Publications by authors named "In Seop Kim"

28 Publications

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Rouxiella aceris sp. nov., isolated from tree sap and the emended description of the genus Rouxiella.

Antonie Van Leeuwenhoek 2021 Apr 11. Epub 2021 Apr 11.

Department of Biological Sciences and Biotechnology, Hannam University, Daejon, 34054, Republic of Korea.

Polyphasic taxonomic studies were performed for the seven strains, which were isolated from sap extracted from Acer pictum in Mt. Halla in Jeju, Republic of Korea. Cells of all the isolates were Gram-reaction-negative, facultatively anaerobic, short rods and contained the major isoprenoid quinone of Q-8, the predominant fatty acids of C and C cyclo and the major polar lipids including phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospholipid. The G + C contents of the genomic DNAs were 50.6-51.3%.The 16S rRNA gene-based phylogeny exhibited that the seven isolates formed two distinct sublines within the family Yersiniaceae. In the 92 core gene analysis, strain SAP-1 formed a subline at the base of radiation of the genus Rouxiella and its assignment to the genus Rouxiella was supported by high amino acid identity values (82.0-83.4%), albeit with sharing low 16S rRNA gene identities (96.0-96.9%). The average nucleotide identity and digital DNA-DNA hybridisation values together with phenotypic differences showed that strains SAP-1, SAP-7, SAP-8 and SAP-13 belonged to a new species of the genus Rouxiella, while strains SAP-2, SAP-3 and SAP-27 were strains of Rouxiella silvae. On the basis of data obtained here, Rouxiella aceris sp. nov. (type strain, SAP-1 = KCTC 72599 = CCM 9078) is proposed, with the emended description of the genus Rouxiella.
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http://dx.doi.org/10.1007/s10482-021-01572-0DOI Listing
April 2021

Duganella aceris sp. nov., isolated from tree sap and proposal to transfer of Rugamonas aquatica and Rugamonas rivuli to the genus Duganella as Duganella aquatica comb. nov., with the emended description of the genus Rugamonas.

Arch Microbiol 2021 Mar 22. Epub 2021 Mar 22.

Institute of Jeju Microbial Resources, BioPS Co., Ltd., Cheju, 63243, Republic of Korea.

A Gram-reaction-negative, strictly aerobic, betaproteobacterial strain, designated SAP-35, was isolated from sap extracted from Acer pictum in Mt. Halla in Jeju, Republic of Korea, and its taxonomic status was examined by a polyphasic approach. Cells of the organism were non-sporulating, motile rods and grew at 4-30 °C, pH 6-7 and in the absence of NaCl. 16S rRNA gene- and whole genome-based phylogenetic analyses showed that strain SAP-35 belonged to the family Oxalobacteraceae and was closely related to Rugamonas rivuli (98.9% 16S rRNA gene sequence similarity) and Rugamonas aquatica (98.4%). The phylogenomic clustering and average amino acid identity values supported that strain SAP-35 belonged to the genus Duganella and two Rugamonas species should be transferred to the genus Duganella. The major isoprenoid quinone of the isolate was Q-8. The major polar lipids were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospholipid. The predominant fatty acids were summed feature 3, C and C cyclo. The G + C content of genome was 64.9%. The average nucleotide identity and dDDH values between strain SAP-35 and the members of the genera Rugamonas and Duganella were < 85.1% and < 49%, respectively. Based on the combined data presented here, strain SAP-35 (= KCTC 72227 = NBRC 113903) represents a novel species of the genus Duganella, for which the name Duganella aceris sp. nov. is proposed. Also, Rugamonas aquatica Lu et al. (Int J Syst Evol Microbiol 70: 3328-3334, 2020) and Rugamonas aquatica Lu et al. 2020 are reclassified as Duganella aquatica comb. nov., with the emended description of the genus Rugamonas.
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http://dx.doi.org/10.1007/s00203-021-02191-zDOI Listing
March 2021

gen. nov., sp. nov., a new member of the family isolated from sap drawn from .

Int J Syst Evol Microbiol 2019 Jun 2;71(3). Epub 2021 Feb 2.

Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea.

