• Korean Journal of Microbiology
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• v.55 no.2
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• pp.160-163
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• 2019

Senegalimassilia sp. KGMB 04484 was isolated from fecal samples obtained from a healthy Korean. The whole-genome sequence of Senegalimassilia sp. KGMB 04484 was analyzed using the PacBio Sequel platform. The genome comprises a 2,748,041 bp chromosome with a G+C content of 61.18%, 2,300 total genes, 2,139 protein-coding gene, 21 rRNA genes, and 51 tRNA genes. Also, we found that strain KGMB 04484 had some genes for hydrolysis enzyme, fatty acid biosynthesis and metabolism in its genome based on the result of genome analysis. Those genes of KGMB 04484 may be related to regulation of human health and digest.

• Korean Journal of Microbiology
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• v.54 no.4
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• pp.456-459
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• 2018

The genus of Olsenella has been isolated from vertebrate animal mouth, rumen, and feces. Olsenella sp. KGMB 04489 was isolated from fecal samples obtained from a healthy Korean. The whole-genome sequence of Olsenella sp. KGMB 04489 was analyzed using the PacBio Sequel platform. The genome comprises a 2,108,034 bp chromosome with a G + C content of 65.50%, 1,838 total genes, 13 rRNA genes, and 52 tRNA genes. Also, we found that strain KGMB 04489 had some genes for hydrolysis enzymes, and antibiotic biosynthesis and resistance in its genome based on the result of genome analysis.

• The Plant Pathology Journal
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• v.39 no.4
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• pp.409-416
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• 2023

Bacterial leaf blight of carrots caused by Xanthomonas hortorum pv. carotae (Xhc) is an important worldwide seed-borne disease. In 2012 and 2013, symptoms similar to bacterial leaf blight were found in carrot farms in Jeju Island, Korea. The phenotypic characteristics of the Korean isolation strains were similar to the type strain of Xhc. Pathogenicity showed symptoms on the 14th day after inoculation on carrot plants. Identification by genetic method was multi-position sequencing of the isolated strain JJ2001 was performed using four genes (danK, gyrB, fyuA, and rpoD). The isolated strain was confirmed to be most similar to Xhc M081. Furthermore, in order to analyze the genetic characteristics of the isolated strain, whole genome analysis was performed through the next-generation sequencing method. The draft genome size of JJ2001 is 5,443,372 bp, which contains 63.57% of G + C and has 4,547 open reading frames. Specifically, the classification of pathovar can be confirmed to be similar to that of the host lineage. Plant pathogenic factors and determinants of the majority of the secretion system are conserved in strain JJ2001. This genetic information enables detailed comparative analysis in the pathovar stage of pathogenic bacteria. Furthermore, these findings provide basic data for the distribution and diagnosis of Xanthomonas hortorum pv. carotae, a major plant pathogen that infects carrots in Korea.

• Korean Journal of Microbiology
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• v.55 no.3
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• pp.296-299
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• 2019

The genus of Bacteroides has been isolated from vertebrate animal feces. Bacteroides sp. KGMB 02408 was isolated from fecal samples obtained from a healthy Korean. The wholegenome sequence of Bacteroides sp. KGMB 02408 was analyzed using the PacBio Sequel platform. The genome comprises a 5,771,427 bp chromosome with a G + C content of 39.50%, 5,005 total genes, 18 rRNA genes, and 74 tRNA genes. Furthermore, we found that strain KGMB 02408 had some genes for oxidoreductases and menaquinone biosynthesis in its genome based on the result of genome analysis.

• Journal of Microbiology and Biotechnology
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• v.26 no.3
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• pp.488-492
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• 2016

Rhodococcus species have become increasingly important owing to their ability to degrade a wide range of toxic chemicals and produce bioactive compounds. Here, we report isolation of the Rhodococcus sp. KB6, which is a new leaf-inhabiting endophytic bacterium that suppresses black rot disease in sweet potato leaves. We determined the 7.0 Mb draft genome sequence of KB6 and have predicted 19 biosynthetic gene clusters for secondary metabolites, including heterobactins, which are a new class of siderophores. Notably, we showed the first internal colonization of host plants with Rhodococcus sp. KB6 and discuss its potential as a biocontrol agent for sustainable agriculture.

• Journal of Microbiology and Biotechnology
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• v.30 no.4
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• pp.505-514
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• 2020

The symbiotic nature of the relationship between algae and marine bacteria is well-studied among the complex microbial interactions. The mutual profit between algae and bacteria occurs via nutrient and vitamin exchange. It is necessary to analyze the genome sequence of a bacterium to predict its symbiotic relationships. In this study, the genome of a marine bacterium, Pseudoruegeria sp. M32A2M, isolated from the south-eastern isles (GeoJe-Do) of South Korea, was sequenced and analyzed. A draft genome (91 scaffolds) of 5.5 Mb with a DNA G+C content of 62.4% was obtained. In total, 5,101 features were identified from gene annotation, and 4,927 genes were assigned to functional proteins. We also identified transcription core proteins, RNA polymerase subunits, and sigma factors. In addition, full flagella-related gene clusters involving the flagellar body, motor, regulator, and other accessory compartments were detected even though the genus Pseudoruegeria is known to comprise non-motile bacteria. Examination of annotated KEGG pathways revealed that Pseudoruegeria sp. M32A2M has the metabolic pathways for all seven vitamin Bs, including thiamin (vitamin B1), biotin (vitamin B7), and cobalamin (vitamin B12), which are necessary for symbiosis with vitamin B auxotroph algae. We also identified gene clusters for seven secondary metabolites including ectoine, homoserine lactone, beta-lactone, terpene, lasso peptide, bacteriocin, and non-ribosomal proteins.

