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Tae-Kwang Oh

Publications and source records attributed to Tae-Kwang Oh.

85 records · Page 5Linked to original sources
PubMed2004

Transfer of Bacillus halodenitrificans Denariaz et al. 1989 to the genus Virgibacillus as Virgibacillus halodenitrificans comb. nov.

A Gram-variable, endospore-forming moderately halophilic rod, strain SF-121, was isolated from a marine solar saltern of the Yellow Sea in Korea. The result of 16S rRNA gene sequence analysis showed that strain SF-121 has highest sequence similarity (99.7 %) with the type strain of Bacillus halodenitrificans. Phylogenetic analyses based on 16S rRNA gene sequences revealed that B. halodenitrificans DSM 10037(T) and strain SF-121 are more closely related to the genus Virgibacillus than to the genus Bacillus. Strain SF-121 and B. halodenitrificans DSM 10037(T) exhibited 16S rRNA gene similarity levels of 95.3-97.5 % with the type strains of Virgibacillus species and 94.0 % with the type strain of Bacillus subtilis. DNA-DNA relatedness and phenotypic data indicated that B. halodenitrificans DSM 10037(T) and strain SF-121 are members of the same species. B. halodenitrificans DSM 10037(T) and strain SF-121 exhibited DNA-DNA relatedness values of 9-11 % with the type strains of Virgibacillus carmonensis and Virgibacillus marismortui. On the basis of the phenotypic, chemotaxonomic, phylogenetic and genetic data, B. halodenitrificans should be reclassified in the genus Virgibacillus as Virgibacillus halodenitrificans comb. nov.

Bacillaceae↗
PubMed2004

Shewanella marisflavi sp. nov. and Shewanella aquimarina sp. nov., slightly halophilic organisms isolated from sea water of the Yellow Sea in Korea.

Two Gram-negative, motile, non-spore-forming, rod-shaped organisms, strains SW-117(T) and SW-120(T), were isolated from sea water of the Yellow Sea in Korea and subjected to a polyphasic taxonomic study. Strains SW-117(T) and SW-120(T) simultaneously contained both menaquinones (MK) and ubiquinones (Q) as isoprenoid quinones; the predominant menaquinone was MK-7 and the predominant ubiquinones were Q-7 and Q-8. The major fatty acid detected in the two strains was iso-C(15 : 0). The DNA G+C content of strains SW-117(T) and SW-120(T) was 51 and 54 mol%, respectively. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains SW-117(T) and SW-120(T) fall within the radiation of the cluster comprising Shewanella species. Strains SW-117(T) and SW-120(T) showed a 16S rRNA gene sequence similarity of 97.4 % and a DNA-DNA relatedness level of 10.1 %. Strains SW-117(T) and SW-120(T) exhibited 16S rRNA gene sequence similarity levels of 93.8-98.5 % and 92.4-97.0 %, respectively, to Shewanella species. Strain SW-117(T) exhibited DNA-DNA relatedness levels of 8.3-20.3 % to the type strains of six phylogenetically related Shewanella species. On the basis of phenotypic, phylogenetic and genetic data, strains SW-117(T) and SW-120(T) were classified in the genus Shewanella as two distinct novel species, for which the names Shewanella marisflavi sp. nov. (type strain, SW-117(T)=KCCM 41822(T)=JCM 12192(T)) and Shewanella aquimarina sp. nov. (type strain, SW-120(T)=KCCM 41821(T)=JCM 12193(T)) are proposed, respectively.

Bacterial Typing Techniques↗
PubMed2004

Porphyrobacter donghaensis sp. nov., isolated from sea water of the East Sea in Korea.

Two Gram-negative, motile, non-spore-forming, bacteriochlorophyll a-containing slightly halophilic strains, SW-132(T) and SW-158, were isolated from sea water of the East Sea in Korea, and subjected to a polyphasic taxonomic study. The two isolates were characterized chemotaxonomically as having Q-10 as the predominant respiratory lipoquinone and major amounts of unsaturated fatty acids C(18 : 1)omega7c and C(17 : 1)omega6c. The DNA G+C contents of the two strains were in the range 66.8-65.9 mol%. The 16S rRNA gene sequences of strains SW-132(T) and SW-158 were 99.9 % (1 nt difference) similar and their mean level of DNA-DNA relatedness was 86 %. The 16S rRNA gene sequence analysis showed that strains SW-132(T) and SW-158 are phylogenetically closely related to Porphyrobacter species and Erythromicrobium ramosum. Similarities between the 16S rRNA gene sequences of strains SW-132(T) and SW-158 and the type strains of Porphyrobacter species and E. ramosum ranged from 97.8 to 99.0 %. DNA-DNA relatedness data indicated that strains SW-132(T) and SW-158 are members of a genomic species that is separate from the four Porphyrobacter species. On the basis of phenotypic and phylogenetic data and genetic distinctiveness, strains SW-132(T) (=KCTC 12229(T)=DSM 16220(T)) and SW-158 (=KCTC 12230) are classified as a novel Porphyrobacter species, for which the name Porphyrobacter donghaensis sp. nov. is proposed.