A Gram-negative, facultatively anaerobic bacterium, designated SAP-6, was isolated from sap extracted from in Mt. Halla in Jeju, Republic of Korea and its precise taxonomic status was determined by a polyphasic approach. Cells were non-sporulating, motile, short rods and showed growth at 4-37 °C, pH 6.0-8.0 and 0-4% NaCl. Phylogenomic analysis based on 92 core gene sequences showed that strain SAP-6 belonged to the family and formed a distinct clade between members of the genera and with gene support index of 89. The closest phylogenetic neighbours were DSM 19580 (97.3% 16S rRNA gene sequence similarity) and HS1 (96.8%), with the average amino acid identity values of 75.3% and 74.0%, respectively. The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospholipid. The major isoprenoid quinones were Q-7 and Q-8. The predominant fatty acids were C, C cyclo and summed feature 3. The DNA G+C content was 57.0%. On the basis of data presented here, strain SAP-6 (=KCTC 52622=DSM 104038) represents a novel species of a new genus in the family , for which the name gen. nov., sp. nov. is proposed.
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http://dx.doi.org/10.1099/ijsem.0.004674DOI Listing
June 2019

Hongsoonwoonella zoysiae gen. nov., sp. nov., a new member of the family Stappiaceae isolated from a tidal mudflat.

Arch Microbiol 2021 May 2;203(4):1335-1343. Epub 2021 Jan 2.

Department of Biological Sciences and Biotechnology, Hannam University, Daejon, 34054, Republic of Korea.

A Gram stain-negative bacterial strain, designated SY4-7, was isolated from rhizosphere mudflat of a halophyte (Zoysia sinica) collected around Seonyu Island, Republic of Korea. Cells of the organism were strictly aerobic, non-sporulating, non-motile rods and grew at 20-42 °C, pH 6-8 and 1-6% (w/v) NaCl. The 16S rRNA gene-based phylogenetic analyses revealed that strain SY4-7 formed an independent cluster separated from the recognized genera of the family Stappiaceae, which was also supported by phylogenomic analysis-based 92-core gene sequences. The type stains of the phylogenetically closest relatives were Stappia indica (95.6% sequence similarity), Stappia stellulata (95.1%) and Roseibium hamelinense (95.1%). The isoprenoid quinone was Q-10. The polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, three unidentified aminophospholipids, an unidentified phosphoglycolipid, an unidentified aminolipid, two unidentified phospholipids and an unidentified lipid. The major cellular fatty acids are Cω7c and C cyclo ω8c. The G + C content of the genomic DNA is 60.7%. Discrimination of the organism from all the recognized genera of the family Stappiaceae was apparent by the chemotaxonomic and phylogenetic features. Based on the results presented here, strain SY4-7 (= KCTC 72226 = NBRC 113902) represents a novel species of a new genus in the family Stappiaceae, for which the name Hongsoonwoonella zoysiae sp. nov. is proposed.
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http://dx.doi.org/10.1007/s00203-020-02083-8DOI Listing
May 2021

sp. nov., isolated from a rhizosphere mudflat of a halophyte and proposal to reclassify Lee . 2019. and Yoon . 2003 as comb. nov. and comb. nov., respectively.

Int J Syst Evol Microbiol 2020 Dec;70(12):6257-6265

Department of Biological Sciences and Biotechnology, Hannam University, Daejon 34054, Republic of Korea.

A marine alphaproteobacterium, designated as strain GH3-10, was isolated from the rhizosphere mud of a halophyte () collected at the seashore of Gangwha Island, Republic of Korea. The isolate was found to be Gram-stain-negative, strictly aerobic, catalase- and oxidase-positive, non-motile, short rods and produced orange-coloured colonies. The 16S rRNA gene- and whole genome-based phylogenetic analyses exhibited that strain GH3-10 belonged to the genus and was most closely related to s21-N3 (98.7 % 16S rRNA gene sequence similarity) and KCTC 23554 (98.4 %). The major respiratory quinone was ubiquinone-10. The polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid and an unidentified lipid. The major fatty acids were C7, summed feature 3 (C7 and/or C6) and C7 10-methyl. The DNA G+C content was 61.3 mol% (by genome). Average nucleotide identity and DNA-DNA relatedness values between the isolate and its phylogenetically closest relatives, together with phenotypic distinctness warranted the taxonomic description of a new species. On the basis of data obtained by a polyphasic approach, strain GH3-10 (=KCTC 62379=JCM 32444) represents a novel species of the genus , for which the name sp. nov. is proposed. According to phylogenetic coherence based on 16S rRNA genes and core genomes, it is also proposed that Lee . 2019. and Yoon . 2003 be transferred to comb. nov. and comb. nov., respectively.
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http://dx.doi.org/10.1099/ijsem.0.004524DOI Listing
December 2020

gen. nov., sp. nov., a new member of the family isolated from a cave.

