Journal of Microbiology

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Genome-based classification of Paraniabella aurantiaca gen. nov., sp. nov., isolated from soil and taxonomic reclassification of five species within the genus Niabella: Yong-Seok Kim, Yerang Yang, Miryung Kim, Do-Hoon Lee, Chang-Jun Cha; J. Microbiol. 2025;63(10):e2505005. Published online October 31, 2025; DOI: https://doi.org/10.71150/jm.2505005

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Abstract PDF Supplementary Material: A Gram-stain-negative, aerobic, non-motile, rod-shaped, and orange-pigmented bacterium, designated CJ426^T, was isolated from ginseng soil in Anseong, Korea. Strain CJ426^T grew optimally on Reasoner’s 2A agar at 30°C and pH 7.0 in the absence of NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain CJ426^T belonged to the family Chitinophagaceae and had the highest sequence similarity with Niabella hibiscisoli KACC 18857^T (98.7%). The 16S rRNA gene sequence similarities with other members of the genus Niabella ranged from 92.3% to 98.1%. Phylogenomic analyses and overall genomic relatedness indices, including average nucleotide identity, average amino acid identity, and the percentage of conserved proteins values, supported the classification of strain CJ426^T as a representative of a novel genus within the family Chitinophagaceae. Furthermore, genome-based analyses suggested that five members of the genus Niabella, including N. aquatica, N. defluvii, N. ginsengisoli, N. hibiscisoli, and, N. yanshanensis, should be separated from other Niabella species and be assigned as a novel genus. The major isoprenoid quinone of strain CJ426^T was menaquinone-7 (MK-7). The predominant polar lipids were phosphatidylethanolamine and six unidentified aminolipids. The major fatty acids were iso-C_15:0, iso-C_15:1 G, and iso-C_17:0 3-OH. The genome of strain CJ426^T was 6.3 Mbp in size, consisting of three contigs, with a G + C content of 41.9%. Based on a polyphasic taxonomic approach, strain CJ426^T represents a novel genus and species within the family Chitinophagaceae, for which the name Paraniabella aurantiaca gen. nov., sp. nov. is proposed. The type strain is CJ426^T (= KACC 23908^T = JCM 37728^T).

Journal Article

Flavobacterium psychrotrophum sp. nov. and Flavobacterium panacagri sp. nov., Isolated from Freshwater and Soil: Yong-Seok Kim , Eun-Mi Hwang , Chang-Myeong Jeong , Chang-Jun Cha; J. Microbiol. 2023;61(10):891-901. Published online October 18, 2023; DOI: https://doi.org/10.1007/s12275-023-00081-1

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Two novel bacterial strains CJ74T and CJ75T belonging to the genus Flavobacterium were isolated from freshwater of Han River and ginseng soil, South Korea, respectively. Strain CJ74T was Gram-stain-negative, aerobic, rod-shaped, non-motile, and non-flagellated, and did not produce flexirubin-type pigments. Strain CJ75T was Gram-stain-negative, aerobic, rodshaped, motile by gliding, and non-flagellated, and produced flexirubin-type pigments. Both strains were shown to grow optimally at 30 °C in the absence of NaCl on R2A medium. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains CJ74T and CJ75T belonged to the genus Flavobacterium and were most closely related to Flavobacterium niveum TAPW14T and Flavobacterium foetidum CJ42T with 96.17% and 97.29% 16S rRNA sequence similarities, respectively. Genomic analyses including the reconstruction of phylogenomic tree, average nucleotide identity, and digital DNA-DNA hybridization suggested that they were novel species of the genus Flavobacterium. Both strains contained menaquinone 6 (MK-6) as the primary respiratory quinone and phosphatidylethanolamine as a major polar lipid. The predominant fatty acids of both strains were iso-C15:0 and summed feature 3 ( C16:1 ω7c and/or C16: 1 ω6c). Based on the polyphasic taxonomic study, strains CJ74T and CJ75T represent novel species of the genus Flavobacterium, for which names Flavobacterium psychrotrophum sp. nov. and Flavobacterium panacagri sp. nov. are proposed, respectively. The type strains are CJ74T (=KACC 19819T =JCM 32889T) and CJ75T (=KACC 23149T =JCM 36132T).

