyonensis BB-MW15T (96.4 %) based on 16S rRNA gene sequences. The major cellular fatty acids of strain CAU 1492T were cyclo-C19 : 0 ω8c and summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c). The polar lipid pattern was composed of phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid and an unidentified aminolipid. The strain contained Q-10 as the sole respiratory quinone. The draft genome of strain CAU 1492T was 4.63 Mb with a DNA G+C content of 63.1 mol%. The genome includes 4292 protein-coding genes and a five rRNA operons. On the basis of the phenotypic, chemotaxonomic and genomic data, strain CAU 1492T represents a novel genus in the family Rhodobacteraceae for which the name Arenibacterium halophilum gen. nov., sp. nov. is proposed. The type strain of Arenibacterium halophilum is CAU 1492T (=KCTC 62998T=NBRC 113696T).
- Published
- 2020
22. Pseudoalteromonas caenipelagi sp. nov., isolated from a tidal flat
- Author
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Wonyong Kim, Jung-Hoon Yoon, Seo Yeon Lee, and Sooyeon Park
- Subjects
Phylogenetic tree ,biology ,Strain (chemistry) ,General Medicine ,Flagellum ,biology.organism_classification ,16S ribosomal RNA ,Microbiology ,chemistry.chemical_compound ,Pseudoalteromonas ,chemistry ,Clade ,Gene ,Ecology, Evolution, Behavior and Systematics ,DNA - Abstract
A Gram-stain-negative, aerobic, non-spore-forming, motile by single polar flagellum and ovoid or rod-shaped bacterial strain, designated JBTF-M23T, was isolated from tidal flat sediment collected from the Yellow Sea, Republic of Korea. Neighbour-joining phylogenetic tree of 16S rRNA gene sequences showed that strain JBTF-M23T fell within the clade comprising the type strains of Pseudoalteromonas species, clustering with the type strains of P. byunsanensis and P. amylolytica . Strain JBTF-M23T exhibited the highest 16S rRNA gene sequence similarity value (98.6 %) to the type strain of P. rubra and sequence similarities of 98.3 and 97.7 % to the type strains of P. byunsanensis and P. amylolytica, respectively. The DNA G+C content of strain JBTF-M23T from genomic sequence data was 41.98 %. The ANI and dDDH values between strain JBTF-M23T and the type strains of P. rubra , P. byunsanensis and P. amylolytica were 71.3–76.6 and 19.4–19.9 %, respectively. Strain JBTF-M23T contained Q-8 as the predominant ubiquinone and C16 : 1 ω7c and/or C16 : 1 ω6c, C16 : 0 and C18 : 1 ω7c as the major fatty acids. The major polar lipids of strain JBTF-M23T were phosphatidylethanolamine and one unidentified aminolipid. Distinguished phenotypic properties, along with the phylogenetic and genetic distinctiveness, revealed that strain JBTF-M23T is separated from recognized Pseudoalteromonas species. On the basis of the data presented, strain JBTF-M23Tis considered to represent a novel species of the genus Pseudoalteromonas , for which the name Pseudoalteromonas caenipelagi sp. nov. is proposed. The type strain is JBTF-M23T(=KACC 19900T=NBRC 113647T).
- Published
- 2020
23. Endolichenic Fungal Community Analysis by Pure Culture Isolation and Metabarcoding: A Case Study of
- Author
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Ji Ho, Yang, Seung-Yoon, Oh, Wonyong, Kim, and Jae-Seoun, Hur
- Abstract
Lichen is a symbiotic mutualism of mycobiont and photobiont that harbors diverse organisms including endolichenic fungi (ELF). Despite the taxonomic and ecological significance of ELF, no comparative investigation of an ELF community involving isolation of a pure culture and high-throughput sequencing has been conducted. Thus, we analyzed the ELF community in
- Published
- 2022
24. Lactococcus chungangensis CAU 28 alleviates diet-induced obesity and adipose tissue metabolism in vitro and in mice fed a high-fat diet
- Author
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Wonyong Kim, Jong-Hwa Kim, Yena Kim, and Qi Zhang
- Subjects
Male ,medicine.medical_specialty ,Mice, Obese ,Adipokine ,White adipose tissue ,Biology ,Diet, High-Fat ,Weight Gain ,Mice ,chemistry.chemical_compound ,Insulin resistance ,3T3-L1 Cells ,Internal medicine ,Lactococcus ,Genetics ,medicine ,Animals ,Obesity ,Adipogenesis ,Triglyceride ,Adiponectin ,Cholesterol ,Leptin ,Cell Differentiation ,medicine.disease ,Mice, Inbred C57BL ,PPAR gamma ,Endocrinology ,Adipose Tissue ,chemistry ,Animal Science and Zoology ,Food Science ,Lipoprotein - Abstract
Obesity, which has become a major public health problem, can arise from complex dyslipidemia, insulin resistance, and immune responses, among other mechanisms. Some Lactobacillus strains effectively ameliorate obesity; however, the beneficial effects of Lactococcus spp., which are often used as dairy starters, remain unclear. In the present study, we evaluated the efficacy of Lactococcus chungangensis CAU 28 using the 3T3-L1 cell line and obese mice fed a high-fat diet. Overall, administration of Lc. chungangensis CAU 28 effectively resolved obesity associated with weight gain and lipid accumulation. In differentiated 3T3-L1 cells, Lc. chungangensis CAU 28 treatment significantly diminished the total lipid quantity, inhibited triglyceride formation, and prevented the proliferation of adipogenic transcription factors (fatty acid synthase, adiponectin, peroxisome proliferator-activated receptor-gamma, and CCAAT-enhancer-binding protein-α) associated with lipid accumulation. In the obesity mouse model, wherein the intake of Lc. chungangensis CAU 28 effectively reduced body weight gain, along with fat differentiation and accumulation (white fat; abdominal and subcutaneous). Furthermore, Lc. chungangensis CAU 28 increased serum adiponectin levels, decreased serum leptin levels, and effectively regulated adipokine secretion. It also increased the high-density lipoprotein:cholesterol ratio, reduced total cholesterol and triglyceride levels, reduced the low-density lipoprotein:cholesterol ratio, and affected obesity-regulated inflammatory cytokines IL-6, tumor necrosis factor-α, IFN-γ, and IL-1β. Additionally, Lc. chungangensis CAU 28 was associated with an increase in the CD3+CD4+CD8- phenotype among obese mice. Thus, the administration of Lc. chungangensis CAU 28 induced antiobesity effects, suggesting potential applications of this species as a supplement for obesity mitigation.