Int J Syst Evol Microbiol 2020 Oct 10;70(10):5503-5511. Epub 2020 Sep 10.

Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 17035, Republic of Korea.

Two Gram-stain-positive, strictly aerobic, non-spore-forming actinobacterial strains, designated YC2-7 and YC5-17, were isolated from the Yongcheondonggul (larva cave) in Jeju, Republic of Korea and their taxonomic ranks were examined by a polyphasic approach. The 16S rRNA gene tree showed that the novel isolates occupied an independent position separated from recognized genera of the family . In the 92 core gene-based phylogenomic analysis, strain YC2-7 was loosely associated with the type strain of with 66.2 % average amino acid identity. The 16S rRNA gene sequence simairity between the isolate and members of the family was below 96.7 %. The cell-wall peptidoglycan was meso-diaminopimelic acid as a diagnostic diamino acid. Whole-cell sugars consisted of arabinose, galactose and glucose. The predominant menaquinone was MK-8(H4, ω-cycl). The major polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. The cellular fatty acids consisted mainly of saturated and unsaturated components with small amounts of tuberculostearic acid. Mycolic acids of 52-58 carbon atoms were present. The DNA G+C content of the genome was 63.8 mol%. On the basis of combination of morphological and chemotaxonomic differences, in addition to phylogenetic distinctness, the novel isolates are considered to constitute members of a novel species of a new genus in the family , for which the name gen. nov., sp. nov. is proposed. The type strain is YC2-7 (=KACC 19965=DSM 108733).
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http://dx.doi.org/10.1099/ijsem.0.004444DOI Listing
October 2020

gen. nov., sp. nov., a new member of the family isolated from a tidal mudflat.

Int J Syst Evol Microbiol 2020 Oct 27;70(10):5235-5242. Epub 2020 Aug 27.

Department of Biological Sciences and Biotechnology, Hannam University, Daejon 34054, Republic of Korea.

A strictly aerobic, Gram-stain-negative, non-motile, ovoid- and rod-shaped bacterium, designated strain GH1-50, was isolated from a tidal mudflat sample collected from Dongmak seashore on Gangwha Island, Republic of Korea. The organism showed growth at 20-40 °C (optimum, 30 °C), pH 7-8 (optimum, pH 7) and 2-6  % (w/v) NaCl (optimum, 5 %). The genes were present but bacteriochlorophyll a was not detected. The major isoprenoid quinone was Q-10. The polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylinositol, an unidentified aminolipid and five unidentified lipids. The predominant cellular fatty acids were C7c, C7c 11-methyl and C. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that the isolate belonged to the family and was loosely associated with members of the recognized genera. The closest relative was the type strain of (96.8 % similarity) followed by (96.4 %). Other members of the family shared 16S rRNA gene similarity values below 96.0 % to the novel isolate. The DNA G+C content calculated from the draft genome sequence was 64.0 %. The average amino acid identity, average nucleotide identity and digital DNA-DNA hybridization values between genome sequences of strain GH1-50 and all the type strains of the recognized taxa compared were <70.0, <84.1 and <20.5 %, respectively. Based on data obtained by a polyphasic approach, strain GH1-50 (=KCTC 72224=NBRC 113929) represents a novel species of a new genus in the family , for which the name gen. nov., sp. nov. is proposed.
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http://dx.doi.org/10.1099/ijsem.0.004401DOI Listing
October 2020

Rahnella aceris sp. nov., isolated from sap drawn from Acer pictum.

Arch Microbiol 2020 Nov 26;202(9):2411-2417. Epub 2020 Jun 26.

Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea.