• Animal Bioscience
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• v.37 no.2_spc
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• pp.396-403
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• 2024

Objective: Monofluoroacetate (MFA) is a potent toxin that blocks ATP production via the Krebs cycle and causes acute toxicity in ruminants consuming MFA-containing plants. The rumen bacterium, Cloacibacillus porcorum strain MFA1 belongs to the phylum Synergistota and can produce fluoride and acetate from MFA as the end-products of dehalorespiration. The aim of this study was to identify the genomic basis for the metabolism of MFA by this bacterium. Methods: A draft genome sequence for C. porcorum strain MFA1 was assembled and quantitative transcriptomic analysis was performed thus highlighting a candidate operon encoding four proteins that are responsible for the carbon-fluorine bond cleavage. Comparative genome analysis of this operon was undertaken with three other species of closely related Synergistota bacteria. Results: Two of the genes in this operon are related to the substrate-binding components of the glycine reductase protein B (GrdB) complex. Glycine shares a similar structure to MFA suggesting a role for these proteins in binding MFA. The remaining two genes in the operon, an antiporter family protein and an oxidoreductase belonging to the radical S-adenosyl methionine superfamily, are hypothesised to transport and activate the GrdB-like protein respectively. Similar operons were identified in a small number of other Synergistota bacteria including type strains of Cloacibacillus porcorum, C. evryensis, and Pyramidobacter piscolens, suggesting lateral transfer of the operon as these genera belong to separate families. We confirmed that all three species can degrade MFA, however, substrate degradation in P. piscolens was notably reduced compared to Cloacibacillus isolates possibly reflecting the loss of the oxidoreductase and antiporter in the P. piscolens operon. Conclusion: Identification of this unusual anaerobic fluoroacetate metabolism extends the known substrates for dehalorespiration and indicates the potential for substrate plasticity in amino acid-reducing enzymes to include xenobiotics.

• Korean Journal of Microbiology
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• v.55 no.3
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• pp.274-277
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• 2019

Ruminococcus sp. KGMB03662 was isolated from fecal samples obtained from a healthy Korean. The whole-genome sequence of Ruminococcus sp. KGMB03662 was analyzed using the PacBio Sequel platform. The genome comprises a 2,707,502 bp chromosome with a G + C content of 43.09%, 2,484 total genes, 2,367 protein-coding gene, 14 rRNA genes, and 53 tRNA genes. In the draft genome, genes involved in the hydrolysis enzyme, fatty acid biosynthesis, fatty acid metabolite, antibiotic biosynthesis, and antibiotic resistance have been identified. Those genes of KGMB03662 may be related to the regulation of human health and disease.

• Research in Plant Disease
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• v.21 no.2
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• pp.74-81
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• 2015

The specific and sensitive nested-PCR method to detect Acidovorax citrulli, a causal agent of bacterial fruit blotch on cucurbitaceae, was developed. PCR primers were designed from the draft genome sequence which was obtained with the Next Generation Sequencing of A. citrulli KACC10651, and the nested-PCR primer set (Ac-ORF 21F/Ac-ORF 21R) were selected by checking of specificity to A. citrulli with PCR assays. The selected nested-PCR primer amplified the 140 bp DNA only from A. citrulli strains, and detection sensitivity of the nested PCR increased 10,000 times of $1^{st}$ PCR detection limit (10 ng genomic DNA/PCR). The nested PCR detected A. citrulli from the all samples of seed surface wash (external seed detection) of the artificially inoculated watermelon seeds with $10^1cfu/ml$ and above population of A. citrulli while the nested PCR could not detected A. citrulli from the mashed seed suspension (internal seed detection) of the all artificially inoculated watermelon seeds. When the naturally infested watermelon seeds (10% seed infested rate with grow-out test) used, the nested PCR detected A. citrulli from 2 seed samples out of 10 replication samples externally and 5 seed samples out of 10 replication samples internally. We believe that the nested-PCR developed in this study will be useful method to detect A. citrulli from the Cucurbitaceae seeds.

• Journal of Microbiology and Biotechnology
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• v.28 no.5
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• pp.776-783
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• 2018

The agarase gene gaa16a was identified from a draft genome sequence of Gilvimarinus agarilyticus JEA5, an agar-utilizing marine bacterium. Recently, three agarase-producing bacteria, G. chinensis, G. polysaccharolyticus, and G. agarilyticus, in the genus Gilvimarinus were reported. However, there have been no reports of the molecular characteristics and biochemical properties of these agarases. In this study, we analyzed the molecular characteristics and biochemical properties of agarases in Gilvimarinus. Gaa16A comprised a 1,323-bp open reading frame encoding 441 amino acids. The predicted molecular mass and isoelectric point were 49 kDa and 4.9, respectively. The amino acid sequence of Gaa16A showed features typical of glycosyl hydrolase family 16 (GH16) ${\beta}$-agarases, including a GH16 domain, carbohydrate-binding region (RICIN domain), and signal peptide. Recombinant Gaa16A (excluding the signal peptide and carbohydrate-binding region, rGaa16A) was expressed as a fused protein with maltose-binding protein at its N-terminus in Escherichia coli. rGaa16A had maximum activity at $55^{\circ}C$ and pH 7.0 and 103 U/mg of specific activity in the presence of 2.5 mM $CaCl_2$. The enzyme hydrolyzed agarose to yield neoagarotetraose as the main product. This enzyme may be useful for industrial production of functional neoagaro-oligosaccharides.