Bacterial Typing Techniques↗
PubMed2003

Halobacillus locisalis sp. nov., a halophilic bacterium isolated from a marine solar saltern of the Yellow Sea in Korea.

A Gram-positive, motile, endospore-forming and rod-shaped halophilic bacterial strain MSS-155 (KCTC 3788 and KCCM 41687) was isolated from a marine solar saltern of the Yellow Sea in Korea and was subjected to a polyphasic taxonomic study. This organism grew at temperature of 10.0-42.0 degrees C with an optimum of 35 degrees C. Strain MSS-155 grew optimally in the presence of 10% NaCl and did not grow in the absence of NaCl. The cell wall peptidoglycan type of strain MSS-155 was A4beta based on l-Orn- d-Asp. Strain MSS-155 was also characterized chemotaxonomically by having menaquinone-7 (MK-7) as the predominant isoprenoid quinone and anteiso-C15:0 as the major fatty acid. The DNA G + C content was 44.0 mol%. Phylogenetic analysis based on 16S rDNA sequences showed that strain MSS-155 falls within the radiation of the cluster comprising Halobacillus species. Levels of 16S rDNA sequence similarity between strain MSS-155 and the type strains of four Halobacillus species were in the range 97.6-98.8%. Strain MSS-155 exhibited levels of DNA-DNA relatedness of 6.2-11.2% to the type strains of Halobacillus species described previously. On the basis of phenotypic properties, phylogeny, and genomic data, strain MSS-155 should be placed in the genus Halobacillus as a member of a novel species, for which we propose the name Halobacillus locisalis sp. nov.

Bacillaceae↗
PubMed2003

Bacillus marisflavi sp. nov. and Bacillus aquimaris sp. nov., isolated from sea water of a tidal flat of the Yellow Sea in Korea.

Two Gram-positive or Gram-variable, endospore-forming, moderately halophilic rods (strains TF-11(T) and TF-12(T)) were isolated from a tidal flat of the Yellow Sea in Korea and were subjected to a polyphasic taxonomic study. Strains TF-11(T) and TF-12(T) had cell-wall peptidoglycan based on meso-diaminopimelic acid. The predominant menaquinone found in the two strains was MK-7. The cellular fatty acid profiles of both strains contained large amounts of branched and saturated fatty acids. The major fatty acids were anteiso-C(15 : 0) and iso-C(15 : 0). The DNA G+C contents of strains TF-11(T) and TF-12(T) were respectively 49 and 38 mol%. Phylogenetic analysis based on 16S rDNA sequences showed that strains TF-11(T) and TF-12(T) fell within the radiation of the cluster comprising Bacillus species. The level of 16S rDNA sequence similarity between strains TF-11(T) and TF-12(T) was 98.3 %. Strains TF-11(T) and TF-12(T) exhibited levels of 16S rDNA sequence similarity of less than 96.0 and 96.3 %, respectively, to Bacillus species. The mean level of DNA-DNA relatedness between the two strains was approximately 7 %. On the basis of phenotypic and phylogenetic data and genomic distinctiveness, strains TF-11(T) and TF-12(T) should be placed in the genus Bacillus as two distinct novel species, for which the names Bacillus marisflavi sp. nov. (type strain TF-11(T)=KCCM 41588(T)=JCM 11544(T)) and Bacillus aquimaris sp. nov. (type strain TF-12(T)=KCCM 41589(T)=JCM 11545(T)) are proposed.

Bacillus↗
PubMed2003

Transfer of Pseudomonas elongata Humm 1946 to the genus Microbulbifer as Microbulbifer elongatus comb. nov.

Phylogenetic analysis based on 16S rDNA sequences revealed that Pseudomonas elongata Humm 1946 is more closely related to the genus Microbulbifer than to authentic pseudomonads. The type strain of P. elongata (DSM 6810(T)) exhibited 16S rDNA similarity levels of 97.5 and 98.2 % to the type strains of Microbulbifer hydrolyticus and Microbulbifer salipaludis, respectively, but of less than approximately 92 % to Pseudomonas species with known 16S rDNA sequences. Respiratory lipoquinone and cellular fatty acid analyses showed that the type strain of P. elongata has characteristics similar to those of the genus Microbulbifer, not those of the genus Pseudomonas. P. elongata DSM 6810(T) contained ubiquinone-8 as the predominant respiratory lipoquinone and iso-C(15 : 0) as the major fatty acid. DNA-DNA relatedness data indicate that P. elongata is a species distinct from M. hydrolyticus and M. salipaludis. Therefore, on the basis of these data, P. elongata Humm 1946 should be transferred to the genus Microbulbifer as Microbulbifer elongatus comb. nov.

