• Journal of Microbiology and Biotechnology
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• v.32 no.7
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• pp.855-861
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• 2022

A white-pigmented, non-motile, gram-negative, and rod-shaped bacterium, designated CYS-02^T, was isolated from soil sampled at Suwon, Gyeonggi-do, Republic of Korea. Cells were strictly aerobic, grew optimally at 20-28℃ and hydrolyzed Tween 40. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain CYS-02^T formed a lineage within the family Comamonadaceae and clustered as members of the genus Variovorax. The closest members were Variovorax guangxiensis DSM 27352^T (98.6% sequence similarity), Variovorax paradoxus NBRC 15149^T (98.5%), and Variovorax gossypii JM-310^T (98.3%). The principal respiratory quinone was Q-8 and the major polar lipids contain phosphatidylethanolamine (PE), phosphatidylethanolamine (PG), and diphosphatidylglycerol (DPG). The predominant cellular fatty acids were C_16:0, summed feature 3 (C_16:1ω7c and/or C_16:1ω6c) and summed feature 8 (C_18:1ω7c and/or C_18:1ω6c). The DNA GC content was 67.7 mol%. The ANI and dDDH values between strain CYS-02T and the closest members in the genus Variovorax were ≤ 79.0 and 22.4%, respectively, and the AAI and POCP values between CYS-02^T and the other related species in the family Comamonadaceae were > 70% and > 50%, respectively. The genome of strain CYS-02^T showed a putative terpene biosynthetic cluster responsible for antioxidant activity which was supported by DPPH radical scavenging activity test. Based on genomic, phenotypic and chemotaxonomic analyses, strain CYS-02^T was classified into a novel species in the genus Variovorax, for which the name Variovorax terrae sp. nov., has been proposed. The type strain is CYS-02^T (= KACC 22656^T = NBRC 00115645^T).

• Journal of Species Research
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• v.6 no.1
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• pp.15-24
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• 2017

During the extensive survey of the prokaryotic species diversity in Korea, bacterial strains belonging to Betaproteobacteria and Epsilonproteobacteria were isolated from various sources including freshwater, sediment, soil and fish. A total of 23 isolates were obtained, among which 22 strains were assigned to the class Betaproteobacteria and one strain to the class Epsilonproteobacteria. The 22 betaproteobacterial strains were further assigned to Comamonadaceae (11 strains), Burkholderiaceae (6 strains), Oxalobacteraceae (2 strains), Neisseriaceae (1 strain) and unclassified family groups (2 strains). For the strains of Burkholderiaceae, 3 strains were identified as 3 species of Burkholderia, and 2 strains were as 2 species of Cupriavidus. For the strains of Comamonadaceae, 4 strains were identified as 2 species of the genus Hydrogenophaga, 2 strains as 2 species of Acidovorax, 2 strains as 2 species of Limnohabitans, and each of the remaining strains as single species of Comamonas, Curvibacter and Rhodoferax, respectively. For the strains of Oxalobacteraceae, 1 strain was identified as a species of Undibacterium, and the other strain as a species of Herbaspirillum. The strain belonging to Neisseriaceae was identified as a species of Iodobacter. The remaining strains of Betaproteobacteria were identified as species of Sphaerotilus and Methylibium respectively (family unassigned). The epsilonproteobacterial strain was identified as a species of Arcobacter of the family Camplyobacteraceae. The detailed description of each unrecorded species is provided.

• Journal of Microbiology and Biotechnology
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• v.24 no.11
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• pp.1490-1494
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• 2014

To probe the genomic properties of microbes thriving in desert lakes, we sequenced the full genome of a betaproteobacterial strain (SL110) belonging to the understudied genus Caenimonas of the family Comamonadaceae. This strain was isolated from a freshwater lake in the western Gobi Desert, Northern China. Its genome contains genes encoding carbon monoxide dehydrogenase, nitrate reductase, nitrite reductase, nitric oxide reductase, and sulfur oxidation enzymes, highlighting the potentially important contribution of this group of bacteria to the cycling of inorganic elements in nature. Unexpectedly, a coenzyme $F_{420}$ biosynthesis gene cluster was identified. A further search for $F_{420}$ biosynthesis gene homologs in genomic databases suggests the possible widespread presence of $F_{420}$ biosynthesis gene clusters in proteobacterial genomes.