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Reviews

[Minireview]Biodegradation of plastics: mining of plastic-degrading microorganisms and enzymes using metagenomics approaches: Dae-Wi Kim , Jae-Hyung Ahn , Chang-Jun Cha; J. Microbiol. 2022;60(10):969-976. Published online September 27, 2022; DOI: https://doi.org/10.1007/s12275-022-2313-7

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Abstract PDF

Plastic pollution exacerbated by the excessive use of synthetic plastics and its recalcitrance has been recognized among the most pressing global threats. Microbial degradation of plastics has gained attention as a possible eco-friendly countermeasure, as several studies have shown microbial metabolic capabilities as potential degraders of various synthetic plastics. However, still defined biochemical mechanisms of biodegradation for the most plastics remain elusive, because the widely used culture-dependent approach can access only a very limited amount of the metabolic potential in each microbiome. A culture-independent approach, including metagenomics, is becoming increasingly important in the mining of novel plastic-degrading enzymes, considering its more expanded coverage on the microbial metabolism in microbiomes. Here, we described the advantages and drawbacks associated with four different metagenomics approaches (microbial community analysis, functional metagenomics, targeted gene sequencing, and whole metagenome sequencing) for the mining of plastic-degrading microorganisms and enzymes from the plastisphere. Among these approaches, whole metagenome sequencing has been recognized among the most powerful tools that allow researchers access to the entire metabolic potential of a microbiome. Accordingly, we suggest strategies that will help to identify plastisphere-enriched sequences as de novo plastic-degrading enzymes using the whole metagenome sequencing approach. We anticipate that new strategies for metagenomics approaches will continue to be developed and facilitate to identify novel plastic-degrading microorganisms and enzymes from microbiomes.

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Overview of bioinformatic methods for analysis of antibiotic resistome from genome and metagenome data: Kihyun Lee , Dae-Wi Kim , Chang-Jun Cha; J. Microbiol. 2021;59(3):270-280. Published online February 23, 2021; DOI: https://doi.org/10.1007/s12275-021-0652-4

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Abstract PDF

Whole genome and metagenome sequencing are powerful approaches that enable comprehensive cataloging and profiling of antibiotic resistance genes at scales ranging from a single clinical isolate to ecosystems. Recent studies deal with genomic and metagenomic data sets at larger scales; therefore, designing computational workflows that provide high efficiency and accuracy is becoming more important. In this review, we summarize the computational workflows used in the research field of antibiotic resistome based on genome or metagenome sequencing. We introduce workflows, software tools, and data resources that have been successfully employed in this rapidly developing field. The workflow described in this review can be used to list the known antibiotic resistance genes from genomes and metagenomes, quantitatively profile them, and investigate the epidemiological and evolutionary contexts behind their emergence and transmission. We also discuss how novel antibiotic resistance genes can be discovered and how the association between the resistome and mobilome can be explored.

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Journal Article

Comparative genomic analysis of pyrene-degrading Mycobacterium species: Genomic islands and ring-hydroxylating dioxygenases involved in pyrene degradation: Dae-Wi Kim , Kihyun Lee , Do-Hoon Lee , Chang-Jun Cha; J. Microbiol. 2018;56(11):798-804. Published online October 24, 2018; DOI: https://doi.org/10.1007/s12275-018-8372-0

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Abstract PDF

The genome sequences of two pyrene-degrading bacterial strains of Mycobacterium spp. PYR10 and PYR15, isolated from the estuarine wetland of the Han river, South Korea, were determined using the PacBio RS II sequencing platform. The complete genome of strain PYR15 was 6,037,017 bp in length with a GC content of 66.5%, and contained 5,933 protein- coding genes. The genome of strain PYR10 was 5,999,427 bp in length with a GC content of 67.7%, and contained 5,767 protein-coding genes. Based on the average nucleotide identity values, these strains were designated as M. gilvum PYR10 and M. pallens PYR15. A genomic comparison of these pyrene-degrading Mycobacterium strains with pyrene- non-degrading strains revealed that the genomes of pyrene-degrading strains possessed similar repertoires of ringhydroxylating dioxygenases (RHDs), including the pyrenehydroxylating dioxygenases encoded by nidA and nidA3, which could be readily distinguished from those of pyrenenon- degraders. Furthermore, genomic islands, containing catabolic gene clusters, were shared only among the pyrenedegrading Mycobacterium strains and these gene clusters contained RHD genes, including nidAB and nidA3B3. Our genome data should facilitate further studies on the evolution of the polycyclic aromatic hydrocarbon-degradation pathways in the genus Mycobacterium.

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Identification and Functional Analysis of a Gene Encoding β-Glucosidase from the Brown-Rot Basidiomycete Fomitopsis palustris: Hwang-Woo Ji , Chang-Jun Cha; J. Microbiol. 2010;48(6):808-813. Published online January 9, 2011; DOI: https://doi.org/10.1007/s12275-010-0482-2

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Abstract PDF: The brown-rot basidiomycete Fomitopsis palustris is known to degrade crystalline cellulose (Avicel) and produce three major cellulases, exoglucanases, endoglucanases, and β-glucosidases. A novel β-glucosidase designated as Cel3A was identified from F. palustris grown at the expense of Avicel. The deduced amino acid sequence of Cel3A showed high homology with those of other fungal β-glucosidases that belong to glycosyl hydrolase (GH) family 3. The sequence analysis also indicated that Cel3A contains the N- and C-terminal domains of GH family 3 and Asp-209 was conserved as a catalytic nucleophile. The cloned gene was successfully expressed in the yeast Pichia pastoris and the recombinant protein exhibited β-glucosidase activity with cellobiose and some degree of thermostability. Considering the size and sequence of the protein, the β-glucosidase identified in this study is different from the protein purified directly from F. palustris in the previous study. Our results suggest that the fungus possesses at least two β-glucosidase genes.