A Gram-reaction-negative, facultatively anaerobic bacterium, designated SAP-19, was isolated from sap extracted from Acer pictum in Mt. Halla in Jeju, Republic of Korea and its taxonomic statue was investigated by a polyphasic approach including genome- and 16S rRNA gene-based phylogenetic analyses. Cells were motile, short rods and showed growth at 20-30 °C, pH 4-9 and 0-6% (w/v) NaCl. The whole genome- and 16S rRNA gene-based phylogenetic analyses exhibited that strain SAP-19 belongs to the genus Rahnella and forms a tight cluster with Rahnella aquatilis. The isolate shared average nucleotide identity of 92.7% and 16S rRNA gene sequence similarity of 99.6% with the type strain of Rahnella aquatilis. The polar lipids contained phosphatidylethanolamine, an unidentified aminophospholipid and an unidentified lipid. The major isoprenoid quinone was Q-8. The predominant fatty acids were C and Ccyclo. The G + C content of the genome was 52.3%. The low average nucleotide identity (92.7%) and digital DNA relatedness (48.6%) values between the isolate and the most closely related strain showed that the isolate can be considered a different genospecies. On the basis of combined data obtained in this study, strain SAP-19 (= KACC 21744 = NBRC 114407) represents a novel species of the genus Rahnella, for which the name Rahnella aceris sp. nov. is proposed.
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http://dx.doi.org/10.1007/s00203-020-01961-5DOI Listing
November 2020

sp. nov., isolated from a cave, and is a later heterosynonym of .

Int J Syst Evol Microbiol 2020 Jul;70(7):4409-4415

Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 17035, Republic of Korea.

A Gram-reaction-positive, strictly aerobic, catalase-positive, oxidase-negative, non-motile actinobacterium, designated C1-24, was isolated from a soil sample collected inside a natural cave. The organism exhibited a rod-coccus developmental cycle during its growth phase. Results of 16S rRNA gene-based phylogenetic analysis showed that the novel strain belonged to the genus and formed a distinct sublineage at the base of the radiation including a cluster. In the results of phylogenomic analysis, the novel strain was loosely associated to . The closest relatives were (98.01 % 16S rRNA gene sequence similarity) and (98.01 %). The genome size was 5.66 Mbp and the DNA G+C content was 64.30 mol%. Whole-cell hydrolysates contained -diaminopimelic acid, arabinose and galactose as the diagnostic diamino acid and sugars. MK-8(H) was the predominant menaquinone. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, an unidentified glycolipid and three unidentified phospholipids. Mycolic acids were present. The major fatty acids were C, Cω9, Cω7 and/or Cω6 and 10-methyl C. Digital DNA-DNA hybridization and average nucleotide identity values revealed that the novel strain should be assigned to a different species. Based on the combined data obtained here, strain C1-24 (=KACC 19964=DSM 109484) represents a new species of the genus , for which sp. nov. is proposed. Also, it is proposed that is a later heterosynonym of based on analyses of 16S rRNA gene and whole-genome sequences.
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http://dx.doi.org/10.1099/ijsem.0.004126DOI Listing
July 2020

gen. nov., sp. nov., a new member of the family isolated from a cave soil.

Int J Syst Evol Microbiol 2020 May;70(5):3340-3347

Jeju Biological Resource Co., Ltd, CTC business Incubator, Jeju 63242, Republic of Korea.

A novel Gram-stain-positive, actinobacterial strain, designated C5-26, was isolated from soil from a natural cave in Jeju, Republic of Korea, and its taxonomic position was investigated using a polyphasic approach. The organism was aerobic, and cells were non-spore-forming, non-motile cocci that occurred singly, in pairs, in triplets, in tetrads, in short chains or in irregular clusters. Colonies of the cells were circular, convex, entire and white. The peptidoglycan type was A4α with an l-Ser-d-Asp interpeptide bridge. The whole-cell sugars comprised glucose, rhamnose, mannose, arabinose, galactose and ribose. The major menaquinone was MK-8(H). The polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and an unidentified phospholipid. The major fatty acids were iso-C and iso-C h. The size of the draft genome was 5.32 Mbp with depth of coverage of 161×. The G+C content of the genomic DNA was 67.1 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that the novel isolate belonged to the family and formed a distinct subcluster at the base of the radiation of the genus . Highest sequence similarities of the novel isolate were found to the type strains of (96.2 %), (95.4 %), (95.4 %) and (95.3 %). The whole genome-based phylogeny supported the novelty of the isolate at the genus level in the family . On the basis of data from this polyphasic study, strain C5-26 (=KCTC 39632=DSM 108676) represents a novel species of a new genus in the family , for which the name gen. nov., sp. nov. is proposed.
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http://dx.doi.org/10.1099/ijsem.0.004177DOI Listing
May 2020

sp. nov., isolated from a tidal mudflat and emended description of the genus .