• Korean Journal of Environmental Biology
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• v.29 no.3
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• pp.154-161
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• 2011

The species diversity of Betaproteobacteria in the Sumunmulbengdui Wetland Area of Jeju Island was studied using culture based techniques, and candidates for novel taxa were screened. Twenty two novel bacterial strains belonging to Betaproteobacteria were isolated, which could be assigned to 16 genera of 4 families, namely Burkholderiaceae (3 strains), Comamonadaceae (8 strains), Oxalobacteraceae (5 strains), Neisseriaceae (5 strains), and an unassigned group belonging to Burkholderiales (1 strain) based 16S rRNA gene sequences. The genus Chromobacterium contained three candidates of novel species, and each of the genera Burkholderia, Comamonas, Pelomonas and Herbaspirillum contained two candidates respectively. Through the analysis of membrane fatty acid profiles and physiological properties using API 20NE as well as morphological and cultural properties, each of the isolates was found to form potentially novel species. Brief description of 22 potential candidates for new species or subspecies is given accordingly.

• Microbiology and Biotechnology Letters
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• v.43 no.2
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• pp.142-149
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• 2015

Bioaerosols are comprised of particles 0.02-100 μm in size that originate in natural and artificial environments, and as a result of human activities. They consist of microorganisms including viruses, bacteria, fungi, and protozoa; fungal spores; microbial toxins; pollen; plant or animal material; expectorated liquid from humans; and glucans (peptidoglycan and β-glucan). Bioaerosols can cause respiratory and other diseases in humans and animals. In this study, bioaerosol samples acquired from agricultural sources, livestock, a sewage treatment plant, a beach, and a pristine area were analyzed to identify and phylogenetically characterize culturable microorganisms. The isolated bacteria exhibited regional differences, with different species dominating. However, Bacillus cereus was isolated in all samples, with a total of 31 strains isolated from all areas, and Acinetobacter baumannii was isolated from an indoor poultry farm. In addition, bacteria determined to be of novel genus or species of the genera Domibacillus, Chryceobacterium, Nocardioides and family Comamonadaceae were isolated from the agricultural, livestock and beach environments.

• Journal of Applied Biological Chemistry
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• v.62 no.1
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• pp.51-56
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• 2019

Biofilms facilitate communication among microorganisms for nutrients and protect them from predators and harmful chemicals such as antibiotics and detergents. Biofilms can also act as cores for the development of clogs in many agricultural irrigation systems and in porous media. In this study, we deployed glass units at a depth of 20 m below the ground surface in the groundwater-surface water mixing zone, and retrieved them after 4 months to investigate the potential colonization of indigenous microbial community and possible mineral-microbe assemblages. We observed the periodic formation of microbial colonies by fluorescence dye staining and microscopy, and analyzed the composition of the microbial community in both the mineral-microbe aggregates and groundwater, by next generation sequencing of the 16S rRNA gene amplicons using MiSeq platform. During the course of incubation, we observed an increase in both the mineral-microbe aggregates and content of extracellular polymeric substances. Interestingly, the microbial community from the aggregates featured a high abundance of iron redox-related microorganisms such as Geobacter sp., Comamonadaceae sp., and Burkholderiales incertae sedis. Therefore, these microorganisms can potentially produce iron-minerals within the sediment-microbe-associated aggregates, and induce biofilm formation within the groundwater borehole and porous media.