Alteromonadaceae↗
PubMed2003

Alteromonas marina sp. nov., isolated from sea water of the East Sea in Korea.

Two Gram-negative, motile, non-spore-forming and moderately halophilic rods (strains SW-47(T) and SW-49) were isolated from sea water of the East Sea in Korea and subjected to a polyphasic taxonomic study. The two strains grew optimally between 30 and 37 degrees C, and grew at 4 and 44 degrees C but not at temperatures above 45 degrees C. They grew optimally in the presence of 2-5 % (w/v) NaCl, but did not grow in the absence of NaCl. Strains SW-47(T) and SW-49 had ubiquinone-8 (Q-8) as the predominant respiratory lipoquinone and C(16 : 1) omega7c and/or iso-C(15 : 0) 2OH, C(16 : 0) and C(18 : 1) omega7c as the major fatty acids, which are consistent with the corresponding data for Alteromonas macleodii. The DNA G+C contents of strains SW-47(T) and SW-49 were 45 and 44 mol%, respectively. Strains SW-47(T) and SW-49 showed a high level of 16S rDNA sequence similarity (99.9 %) and a mean level of DNA-DNA relatedness of 96.5 %. Phylogenetic analyses based on 16S rDNA sequences showed that the two strains form a coherent cluster with A. macleodii. Strains SW-47(T) and SW-49 exhibited levels of 16S rDNA sequence similarity of 99.3 and 99.1 %, respectively, with A. macleodii DSM 6062(T) and of less than 89.4 % with other species used in the phylogenetic analyses. Alteromonas fuliginea CIP 105339(T) was found to be more closely related to the genus Pseudoalteromonas than to the genus ALTEROMONAS: On the basis of phenotypic properties and phylogenetic and genomic data, strains SW-47(T) and SW-49 represent a new species of the genus Alteromonas, for which the name Alteromonas marina (type strain SW-47(T)=KCCM 41638(T)=JCM 11804(T)) is proposed.

Alteromonas↗
PubMed2003

Planococcus maritimus sp. nov., isolated from sea water of a tidal flat in Korea.

Two Gram-positive, motile cocci, strains TF-9(T) and TF-16, were isolated from sea water of a tidal flat in Korea. Phylogenetic analysis based on 16S rDNA sequences showed that the strains fall within the radiation of the cluster comprising Planococcus citreus and Planococcus kocurii, and this cluster joined the clade comprising Planomicrobium species and Planococcus alkanoclasticus and Planococcus psychrophilus with a high bootstrap resampling value. Strains TF-9(T) and TF-16 contained MK-8, MK-7 and MK-6 as the predominant menaquinones. The major fatty acid was anteiso-C(15 : 0). The DNA G+C contents of strains TF-9(T) and TF-16 were respectively 48 and 49 mol%. The level of 16S rDNA identity between strains TF-9(T) and TF-16 was 98.9 %. Strain TF-9(T) and TF-16 respectively exhibited levels of 16S rDNA identity of 97.2-98.4 and 96.9-99.5 % to the type strains of Planococcus kocurii, Planococcus citreus and Planococcus antarcticus. The mean level of DNA-DNA relatedness between strains TF-9(T) and TF-16 was 36.7 %. Strains TF-9(T) and TF-16 respectively exhibited levels of DNA-DNA relatedness of 7.1-43.4 and 3.5-80.9 % to Planococcus citreus DSM 20549(T), Planococcus kocurii DSM 20747(T) and Planococcus antarcticus DSM 14505(T). On the basis of the phenotypic, phylogenetic and genomic data, strain TF-9(T) (=KCCM 41587(T)=JCM 11543(T)) should be placed as a novel species of the genus Planococcus, for which the name Planococcus maritimus sp. nov. is proposed, and strain TF-16 should be classified as a member of Planococcus citreus.

DNA, Bacterial↗
PubMed2003

AhlD, an N-acylhomoserine lactonase in Arthrobacter sp., and predicted homologues in other bacteria.