- Published
- 2020
25. Halarcobacter arenosus sp. nov., isolated from marine sediment
- Author
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Jong-Hwa Kim, Jiseon Jeong, Ampaitip Sukhoom, Wonyong Kim, and Jihye Baek
- Subjects
Arcobacter ,Geologic Sediments ,0303 health sciences ,Phylogenetic tree ,030306 microbiology ,General Medicine ,Biology ,Biochemistry ,Microbiology ,C content ,Bacterial strain ,03 medical and health sciences ,Species Specificity ,RNA, Ribosomal, 16S ,Republic of Korea ,Botany ,Genetics ,16s rrna gene sequencing ,Taxonomy (biology) ,Campylobacteraceae ,Molecular Biology ,Phylogeny ,030304 developmental biology - Abstract
A Gram-stain-negative, slightly curved, rod-shaped bacterial strain CAU 1517T was isolated from marine sediment in Busan, the Republic of Korea. The taxonomic position of strain CAU 1517T was investigated via a polyphasic approach comprising phenotypic, chemotaxonomic and phylogenetic properties. Strain CAU 1517T grew optimally at 30 °C, pH 7.5 and in the presence of 7% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequencing revealed that strain CAU 1517T belongs to the genus Halarcobacter and is most closely related to Halarcobacter bivalviorum LMG 26154T (96.5% similarity). The average nucleotide identity and digital DNA-DNA hybridization values between strain CAU 1517T and members of genus Halarcobacter ranged from were 76.7–78.0% and 19.5–21.2%, respectively. The strain contained menaquinone-6 (MK-6) as the only respiratory quinone, and C16:0, summed feature 3 (C16:1 ω7c/C16:1 ω6c), and summed feature 8 (C18:1ω7c/C18:1ω6c) as the major fatty acids. The polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylethanolamine, and two unidentified aminophospholipids. The G+C content was 28.2 mol%. Therefore, it has been demonstrated that the isolate represents a novel species of the genus Halarcobacter, for which the name Halarcobacter arenosus sp. nov., is proposed. The type strain is CAU 1517T (=KCTC 72232T =NBRC 113955T).
- Published
- 2020
26. Pontimicrobium aquaticum gen. nov., sp. nov., a bacterium in the family Flavobacteriaceae isolated from seawater
- Author
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Thidarat Janthra, Jong-Hwa Kim, Jihye Baek, Jung-Hoon Yoon, Ampaitip Sukhoom, and Wonyong Kim
- Subjects
food.ingredient ,Phylogenetic tree ,Strain (chemistry) ,General Medicine ,Biology ,16S ribosomal RNA ,biology.organism_classification ,Microbiology ,Flavobacteriaceae ,Aquibacter ,food ,Genus ,Genome size ,Ecology, Evolution, Behavior and Systematics ,Bacteria - Abstract
A Gram-stain-negative, yellow-pigmented, non-spore-forming, non-motile, rod-shaped, catalase-positive, strictly aerobic bacterial strain, designated CAU 1491T, was isolated from seawater and its taxonomic position was examined using a polyphasic approach. Cells of strain CAU 1491T grew optimally at 30 °C, pH 7.5 and in 2.0 % (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence of CAU 1491T showed that it formed a distinct lineage within the family Flavobacteriaceae as a separate deep branch, with 97.0 % or lower sequence similarity to representatives of the genera Lacinutrix , Gaetbulibacter and Aquibacter . The major cellular fatty acids of strain CAU 1491T were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH and summed feature 3. The polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylserine, phosphatidylethanolamine and an unidentified phospholipid. The strain contained MK-6 as the sole respiratory quinone. Genome sequencing revealed that strain CAU 1491T has a genome size of 3.13 Mbp and a G+C content of 32.4 mol%. On the basis of the phenotypic, chemotaxonomic and genomic data, strain CAU 1491T represents a new genus and species in the family Flavobacteriaceae for which the name Pontimicrobium aquaticum gen. nov., sp. nov. is proposed. The type strain of Pontimicrobium aquaticum is CAU 1491T (=KCTC 72003T=NBRC 113695T).