• Journal of Microbiology and Biotechnology
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• v.22 no.3
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• pp.311-315
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• 2012

A novel ${\beta}$-proteobacterium, designated BXN5-$27^T$, was isolated from soil of a ginseng field of Baekdu Mountain in China, and was characterized using a polyphasic approach. The strain was Gram-staining-negative, aerobic, motile, non-spore-forming, and rod shaped. Strain BXN5-$27^T$ exhibited ${\beta}$-glucosidase activity that was responsible for its ability to transform ginsenoside $Rb_1$ (one of the dominant active components of ginseng) to compound Rd. Phylogenetic analysis based on 16S rRNA gene sequences showed that this strain belonged to the family Comamonadaceae; it was most closely related to Ramlibacter henchirensis $TMB834^T$ and Ramlibacter tataouinensis$TTB310^T$ (96.4% and 96.3% similarity, respectively). The G+C content of the genomic DNA was 68.1%. The major menaquinone was Q-8. The major fatty acids were $C_{16:0}$, summed feature 4 (comprising $C_{16:1}$ ${\omega}7c$ and/or iso-$C_{15:0}$ 2OH), and $C_{17:0}$ cyclo. Genomic and chemotaxonomic data supported the affiliation of strain BXN5-$27^T$ to the genus Ramlibacter. However, physiological and biochemical tests differentiated it phenotypically from the other established species of Ramlibacter. Therefore, the isolate represents a novel species, for which the name Ramlibacter ginsenosidimutans sp. nov. is proposed, with the type strain being BXN5-$27^T$ (=DSM $23480^T$ = LMG $24525^T$ = KCTC $22276^T$).

• Journal of Species Research
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• v.9 no.2
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• pp.85-104
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• 2020

In 2019, after a comprehensive investigation of indigenous prokaryotic species in Korea, a total of 12 bacterial strains assigned to the phylum Proteobacteria were isolated from soil. With the high 16S rRNA gene sequence similarity (>98.8%) and formation of a robust phylogenetic clade with the closest species, it was determined that each strain belonged to independent, predefined bacterial species. This study identified two species in the family Burkholderiaceae, one species in the family Comamonadaceae, two species in the family Oxalobacteraceae, one species in the family Micrococcaceae, one species in the family Bradyrhizobiaceae, one species in the family Methylobacteriaceae, one species in the family Rhizobiaceae, one species in the family Rhodocyclaceae, and one species in the family Sphingomonadaceae. There is no official report about these 12 species in Korea, so are described as unreported bacterial species in Korea in this study. Gram reaction, basic biochemical characteristics, colony, and cell morphology are also described in the species description section.

• Tuberculosis and Respiratory Diseases
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• v.79 no.3
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• pp.165-178
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• 2016

Background: Although recent metagenomic approaches have characterized the distinguished microbial compositions in airways of asthmatics, these results did not reach a consensus due to the small sample size, non-standardization of specimens and medication status. We conducted a metagenomics approach by using terminal restriction fragment length polymorphism (T-RFLP) analysis of the induced whole sputum representing both the cellular and fluid phases in a relative large number of steroid $na{\ddot{i}}ve$ asthmatics. Methods: Induced whole sputum samples obtained from 36 healthy subjects and 89 steroid-$na{\ddot{i}}ve$ asthma patients were analyzed through T-RFLP analysis. Results: In contrast to previous reports about microbiota in the asthmatic airways, the diversity of microbial composition was not significantly different between the controls and asthma patients (p=0.937). In an analysis of similarities, the global R-value showed a statistically significant difference but a very low separation (0.148, p=0.002). The dissimilarity in the bacterial communities between groups was 28.74%, and operational taxonomic units (OTUs) contributing to this difference were as follows: OTU 789 (Lachnospiraceae), 517 (Comamonadaceae, Acetobacteraceae, and Chloroplast), 633 (Prevotella), 645 (Actinobacteria and Propionibacterium acnes), 607 (Lactobacillus buchneri, Lactobacillus otakiensis, Lactobacillus sunkii, and Rhodobacteraceae), and 661 (Acinetobacter, Pseudomonas, and Leptotrichiaceae), and they were significantly more prevalent in the sputum of asthma patients than in the sputum of the controls. Conclusion: Before starting anti-asthmatic treatment, the microbiota in the whole sputum of patients with asthma showed a marginal difference from the microbiota in the whole sputum of the controls.