Quorum sensing is a signalling mechanism that controls diverse biological functions, including virulence, via N-acylhomoserine lactone (AHL) signal molecules in Gram-negative bacteria. With the aim of isolating strains or enzymes capable of blocking quorum sensing by inactivating AHL, bacteria were screened for AHL degradation by their ability to utilize N-3-oxohexanoyl-L-homoserine lactone (OHHL) as the sole carbon source. Among four isolates, strain IBN110, identified as Arthrobacter sp., was found to grow rapidly on OHHL, and to degrade various AHLs with different lengths and acyl side-chain substitutions. Co-culture of Arthrobacter sp. IBN110 and the plant pathogen Erwinia carotovora significantly reduced both the AHL amount and pectate lyase activity in co-culture medium, suggesting the possibility of applying Arthrobacter sp. IBN110 in the control of AHL-producing pathogenic bacteria. The ahlD gene from Arthrobacter sp. IBN110 encoding the enzyme catalysing AHL degradation was cloned, and found to encode a protein of 273 amino acids. A mass spectrometry analysis showed that AhlD probably hydrolyses the lactone ring of N-3-hexanoyl-L-homoserine lactone, indicating that AhlD is an N-acylhomoserine lactonase (AHLase). A comparison of AhlD with other known AHL-degrading enzymes, Bacillus sp. 240B1 AiiA, a Bacillus thuringiensis subsp. kyushuensis AiiA homologue and Agrobacterium tumefaciens AttM, revealed 25, 26 and 21 % overall identities, respectively, in the deduced amino acid sequences. Although these identities were relatively low, the HXDH approximately H approximately D motif was conserved in all the AHLases, suggesting that this motif is essential for AHLase activity. From a genome database search based on the conserved motif, putative AhlD-like lactonase genes were found in several other bacteria, and AHL-degrading activities were observed in Klebsiella pneumoniae and Bacillus stearothermophilus. Furthermore, it was verified that ahlK, an ahlD homologue, encodes an AHL-degrading enzyme in K. pneumoniae. Accordingly, the current results suggest the possibility that AhlD-like AHLases could exist in many other micro-organisms.

Agrobacterium tumefaciens↗
PubMed2002

Novel zinc-binding center and a temperature switch in the Bacillus stearothermophilus L1 lipase.

The bacterial thermoalkalophilic lipases optimally hydrolyze saturated fatty acids at elevated temperatures. They also have significant sequence homology with staphylococcal lipases, and both the thermoalkalophilic and staphylococcal lipases are grouped as the lipase family I.5. We report here the first crystal structure of the lipase family I.5, the structure of a thermoalkalophilic lipase from Bacillus stearothermophilus L1 (L1 lipase) determined at 2.0-A resolution. The structure is in a closed conformation, and the active site is buried under a long lid helix. Unexpectedly, the structure exhibits a zinc-binding site in an extra domain that accounts for the larger molecular size of the family I.5 enzymes in comparison to other microbial lipases. The zinc-coordinated extra domain makes tight interactions with the loop extended from the C terminus of the lid helix, suggesting that the activation of the family I.5 lipases may be regulated by the strength of the interactions. The unusually long lid helix makes strong hydrophobic interactions with its neighbors. The structural information together with previous biochemical observations indicate that the temperature-mediated lid opening is triggered by the thermal dissociation of the hydrophobic interactions.

Amino Acid Sequence↗
PubMed1998

Specific probiotic characterization of Weissella hellenica DS-12 isolated from flounder intestine.

A total of 199 microorganisms were isolated from the intestinal contents of flounder (Paralichthys olivaceus) in a fish farm in Seoul, Korea. Among these strains, DS-12 was selected as a candidate for flounder probiotics because of its excellent exhibition of antimicrobial activity against fish pathogens such as edwardsiella, pasteurella, aeromonas, and vibrio, and initiate growth in 10% NaCl, 10% bile, and in broth at pH 3 for 90 min. This strain was Gram-positive, and catalase-negative coccoid rods that produced gas from glucose and formed more than 90% of lactate as the D(-) isomer. This organism is positioned at a cluster in the genus Weissella on the phylogenetic tree based on 16S rRNA sequences, which were assigned to Weissella hellenica on the basis of DNA-DNA relatedness. However, the type strain of W. hellenica JCM 10103(T) had no antibacterial activity against the fish pathogenic bacteria and was found to be quite different from the DS-12 strain in some sugar fermentation patterns of alpha-methyl-D-glucoside, esculine, cellobiose, melibiose, D-raffinose, and D-turanose, being especially unable to grow at 15 and 35 degrees C in 7% NaCl and 10% bile. The results obtained in the present study demonstrated that the type strain of W. hellenica had no probiotic characteristics, but the strain DS-12 could be used as a specific probiotic for flounder.

Journal Article↗