- Published
- 2020
27. Aureimonas fodinaquatilis sp. nov., isolated from coal mine wastewater
- Author
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Wonyong Kim, Ampaitip Sukhoom, Jong-Hwa Kim, Jung-Sook Lee, and Jihye Baek
- Subjects
food.ingredient ,Wastewater ,Biochemistry ,Microbiology ,03 medical and health sciences ,food ,Species Specificity ,Phylogenetics ,RNA, Ribosomal, 16S ,Republic of Korea ,Genetics ,Molecular Biology ,Phospholipids ,Phylogeny ,Alphaproteobacteria ,030304 developmental biology ,Gram ,Base Composition ,0303 health sciences ,Phylogenetic tree ,Strain (chemistry) ,030306 microbiology ,Chemistry ,Fatty Acids ,Nucleic Acid Hybridization ,Aureimonas frigidaquae ,General Medicine ,16S ribosomal RNA ,Coal ,Aureimonas ,Aureimonas altamirensis ,Genome, Bacterial - Abstract
A Gram stain-negative, aerobic, non-motile, short, rod-shaped bacterial strain CAU 1482T was isolated from coal mine wastewater in Hongcheon, Korea. It grew well at 30 °C, pH 8.5, 2% NaCl (w/v). 16S rRNA-based phylogeny indicated that CAU 1482T forms a distinct lineage within Aureimonas with high similarity to Aureimonas frigidaquae CW5T (98.2%), Aureimonas altamirensis S21BT (98.0%), and Aureimonas glaciei B5-2T (96.3%). The predominant cellular fatty acids were C18:1 2-OH, C16:0, C18:1 ω7c, and/or C18:1 ω6c (summed feature 8), with Q-10 as the major isoprenoid quinone. The polar lipid profile comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, two unidentified aminolipids, and three unidentified lipids. The 3.9-Mb genome included 8 contigs and 3599 protein-coding genes with a 56.7 mol% G + C content. Average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strain CAU 1482T and closely related strains of A. frigidaquae CW5T and A. altamirensis S21BT were 72.2‒72.4% and 18.7‒18.8%, respectively. These phenotypic, chemotaxonomic, and phylogenetic data support CAU 1482T as a novel Aureimonas species, for which the name Aureimonas fodinaquatilis sp. nov. is proposed. The type strain is CAU 1482T (= KCTC 62995T = NBRC 113692T).
- Published
- 2020
28. Shewanella insulae sp. nov., isolated from a tidal flat
- Author
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Jung-Hoon Yoon, In Kyu Kim, Sooyeon Park, and Wonyong Kim
- Subjects
food.ingredient ,Phylogenetic tree ,Strain (chemistry) ,Aquimarina ,General Medicine ,Biology ,biology.organism_classification ,16S ribosomal RNA ,Microbiology ,Shewanella ,Nucleic acid thermodynamics ,food ,Phylogenetics ,Gene ,Ecology, Evolution, Behavior and Systematics - Abstract
A Gram-stain-negative, aerobic, non-spore-forming, motile by single polar flagellum and ovoid or rod-shaped bacterial strain, designated JBTF-M18T, was isolated from tidal-flat sediment collected from the Yellow Sea, Republic of Korea. The neighbour-joining phylogenetic tree of 16S rRNA gene sequences showed that strain JBTF-M18T fell within the clade comprising the type strains of Shewanella species. Strain JBTF-M18T exhibited 16S rRNA gene sequence similarity values of 97.1–98.8 % to the type strains of S. loihica , S. aquimarina , S. waksmanii and S. marisflavi and of less than 96.9 % to the type strains of the other Shewanella species. The average nucleotide identity and digital DNA–DNA hybridization values between strain JBTF-M18T and the type strains of S. waksmanii and S. loihica were 72.0 and 89.5% and 18.9 and 38.1 %, respectively. DNA–DNA relatedness values between strain JBTF-M18T and the type strains of S. aquimarina and S. marisflavi were 14 and 19 %, respectively. The DNA G+C content of strain JBTF-M18T from genomic sequence data was 52.9 %. Strain JBTF-M18Tcontained MK-6 as the predominant menaquinone and Q-7 and Q-8 as the predominant ubiquinones. It had iso-C15 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and C16 : 0 as the major fatty acids. The major polar lipids of strain JBTF-M18T were phosphatidylethanolamine and phosphatidylglycerol. Distinguished phenotypic properties, along with the phylogenetic and genetic distinctiveness, revealed that strain JBTF-M18T is separated from recognized Shewanella species. On the basis of the data presented, strain JBTF-M18T is considered to represent a novel species of the genus Shewanella , for which the name Shewanella insulae sp. nov. is proposed. The type strain is JBTF-M18T (=KACC 19869T=NBRC 113583T).
- Published
- 2020
29. Ruegeria sediminis sp. nov., isolated from tidal flat sediment
- Author
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Wonyong Kim, Jihye Baek, Jong-Hwa Kim, and Ampaitip Sukhoom
- Subjects
Phylogenetic tree ,Strain (chemistry) ,Ruegeria ,General Medicine ,Biology ,16S ribosomal RNA ,biology.organism_classification ,Microbiology ,DNA sequencing ,Proteobacteria ,Rhodobacteraceae ,Genome size ,Ecology, Evolution, Behavior and Systematics - Abstract
A Gram-stain-negative, aerobic, non-motile, rod-shaped bacterial strain, designated CAU 1488T, was isolated from tidal flat sediment, and its taxonomic position was investigated using a polyphasic approach. The organism grew optimally at a temperature of 30 °C, at pH 7.0–7.5 and in the presence of 0–6 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CAU 1488T forms a lineage distinct from Ruegeria marisrubri ZGT 118T (97.9 %), Ruegeria marina ZH17T (97.6 %), Ruegeria lacuscaerulensis ITI 1157T (97.5 %), Ruegeria pomeroyi DSS-3T (97.1 %), Ruegeria profundi ZGT108T (97.0 %), Ruegeria intermedia CC-GIMAT-2T (96.8 %), Ruegeria atlantica CECT 4292T (96.7 %) and Ruegeria kandeliae J95T (95.9 %). Genome sequencing revealed that CAU 1488T had a genome size of 4.23 Mbp and a G+C content of 63.2 mol%. Overall genome related indexes including average nucleotide identity and digital DNA–DNA hybridization values were 75.0–83.0 % and 26.2 %, which are below the cutoffs of 95 and 70 %, respectively, indicating that strain CAU 1488T represents a distinct species from the members of the genus Ruegeria . The predominant quinone was ubiquinone-10 (Q-10). The major fatty acids were summed feature 8 (C18 : 1 ω7c/ω6c; 60.7 %) and its polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and unidentified aminolipids. On the basis of phenotypic, chemotaxonomic and genomic data, strain CAU 1488T constitutes a novel species of the genus Ruegeria , for which the name Ruegeria sediminis sp. nov. is proposed. The type strain is CAU 1488T (=KCTC 62996T=NBRC 113693T).