Int J Syst Evol Microbiol 2020 Jan;70(1):259-266

Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea.

A Gram-reaction-negative bacterial strain, designated GH1-19, was isolated from a tidal mudflat sample collected in Gangwha Island, Republic of Korea. Cells of the novel micro-organism were strictly aerobic, non-sporulating, motile and rod-shaped. Growth occurred at 10-40 °C (optimum, 30 °C), pH 6-9 (pH 8) and in the presence of 1-9 % NaCl (3 %). Comparative analysis of complete or nearly complete 16S rRNA gene sequences exhibited that strain GH1-19 formed a distinct cluster between CAU 1311 (97.42 % sequence similarity) and L1 8-17 (97.35 %). Similarity levels of 16S rRNA gene sequences between the novel strain and other members of the family were below 96.6 %. The isoprenoid quinone was Q-10. The major fatty acids were Cωc, C, summed feature 3 (C7 and/or C6) and C 3-OH. The polar lipids consisted of diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminolipid, an unidentified phospholipid and an unidentified lipid. The G+C content of the DNA was 63.2 mol% (draft genome). DNA-DNA relatedness value between the novel strain and the type strain of was 12.7±9.0 %. On the basis of data from phenotypic, chemotaxonomic and DNA-DNA hybridization studies together with phylogenetic analyses, strain GH1-19 (=KCTC 62376=DSM 106292) represents a novel species of the genus , for which the name sp. nov. is proposed, with the emended description of the genus .
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http://dx.doi.org/10.1099/ijsem.0.003749DOI Listing
January 2020

sp. nov., a new actinobacterium isolated from a cave.

Int J Syst Evol Microbiol 2019 Oct;69(10):3128-3134

Department of Biological Sciences and Biotechnology, Hannam University, Daejon 34054, Republic of Korea.

A novel Gram-stain-positive actinobacterial strain, designated C9-28, was isolated from soil sampled in a natural cave on Jeju Island, Republic of Korea. Strain C9-28 morphologically exhibited a rod-coccus life cycle and grew at 10-37 °C (optimum, 30 °C), pH 6-9 (optimum, pH 7) and 0-3 % (optimum, absence of NaCl). In the maximum-likelihood tree based on 16S rRNA gene sequences, strain C9-28 formed a sublineage between a clade and the type strain of . The closest relatives of strain C9-28 were the type strains of (98.88 % 16S rRNA gene sequence similarity), (98.88 %) and (98.60 %). The phylogenomic tree based on whole genome sequences supported the distinct position of the novel strain within the genus . The following chemotaxonomic characteristics also supported the assignment to the genus: -diaminopimelic acid; arabinose and galactose in whole-cell hydrolysates; the predominant menaquinone of MK-8(H); and polar lipids including diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, three unidentified glycolipids and two unidentified lipids. The predominant cellular fatty acids were C, summed feature 3 (Cω7 and/or Cω6), Cω9 and C. Based on the values of average nucleotide identity and digital DNA-DNA hybridization from whole genome sequences, and DNA-DNA hybridization between the isolate and the closest relatives, strain C9-28 (=KACC 19823=DSM 107559) represents a novel species of the genus , for which the name sp. nov. is proposed.
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http://dx.doi.org/10.1099/ijsem.0.003601DOI Listing
October 2019

sp. nov., isolated from a rhizosphere mudflat of a halophyte ().

Int J Syst Evol Microbiol 2019 Oct 29;69(10):3287-3292. Epub 2019 Jul 29.

Department of Biological Sciences and Biotechnology, Hannam University, Daej on 34054, Republic of Korea.