Functional Analysis of the Invariant Residue G791 of Escherichia coli 16S rRNA: Woo-Seok Song , Hong-Man Kim , Jae-Hong Kim , Se-Hoon Sim , Sang-Mi Ryou , Sanggoo Kim , Chang-Jun Cha , Philip R. Cunningham , Jeehyeon Bae , Kangseok Lee; J. Microbiol. 2007;45(5):418-421.; DOI: https://doi.org/2595 [pii]

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Abstract PDF: The nucleotide at position 791(G791) of E. coli 16S rRNA was previously identified as an invariant residue for ribosomal function. In order to characterize the functional role of G791, base substitutions were introduced at this position, and mutant ribosomes were analyzed with regard to their protein synthesis ability, via the use of a specialized ribosome system. These ribosomal RNA mutations attenuated the ability of ribosomes to conduct protein synthesis by more than 65%. A transition mutation (G to A) exerted a moderate effect on ribosomal function, whereas a transversion mutation (G to C or U) resulted in a loss of protein synthesis ability of more than 90%. The sucrose gradient profiles of ribosomes and primer extension analysis showed that the loss of protein-synthesis ability of mutant ribosomes harboring a base substitution from G to U at position 791 stems partially from its inability to form 70S ribosomes. These findings show the involvement of the nucleotide at position 791 in the association of ribosomal subunits and protein synthesis steps after 70S formation, as well as the possibility of using 16S rRNA mutated at position 791 for the selection of second-site revertants in order to identify ligands that interact with G791 in protein synthesis.

Identification of Genes for Mycothiol Biosynthesis in Streptomyces coelicolor A3(2): Joo-Hong Park , Chang-Jun Cha , Jung-Hye Roe; J. Microbiol. 2006;44(1):121-125.; DOI: https://doi.org/2327 [pii]

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Abstract PDF: Mycothiol is a low molecular weight thiol compound produced by a number of actinomycetes, and has been suggested to serve both anti-oxidative and detoxifying roles. To investigate the metabolism and the role of mycothiol in Streptomyces coelicolor, the biosynthetic genes (mshA, B, C, and D) were predicted based on sequence homology with the mycobacterial genes and confirmed experimentally. Disruption of the mshA, C, and D genes by PCR targeting mutagenesis resulted in no synthesis of mycothiol, whereas the mshB mutation reduced its level to about 10% of the wild type. The results indicate that the mshA, C, and D genes encode non-redundant biosynthetic enzymes, whereas the enzymatic activity of MshB (acetylase) is shared by at least one other gene product, most likely the mca gene product (amidase).

Purification and Characterization of Thermostable β-Glucosidase from the Brown-Rot Basidiomycete Fomitopsis palustris Grown on Microcrystalline Cellulose: Jeong-Jun Yoon , Ki-Yeon Kim , Chang-Jun Cha; J. Microbiol. 2008;46(1):51-55.; DOI: https://doi.org/10.1007/s12275-007-0230-4

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Abstract PDF

An extracellular β-glucosidase was purified 154-fold to electrophoretic homogeneity from the brown-rot basidiomycete Fomitopsis palustris grown on 2.0% microcrystalline cellulose. SDS-polyacrylamide gel electrophoresis gel gave a single protein band and the molecular mass of purified enzyme was estimated to be approximately 138 kDa. The amino acid sequences of the proteolytic fragments determined by nano-LC- MS/MS suggested that the protein has high homology with fungal β-glucosidases that belong to glycosyl hydrolase family 3. The Kms for p-nitorophenyl-β-D-glucoside (p-NPG) and cellobiose hydrolyses were 0.117 and 4.81 mM, and the Kcat values were 721 and 101.8 per sec, respectively. The enzyme was competitively inhibited by both glucose (Ki= 0.35 mM) and gluconolactone (Ki= 0.008 mM), when p-NPG was used as substrate. The optimal activity of the purified β-glucosidase was observed at pH 4.5 and 70°C. The F. palustris protein exhibited half-lives of 97 h at 55°C and 15 h at 65°C, indicating some degree of thermostability. The enzyme has high activity against p-NPG and cellobiose but has very little or no activity against p-nitrophenyl-β-lactoside, p-nitrophenyl-β-xyloside, p-nitrophenyl-α-arabinofuranoside, xylan, and carboxymethyl cellulose. Thus, our results revealed that the β-glucosidase from F. palustris can be classified as an aryl-β-glucosidase with cellobiase activity.

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