- Published
- 2020
30. Gramella sabulilitoris sp. nov., isolated from a marine sand
- Author
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Jung-Hoon Yoon, In Kyu Kim, Wonyong Kim, and Sooyeon Park
- Subjects
0106 biological sciences ,0301 basic medicine ,Gramella echinicola ,Phylogenetic tree ,Strain (biology) ,General Medicine ,Biology ,16S ribosomal RNA ,010603 evolutionary biology ,01 natural sciences ,Microbiology ,C content ,03 medical and health sciences ,030104 developmental biology ,Data sequences ,Gramella sediminilitoris ,Botany ,Clade ,Ecology, Evolution, Behavior and Systematics - Abstract
A Gram-stain-negative, aerobic, non-spore-forming, motile by gliding and rod-shaped bacterial strain, designated HSMS-1T, was isolated from a marine sand collected from the Yellow Sea, Republic of Korea, and identified by a polyphasic taxonomic approach. The neighbour-joining phylogenetic tree of 16S rRNA gene sequences showed that HSMS-1T fell within the clade comprising the type strains of species of the genus Gramella . HSMS-1T exhibited 16S rRNA gene sequence similarity values of 99.0 and 98.7 % to the type strains of Gramella echinicola and Gramella sediminilitoris and of 93.3–98.5 % to the type strains of the other species of the genus Gramella . The ANI and dDDH values between HSMS-1T and the type strains of G. echinicola , Gramella gaetbulicola , Gramella forsetii , Gramella salexigens , Gramella portivictoriae and Gramella flava were 72.6–79.3 % and 17.4–22.2 %, respectively. Mean DNA–DNA relatedness value between HSMS-1T and the type strain of G. sediminilitoris was 18 %. HSMS-1T contained MK-6 as the predominant menaquinone and iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 0 3-OH and iso-C16 : 0 as the major fatty acids. The major polar lipid of HSMS-1T was phosphatidylethanolamine. The DNA G+C content of HSMS-1T from genomic sequence data was 39.2 %. Distinguishing phenotypic properties, along with the phylogenetic and genetic distinctiveness, revealed that HSMS-1T is separated from recognized species of the genus Gramella . On the basis of the data presented, strain HSMS-1T is considered to represent a novel species of the genus Gramella , for which the name Gramella sabulilitoris sp. nov. is proposed. The type strain is HSMS-1T(=KACC 19899T=NBRC 113648T).
- Published
- 2020
31. Thalassococcus arenae sp. nov. isolated from sea sand
- Author
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Veeraya Weerawongwiwat, Jong-Hwa Kim, Jung-Sook Lee, Jung-Hoon Yoon, Ampaitip Sukhoom, and Wonyong Kim
- Subjects
DNA, Bacterial ,Ubiquinone ,Fatty Acids ,General Medicine ,Sequence Analysis, DNA ,Biochemistry ,Microbiology ,Bacterial Typing Techniques ,Sand ,RNA, Ribosomal, 16S ,Genetics ,Seawater ,Rhodobacteraceae ,Molecular Biology ,Phospholipids ,Phylogeny - Abstract
A Gram-negative, aerobic, rod-shaped bacterium, designated strain CAU 1522
- Published
- 2022
32. Alleviation effects of
- Author
-
Jong-Hwa, Kim and Wonyong, Kim
- Subjects
Inflammation ,Male ,Plant Extracts ,Polyphenols ,Mice, Inbred Strains ,Administration, Cutaneous ,Plant Roots ,Cell Line ,Dermatitis, Atopic ,Disease Models, Animal ,Mice ,Anti-Allergic Agents ,Animals ,HaCaT Cells ,Humans ,Rubus - Abstract
Atopic dermatitis (AD) is an inflammatory skin disease characterized by chronic inflammatory dermatitis with immunological manifestations. The aim of this study was to investigate the effects of polyphenol-containing
- Published
- 2022
33. Muricauda lutisoli sp. nov., isolated from mudflat
- Author
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Jiseon Jeong, Veeraya Weerawongwiwat, Jong-Hwa Kim, Ampaitip Sukhoom, Kijeong Kim, and Wonyong Kim
- Subjects
DNA, Bacterial ,RNA, Ribosomal, 16S ,Fatty Acids ,Genetics ,Seawater ,Vitamin K 2 ,General Medicine ,Sequence Analysis, DNA ,Molecular Biology ,Biochemistry ,Microbiology ,Phylogeny ,Bacterial Typing Techniques - Abstract
A Gram-negative, nonmotile, rod-shaped bacterium, designated strain CAU 1631
- Published
- 2022
34. Sneathiella sedimenti sp. nov., isolated from marine sediment
- Author