The taxonomic status of a Gram-reaction-negative, aerobic, motile, rod-shaped bacterium, designated strain GH3-15, was examined by a polyphasic approach. The strain, which was isolated from the rhizosphere mudflat of a halophyte at the seashore of Gangwha Island, Republic of Korea, was found to belong to the family based on 16S rRNA gene sequences. The closest phylogenetic neighbour was SM1501 (98.3 % sequence similarity). Levels of 16S rRNA gene sequence similarity of strain GH3-15 to other members of the family were <97.1 %. The respiratory quinone was Q-10. The major fatty acids were Cω6, Cω7, C 2-OH, 11-methyl Cω7 and C. The polar lipids were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and sphingoglycolipid. The novel isolate exhibited growth at 20-40 °C, at pH 5-9, and in the presence of 1-7 % (w/v) NaCl. DNA relatedness between strain GH3-15 and its closet relative was 32.9±8.8 %. On the basis of phenotypic, chemotaxonomic and DNA-DNA hybridization data, in addition to a distinct phylogenetic position, strain GH3-15 (=KCTC 62380=JCM 32445) represents a novel species of the genus for which the name sp. nov. is proposed.
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http://dx.doi.org/10.1099/ijsem.0.003625DOI Listing
October 2019

Amycolatopsis acidiphila sp. nov., a moderately acidophilic species isolated from coal mine soil.

Int J Syst Evol Microbiol 2017 Sep 31;67(9):3387-3392. Epub 2017 Aug 31.

Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, 99 Daehak-ro, Yuseong, Daejeon 34134, Republic of Korea.

Little is known on members of the genus Amycolatopsis inhabiting acidic habitats. In this study, a moderately acidophilic Amycolatopsis strain, designated 2-5T, was isolated from coal mine soil, and subjected to a polyphasic taxonomic characterization. Analysis based on 16S rRNA gene sequences indicated that the strain was most closely related to the type strain of Amycolatopsis bartoniae, sharing 99.30 % similarity, while similarity to all other Amycolatopsis species was less than 97 %. The DNA-DNA relatedness between the new isolate and the type strain of A. bartoniae was 56.5±0.7 %. The optimal pH range of the isolate for growth was 5.5-6.0, but growth also occurred at pH 4.5 and 7.5. The isolate tolerated up to 6 % (w/v) NaCl (optimum, 0 %), and the temperature range for growth was 15-40 °C (optimum, 30 °C). The isolate was able to utilize most substrates tested for sole carbon sources, showing its metabolic versatility. The isolate exhibited antimicrobial activity against Serratia marcescens and weak antifungal activity against Fusarium proliferatum. The chemotaxonomic profiles of strain 2-5T included polar lipids containing phosphatidylethanolamine, phsphatidylmethylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol dimannosides, fatty acids containing C17 : 1ω6c and iso-C16 : 0 as the major components, MK-9(H4) as the predominant menaquinone, and meso-diaminopimelic acid and arabinose, galactose, glucose and ribose as the diagnostic diamino acid and sugars in the cell wall. The combined phenotypic, chemotaxonomic and genotypic analyses clearly indicated that the isolate merits recognition as represnting a novel species of Amycolatopsis, for which the name Amycolatopsis acidiphila sp. nov. is proposed. The type strain is 2-5T (=KCTC 39523T=JCM 30562T).
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http://dx.doi.org/10.1099/ijsem.0.002126DOI Listing
September 2017

Human soluble delta-like 1 homolog exerts antitumor effects in vitro and in vivo.

Biochem Biophys Res Commun 2016 06 15;475(2):209-15. Epub 2016 May 15.

Aging Research Center, Korea Research Institute of Bioscience & Biotechnology, Daejeon, 34141, Republic of Korea. Electronic address:

Proteolysis of delta-like 1 homolog (DLK1), a cell-surface transmembrane protein, produces an active soluble form of DLK1 (sDLK1). Both membrane-bound DLK1 and sDLK1 modulate multiple developmental processes including adipogenesis, osteogenesis, chondrogenesis and myogenesis. However, cancer-related functions of DLK1 have not yet been established. We thus evaluated the roles of extracellular sDLK1, comprising six EGF-like domains and juxtamembrane regions, in human pancreatic cancer MIA PaCa-2 cells in vitro and in vivo. We observed that sDLK1 exerted antitumor effects not only in cancer cell migration and anchorage-independent cell growth but also in in vivo tumor growth.
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http://dx.doi.org/10.1016/j.bbrc.2016.05.076DOI Listing
June 2016

Quantitative detection of residual E. coli host cell DNA by real-time PCR.

J Microbiol Biotechnol 2010 Oct;20(10):1463-70

Department of Biological Sciences, Hannam University, Daejon 305-811, Korea.