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Yunjeong Lee, Veeraya Weerawongwiwat, Jong-Hwa Kim, Jung-Hoon Yoon, Min Kuk Suh, Han Sol Kim, Jung-Sook Lee, Ampaitip Sukhoom, and Wonyong Kim
- Subjects
General Medicine ,Microbiology ,Ecology, Evolution, Behavior and Systematics - Abstract
A novel bacterium, designated CAU 1612T, was isolated from coastal sediment sampled in the Republic of Korea. Cells of the strain were Gram-stain-negative, rod-shaped and motile. Optimum growth occurred at 30 °C, at pH 7.0 and with 1.0 % (w/v) NaCl. Based on 16S rRNA gene sequences, phylogenetic analysis revealed that strain CAU 1612T belonged to the genus Sneathiella and showed highest similarity to ‘Sneathiella litorea’ JCM 33810T (98.5 %), followed by Sneathiella chungangensis KCTC 32476T (97.7 %), Sneathiella aquimaris KCTC 12842T (96.0 %), Sneathiella chinensis LMG 23452T (95.5 %), Sneathiella limimaris KCTC 52846T (95.5 %) and Sneathiella glossodoripedis KCTC 12842T (95.4 %). The average nucleotide identity and digital DNA–DNA hybridization values of strain CAU 1612T were estimated to be 68.5–81.7 % and ≤23.7 %, respectively, to members of the genus Sneathiella . The DNA G+C content was 54.1 mol%. The major cellular fatty acids (>10 %) were C16:0, C19 : 0 cyclo ω8c and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The major menaquinone was Q-10 and the predominant polar lipids were phosphatidylmethylethanolamine, phosphatidylethanolamine and phosphatidylglycerol. On the basis of taxonomic evidence, strain CAU 1612T represents a novel species, for which the name Sneathiella sedimenti sp. nov. is proposed. The type strain is CAU 1612T (=KCTC 82427T=MCCC 1K06082T).
- Published
- 2022
35. Marinobacter arenosus sp. nov., a halotolerant bacterium isolated from a tidal flat
- Author
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Yunjeong Lee, Veeraya Weerawongwiwat, Jong-Hwa Kim, Min Kuk Suh, Han Sol Kim, Jung-Sook Lee, Jung-Hoon Yoon, Ampaitip Sukhoom, and Wonyong Kim
- Subjects
DNA, Bacterial ,RNA, Ribosomal, 16S ,Marinobacter ,Genetics ,Sequence Analysis, DNA ,General Medicine ,Molecular Biology ,Biochemistry ,Microbiology ,Phospholipids ,Phylogeny ,Bacterial Typing Techniques - Abstract
A Gram-negative, rod-shaped, motile bacterium, designated strain CAU 1620
- Published
- 2022
36. Marinobacterium arenosum sp. nov., isolated from a coastal sand
- Author
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Yunjeong Lee, Veeraya Weerawongwiwat, Jong-Hwa Kim, Jung-Hoon Yoon, Jung-Sook Lee, Ampaitip Sukhoom, and Wonyong Kim
- Subjects
DNA, Bacterial ,Ubiquinone ,Alteromonadaceae ,Fatty Acids ,General Medicine ,Sequence Analysis, DNA ,Biochemistry ,Microbiology ,Bacterial Typing Techniques ,Sand ,RNA, Ribosomal, 16S ,Genetics ,Molecular Biology ,Phospholipids ,Phylogeny - Abstract
A Gram-negative, aerobic, motile, rod-shaped bacterium, designated strain CAU 1594
- Published
- 2022
37. Multiple reassortment and interspecies transmission events contribute to the diversity of porcine-like human rotavirus C strains detected in South Korea
- Author
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Thoi Cong Truong, Tinh Huu Nguyen, and Wonyong Kim
- Subjects
Rotavirus ,Dogs ,Genotype ,Swine ,Virology ,Animals ,Humans ,Cattle ,General Medicine ,Genome, Viral ,Phylogeny ,Rotavirus Infections - Abstract
Globally, rotavirus C (RVC) causes diarrhoeal outbreaks, mainly in swine, with sporadic incidents in human, bovine, and canine populations. In this study, two human RVC strains, RVC/Human-wt/KOR/CAU13-1-77/2013 and RVC/Human-wt/KOR/CAU14-1-242/2014, were isolated in South Korea, and their complete genome sequences were compared with those of other human- and animal-origin RVC strains found worldwide. Genetic analysis revealed that these viruses have a G4-P[2]-I2-R2-C2-M3-A2-N2-T2-E2-H2 genotype constellation. Phylogenetic analysis indicated that these Korean RVC strains belong to the M3 lineage of the VP3 gene in human RVC from Japan and China and porcine RVC from Japan. These results suggest that RVC circulates in northeast Asia in both the human and porcine populations. These results also provide evidence of interspecies RVC reassortment events.
- Published
- 2022
38. Paenibacillus arenosi sp. nov., a siderophore-producing bacterium isolated from coastal sediment
- Author
-
Jihye Baek, Veeraya Weerawongwiwat, Jong-Hwa Kim, Jung-Hoon Yoon, Jung-Sook Lee, Ampaitip Sukhoom, and Wonyong Kim
- Subjects
DNA, Bacterial ,Base Composition ,Fatty Acids ,Siderophores ,Sequence Analysis, DNA ,General Medicine ,Biochemistry ,Microbiology ,Bacterial Typing Techniques ,RNA, Ribosomal, 16S ,Genetics ,Paenibacillus ,Molecular Biology ,Phospholipids ,Phylogeny - Abstract
In this study, strain CAU 1523
- Published
- 2022
39. Changes in fecal metabolic and lipidomic features by anti-TNF treatment and prediction of clinical remission in patients with ulcerative colitis
- Author
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Seok-Young Kim, Seung Yong Shin, Soo Jung Park, Jong Pil Im, Hyo Jong Kim, Kang-Moon Lee, Ji Won Kim, Sung-Ae Jung, Jun Lee, Sang-Bum Kang, Sung Jae Shin, Eun Sun Kim, You Sun Kim, Tae Oh Kim, Hyun-Soo Kim, Dong Il Park, Hyung Kil Kim, Eun Soo Kim, Young-Ho Kim, Dennis Teng, Jong-Hwa Kim, Wonyong Kim, Maham Saeed, Jung Min Moon, Kisung Kim, Chang Hwan Choi, and Hyung-Kyoon Choi
- Subjects
Gastroenterology - Abstract
Background: Therapeutic targets for ulcerative colitis (UC) and prediction models of antitumor necrosis factor (TNF) therapy outcomes have not been fully reported. Objective: Investigate the characteristic metabolite and lipid profiles of fecal samples of UC patients before and after adalimumab treatment and develop a prediction model of clinical remission following adalimumab treatment. Design: Prospective, observational, multicenter study was conducted on moderate-to-severe UC patients ( n = 116). Methods: Fecal samples were collected from UC patients at 8 and 56 weeks of adalimumab treatment and from healthy controls (HC, n = 37). Clinical remission was assessed using the Mayo score. Metabolomic and lipidomic analyses were performed using gas chromatography mass spectrometry and nano electrospray ionization mass spectrometry, respectively. Orthogonal partial least squares discriminant analysis was performed to establish a remission prediction model. Results: Fecal metabolites in UC patients markedly differed from those in HC at baseline and were changed similarly to those in HC during treatment; however, lipid profiles did not show these patterns. After treatment, the fecal characteristics of remitters (RM) were closer to those of HC than to those of non-remitters (NRM). At 8 and 56 weeks, amino acid levels in RM were lower than those in NRM and similar to those in HC. After 56 weeks, levels of 3-hydroxybutyrate, lysine, and phenethylamine decreased, and dodecanoate level increased in RM similarly to those in HC. The prediction model of long-term remission in male patients based on lipid biomarkers showed a higher performance than clinical markers. Conclusion: Fecal metabolites in UC patients markedly differ from those in HC, and the levels in RM are changed similarly to those in HC after anti-TNF therapy. Moreover, 3-hydroxybutyrate, lysine, phenethylamine, and dodecanoate are suggested as potential therapeutic targets for UC. A prediction model of long-term remission based on lipid biomarkers may help implement personalized treatment.
- Published
- 2023
40. Heat-killed Lactiplantibacillus plantarum LRCC5314 mitigates the effects of stress-related type 2 diabetes in mice via gut microbiome modulation
- Author
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YoHan Nam, Seokmin Yoon, Jihye Baek, Jong-Hwa Kim, Miri Park, KwangWoo Hwang, and Wonyong Kim
- Subjects
General Medicine ,Applied Microbiology and Biotechnology ,Biotechnology - Published
- 2021
41. Pseudomarimonas arenosa gen. nov., sp. nov. isolated from marine sand
- Author
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Veeraya Weerawongwiwat, Jong-Hwa Kim, Jung-Hoon Yoon, Jung-Sook Lee, Ampaitip Sukhoom, and Wonyong Kim
- Subjects
General Medicine ,Microbiology ,Ecology, Evolution, Behavior and Systematics - Abstract
A novel Gram-negative, aerobic, non-motile, rod-shaped, bacterial strain (CAU 1598T) was isolated from marine sand. Strain CAU 1598T grew well at 30 °C, pH 6.5–7.0 and with 3 % NaCl (w/v). Phylogeny results based on 16S rRNA gene sequencing indicated that the identified strain had the highest similarity (94.3%) to Pseudoxanthomonas putridarboris , indicating that strain CAU 1598T belongs to the family Xanthomonadaceae . Further, the fatty acid profile of the strain was primarily composed of C16:0, iso-C15 : 0, iso-C16 : 0, summed feature 3 (consisting of C16 : 1 ω7c/iso-C15 : 0 2-OH) and summed feature 9 (consisting of iso-C17 : 1 ω9c and/or C16 : 0 10-methyl), with ubiquinone-8 as the major isoprenoid quinone. The polar lipid profile included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphoglycolipid, an unidentified aminolipid and an unidentified lipid. The G+C content of the bacterial genome was 62.6 mol% and its 5.4 Mb length encompassed 144 contigs and 4236 protein-coding genes. These phenotypic, chemotaxonomic and phylogenetic data indicate that CAU 1598T belongs to a new genus and species, for which the name Pseudomarimonas arenosa gen. nov., sp. nov. is proposed. The type strain is CAU 1598T (=KCTC 82406T=MCCC 1K05673T).
- Published
- 2021
42. Complete Genome Sequence of Lacticaseibacillus rhamnosus CAU 1365, Isolated from Kimchi
- Author
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Yunjeong Lee, Jong-Hwa Kim, and Wonyong Kim
- Subjects
Immunology and Microbiology (miscellaneous) ,Genome Sequences ,Genetics ,food and beverages ,Molecular Biology - Abstract
Here, we report the whole-genome sequence of Lacticaseibacillus rhamnosus CAU 1365, which was isolated from kimchi. The genome was composed of 1 contig with a total length of 2,991,039 bp and had 2,658 coding sequences, including 62 tRNA genes and 15 rRNA genes.