E. coli has been widely used as a host system to manufacture recombinant proteins for human therapeutic use. Among impurities to be eliminated during the downstream process, residual host cell DNA is a major interest for safety. Residual E. coli host cell DNA in the final products are usually determined using conventional slot blot hybridization assay or total DNA Threshold assay, although these methods are time consuming, expensive, and relatively insensitive. Therefore a sensitive real-time PCR assay for specific detection of residual E. coli DNA was developed and compared with slot blot hybridization assay and Threshold assay to validate the overall capability of these methods. Specific primer pair for amplification of the E. coli 16S rRNA gene was selected to improve the sensitivity, and E. coli host cell DNA was quantified by use of SYBR Green 1. The detection limit of real-time PCR assay in the optimized condition was calculated to be 0.042 pg genomic DNA, which is much higher than those of slot blot hybridization assay and Threshold assay of which detection limit were 2.42 and 3.73 pg genomic DNA, respectively. The real-time PCR assay was validated to be more reproducible, accurate, and precise than slot blot hybridization assay and Threshold assay. The real-time PCR assay may be a useful tool for quantitative detection and clearance validation of residual E. coli DNA during the manufacturing process for recombinant therapeutics.
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http://dx.doi.org/10.4014/jmb.1004.04035DOI Listing
October 2010

Inactivation and removal of influenza A virus H1N1 during the manufacture of plasma derivatives.

Biologicals 2010 Nov 17;38(6):652-7. Epub 2010 Aug 17.

Department of Biological Sciences, College of Life Science and Nanotechnology, Hannam University, Daejon 305-811, Republic of Korea.

Although transmission of pandemic influenza A virus H1N1 2009 is still occurring globally, little has been reported about how this outbreak has affected the safety of plasma derivatives. To evaluate the safety of plasma derivatives, dedicated virus clearance processes used during their production were investigated for their effectiveness in eliminating this virus of recent concern. In this study, influenza A virus H1N1 strain A/NWS/33 (H1N1) was chosen as a surrogate. H1N1 was completely inactivated by fraction IV fractionation as well as pasteurization during the manufacture of albumin. H1N1 was also effectively removed into the precipitate by fraction III fractionation and completely inactivated by low pH incubation as well as pasteurization during the manufacture of intravenous immunoglobulin. H1N1 was completely inactivated within 1 min of solvent/detergent treatment using 0.3% tri (n-butyl) phosphate and 1.0% Triton X-100 and also completely inactivated within 10 min of dry-heat treatment at 98 °C during the manufacture of factor VIII. H1N1 was completely removed by virus filtration process using Viresolve NFP filter and also completely inactivated by pasteurization during the manufacture of anti-thrombin III. These results indicate that all the virus clearance processes commonly used have sufficient H1N1 reducing capacity to achieve a high margin of safety.
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http://dx.doi.org/10.1016/j.biologicals.2010.07.007DOI Listing
November 2010

Inactivation of influenza A virus H1N1 by disinfection process.

Am J Infect Control 2010 Jun 28;38(5):354-60. Epub 2010 Apr 28.

Department of Biological Sciences, Hannam University, Daejeon, South Korea.

Background: Because any patient, health care worker, or visitor is capable of transmitting influenza to susceptible persons within hospitals, hospital-acquired influenza has been a clinical concern. Disinfection and cleaning of medical equipment, surgical instruments, and hospital environment are important measures to prevent transmission of influenza virus from hospitals to individuals. This study was conducted to evaluate the efficacy of disinfection processes, which can be easily operated at hospitals, in inactivating influenza A virus H1N1 (H1N1).

Methods: The effects of 0.1 mol/L NaOH, 70% ethanol, 70% 1-propanol, solvent/detergent (S/D) using 0.3% tri (n-butyl)-phosphate and 1.0% Triton X-100, heat, and ethylene oxide (EO) treatments in inactivating H1N1 were determined. Inactivation of H1N1 was kinetically determined by the treatment of disinfectants to virus solution. Also, a surface test method, which involved drying an amount of virus on a surface and then applying the inactivation methods for 1 minute of contact time, was used to determine the virucidal activity.