- Published
- 2021
43. Evaluation of Antimicrobial Properties of Lichen Substances against Plant Pathogens
- Author
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Jaycee A. Paguirigan, Rundong Liu, Seong Mi Im, Jae-Seoun Hur, and Wonyong Kim
- Subjects
Agronomy and Crop Science - Abstract
Plant pathogens pose major threats on agriculture and horticulture, causing significant economic loss worldwide. Due to the continuous and excessive use of synthetic pesticides, emergence of pesticide resistant pathogens has become more frequent. Thus, there is a growing needs for environmentally-friendly and selective antimicrobial agents with a novel mode of action, which may be used in combination with conventional pesticides to delay development of pesticide resistance. In this study, we evaluated the potentials of lichen substances as novel biopesticides against eight bacterial and twelve fungal plant pathogens that have historically caused significant phytopathological problems in South Korea. Eight lichen substances of diverse chemical origins were extracted from axenic culture or dried specimen, and further purified for comparative analysis of their antimicrobial properties. Usnic acid and vulpinic acid exhibited strong antibacterial activities against Clavibacter michiganensis subsp. michiganensis. In addition, usnic acid and vulpinic acid were highly effective in the growth inhibition of fungal pathogens, such as Diaporthe eres, D. actinidiae, and Sclerotinia sclerotiorum. Intriguingly, the growth of Rhizoctonia solani was specifically inhibited by lecanoric acid, indicating that lichen substances exhibit some degrees of selectivity to plant pathogens. These results suggested that lichen substance can be used as a selective biopesticide for controlling plant disease of agricultural and horticultural significance, minimizing possible emergence of pesticide resistant pathogens in fields.
- Published
- 2021
44. Roseibium limicola sp. nov., isolated from tidal mudflat
- Author
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Han Sol Kim, Ampaitip Sukhoom, Jung-Hoon Yoon, Jung-Sook Lee, Jong-Hwa Kim, Wonyong Kim, Veeraya Weerawongwiwat, and Min Kuk Suh
- Subjects
biology ,Phylogenetic tree ,Strain (chemistry) ,Alphaproteobacteria ,Roseibium hamelinense ,General Medicine ,biology.organism_classification ,16S ribosomal RNA ,Microbiology ,Roseibium ,Rhodobacteraceae ,Ecology, Evolution, Behavior and Systematics ,Bacteria - Abstract
A novel bacterium, designated strain CAU 1637T, was isolated from a tidal mudflat. Cells of strain CAU 1637T were Gram-stain-negative, aerobic, motile with single flagellum and rod-shaped. The optimum conditions for growth were observed at 30 °C, pH 6.0 and in the presence of 2 % (w/v) NaCl. The respiratory quinone was ubiquinone-10. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CAU 1637T was closely related to the genus Roseibium , with the highest similarity to Roseibium aestuarii NRBC 112946T (97.4 %), followed by Roseibium hamelinense NRBC 16783T (96.8 %), Roseibium aquae JCM 19310T (96.4 %), Roseibium sediminis KCTC 52373T (95.8 %) and Roseibium denhamense JCM 10543T (95.3 %). The predominant cellular fatty acids were C18 : 1 ω7c 11-methyl and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The major polar lipids consisted of diphosphatidylglycerol and phosphatidylglycerol. The average nucleotide identity values between the novel isolate and related strains ranged from 71.0 to 76.4 %, and the DNA−DNA hybridization values ranged from 19.3 to 20.3 %. The G+C content was 58.4 mol% and the whole-genome size was 4.6 Mb, which included 17 contigs and 3931 protein-coding genes. Based on the taxonomic data, strain CAU 1637T represents a novel species of the genus Roseibium , for which the name Roseibium limicola sp. nov. is proposed. The type strain is CAU 1637T (=KCTC 82429T=MCCC 1K06080T).
- Published
- 2021
45. Heat-Killed
- Author
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YoHan, Nam, Seokmin, Yoon, Jihye, Baek, Jong-Hwa, Kim, Miri, Park, KwangWoo, Hwang, and Wonyong, Kim
- Subjects
Mice, Inbred C57BL ,Mice ,Hot Temperature ,Diabetes Mellitus, Type 2 ,Lactobacillaceae ,Probiotics ,Animals ,Gastrointestinal Microbiome ,Lactobacillus plantarum - Abstract
The incidence of stress-related type 2 diabetes (stress-T2D), which is aggravated by physiological stress, is increasing annually. The effects of
- Published
- 2021
46. Arenibacterium arenosum sp. nov., isolated from sea sand
- Author
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Jiseon Jeong, Veeraya Weerawongwiwat, Jong-Hwa Kim, Min Kuk Suh, Han Sol Kim, Jung-Sook Lee, Jung-Hoon Yoon, Ampaitip Sukhoom, and Wonyong Kim
- Subjects
DNA, Bacterial ,Ubiquinone ,General Medicine ,Sequence Analysis, DNA ,Silicon Dioxide ,Biochemistry ,Microbiology ,Bacterial Typing Techniques ,Sand ,RNA, Ribosomal, 16S ,Genetics ,Molecular Biology ,Phospholipids ,Phylogeny - Abstract
A Gram-negative, non-motile, short rod-shaped aerobic bacterial strain CAU 1593
- Published
- 2021
47. Thauera sedimentorum sp. nov., Isolated from Coastal Sediment
- Author
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Jihye Baek, Nattira Jaikwang, Jong-Hwa Kim, Jung-Hoon Yoon, Jung-Sook Lee, Ampaitip Sukhoom, and Wonyong Kim
- Subjects
DNA, Bacterial ,Thauera ,RNA, Ribosomal, 16S ,Fatty Acids ,Nucleic Acid Hybridization ,General Medicine ,Sequence Analysis, DNA ,Applied Microbiology and Biotechnology ,Microbiology ,Phospholipids ,Phylogeny ,Bacterial Typing Techniques - Abstract
A Gram-negative, strictly aerobic, rod-shaped, non-spore-forming bacterium, designated CAU 1555
- Published
- 2021
48. Photobacterium arenosum sp. nov., isolated from marine sediment sand
- Author
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Ampaitip Sukhoom, Wonyong Kim, Veeraya Weerawongwiwat, Jong-Hwa Kim, Jung-Sook Lee, Seokmin Yoon, and Jung-Hoon Yoon
- Subjects
Strain (chemistry) ,biology ,Phylogenetic tree ,General Medicine ,biology.organism_classification ,16S ribosomal RNA ,Photobacterium ,Microbiology ,Vibrionaceae ,Gammaproteobacteria ,Botany ,Genome size ,Ecology, Evolution, Behavior and Systematics ,Bacteria - Abstract
A Gram-stain-negative, aerobic, motile, short rod-shaped, catalase-negative and oxidase-positive bacterium, strain CAU 1568T, was isolated from marine sediment sand sampled at Sido Island in the Republic of Korea. The optimum conditions for growth were at 25–30 °C, at pH 6.5–8.5 and with 0–4.0 % (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain CAU 1568T was a member of the genus Photobacterium with high similarity to Photobacterium salinisoli JCM 30852T (97.7 %), Photobacterium halotolerans KACC 17089T (97.3 %) and Photobacterium galatheae LMG F28894T (97.3 %). The predominant cellular fatty acids were C16 : 0, summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c) and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), with Q-8 as the major of isoprenoid quinone. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerols, phosphatidylcholine, phosphatidylethanolamine, phospholipid, two aminophospholipids and three unidentified lipids. The whole genome size of strain CAU 1568T was 4.8 Mb with 50.1 mol% G+C content; including 38 contigs and 4233 protein-coding genes. These taxonomic data support CAU 1568T as representing a novel Photobacterium species, for which the name Photobacterium arenosum sp. nov. is proposed. The type strain of this novel species is CAU 1568T (=KCTC 82404T=MCCC 1K05668T).
- Published
- 2021
49. Multifunctional Probiotic and Functional Properties of
- Author
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Seokmin, Yoon, Hyeokjun, Cho, Yohan, Nam, Miri, Park, Ahyoung, Lim, Jong-Hwa, Kim, Jaewoong, Park, and Wonyong, Kim
- Subjects
Lipopolysaccharides ,Adipogenesis ,Tumor Necrosis Factor-alpha ,Probiotics ,Interleukin-1beta ,Anti-Inflammatory Agents ,Drug Tolerance ,Nitric Oxide ,Bile Acids and Salts ,Interferon-gamma ,Mice ,RAW 264.7 Cells ,Lactobacillaceae ,3T3-L1 Cells ,Fermentation ,Animals ,Cytokines ,Humans ,Caco-2 Cells ,Fermented Foods - Abstract
In this study, the survival capacity (acid and bile salt tolerance, and adhesion to gut epithelial cells) and probiotic properties (enzyme activity-inhibition and anti-inflammatory activities, inhibition of adipogenesis, and stress hormone level reduction) of
- Published
- 2021
50. Chachezhania sediminis sp. nov., isolated from marine sediment
- Author
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Jihye Baek, Wonyong Kim, Jung-Sook Lee, Jong-Hwa Kim, Jung-Hoon Yoon, and Ampaitip Sukhoom
- Subjects
0106 biological sciences ,0301 basic medicine ,Phylogenetic tree ,biology ,Strain (chemistry) ,Alphaproteobacteria ,General Medicine ,biology.organism_classification ,16S ribosomal RNA ,010603 evolutionary biology ,01 natural sciences ,Microbiology ,03 medical and health sciences ,Monophyly ,030104 developmental biology ,Genus ,Botany ,Rhodobacteraceae ,Gene ,Ecology, Evolution, Behavior and Systematics - Abstract
A Gram-stain-negative, aerobic, non-motile, rod-shaped bacterial strain (CAU 1508T) was isolated from marine sediment collected in the Republic of Korea. Growth was observed at 10–45 °C (optimum, 30 °C), pH 4.0–11.0 (optimum, pH 6.0–8.0) and with 0–8.0 % (w/v) NaCl (optimum, 2–4 %). The isolate formed a monophyletic clade in the phylogenetic analyses using 16S rRNA gene and whole-genome sequences, exhibiting the highest similarity to Chachezhania antarctica SM1703T (96.5 %), and representing a distinct branch within the genus Chachezhania (family Rhodobacteraceae ). Its whole genome sequence was 5.59 Mb long, with a G+C content of 65.7 mol% and 2183 predicted genes belonging to six functional categories. The average nucleotide identity and digital DNA–DNA hybridization values between CAU 1508T and C. antarctica SM1703T were 79.1 and 22.2 %, respectively. The predominant cellular fatty acids were C19 : 0 cyclo ω8c and summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, two unidentified phospholipids and one unidentified aminophospholipid. The sole isoprenoid quinone was ubiquinone 10. Phenotypic phylogenetic properties supported the classification of CAU 1508T as representing a novel species of the genus Chachezhania , with the proposed name Chachezhania sediminis sp. nov. The type strain is CAU 1508T (=KCTC 62999T=NBRC 113697T).
- Published
- 2021
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