Results: H1N1 was completely inactivated to undetectable levels in 1 minute of 70% ethanol, 70% 1-propanol, and solvent/detergent treatments in the surface tests as well as in the suspension tests. H1N1 was completely inactivated in 1 minute of 0.1 mol/L NaOH treatment in the suspension tests and also effectively inactivated in the surface tests with the log reduction factor of 3.7. H1N1 was inactivated to undetectable levels within 5 minutes, 2.5 minutes, and 1 minute of heat treatment at 70, 80, and 90 degrees C, respectively in the suspension tests. Also, H1N1 was completely inactivated by EO treatment in the surface tests.

Conclusion: Common disinfectants, heat, and EO tested in this study were effective at inactivating H1N1. These results would be helpful in implementing effective disinfecting measures to prevent hospital-acquired infections.
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http://dx.doi.org/10.1016/j.ajic.2010.03.003DOI Listing
June 2010

[Evaluation of the virus-elimination efficacy of nanofiltration (Viresolve NFP) for the parvovirus B19 and hepatitis A virus].

Korean J Lab Med 2010 Feb;30(1):45-50

Blood Transfusion Research Institute, Korean Red Cross, Seoul, Korea.

Background: The safety of plasma derivatives has been reinforced since 1980s by variable pathogen inactivation or elimination techniques. Nucleic acid amplification test (NAT) for the source plasma has also been implemented worldwide. Recently nanofiltration has been used in some country for ensuring safety of plasma derivatives to eliminate non-enveloped viruses such as parvovirus B19 (B19V) and hepatitis A virus (HAV). We evaluated the efficacy of nanofiltration for the elimination of B19V and HAV.

Methods: To verify the efficacy of nanofiltration, we adopted a 20 nm Viresolve NFP (Millipore, USA) in the scaling down (1:1,370) model of the antithrombin III production. As virus stock solutions, we used B19V reactive plasma and porcine parvovirus (PPV) and HAV obtained from cell culture. And 50% tissue culture infectious dose was consumed as infectious dose. The methods used to evaluate the virus-elimination efficacy were reverse-transcriptase polymerase chain reaction for B19V and the cytopathic effect calculation after filtration for PPV and HAV.

Results: B19V was not detected by RT-PCR in the filtered antithrombin III solutions with initial viral load of 6.42 x 10(5) IU/mL and 1.42 x 10(5) IU/mL before filtration. The virus-elimination efficacy of nanofiltration for PPV and HAV were > or = (3.32) and > or = (3.31), respectively.

Conclusions: Nanofiltration would be an effective method for the elimination of B19V and HAV. It may be used as a substitute for NAT screening of these viruses in source plasma to ensure safety of plasma derivatives in Korea.
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http://dx.doi.org/10.3343/kjlm.2010.30.1.45DOI Listing
February 2010

Complex extracellular interactions of proteases and a protease inhibitor influence multicellular development of Streptomyces coelicolor.

Mol Microbiol 2008 Dec 2;70(5):1180-93. Epub 2008 Oct 2.

School of Biological Sciences, Seoul National University, Seoul 151-742, Korea.

Streptomyces coelicolor produces an extracellular protease inhibitor protein, STI (Streptomyces trypsin inhibitor). We show that post-growth elimination of STI is needed for colonies to develop aerial mycelium efficiently. Inactivation of STI, and thus the normal progression of colony development, at least partly involves an extracellular protease specified by gene SCO5913. Two-hybrid analysis identified two possible targets of STI inhibition (the products of SCO1355 and SCO5447), both extracellular proteases containing a domain homologous with the P-domain of eukaryotic convertases, proteases that mediate the processing of many precursors with important cellular or developmental roles. At least the SCO1355 protease is needed for the normal progression of development. Two components of the proposed cascade are dependent on the tRNA for the rare UUA (leucine) codon, which is specified by the developmental gene bldA. A model is presented that links intracellular regulatory events with an extracellular protease cascade to facilitate normal development.
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http://dx.doi.org/10.1111/j.1365-2958.2008.06471.xDOI Listing
December 2008

Improvement of virus safety of an antihemophilc factor IX by virus filtration process.

J Microbiol Biotechnol 2008 Jul;18(7):1317-25

Department of Biological Sciences, College of Life Science and Nanotechnology, Hannam University, Daejon, Korea.

Viral safety is an important prerequisite for clinical preparations of plasma-derived pharmaceuticals. One potential way to increase the safety of therapeutic biological products is the use of a virus-retentive filter. In order to increase the viral safety of human antihemophilic factor IX, particularly in regard to non-enveloped viruses, virus removal process using a polyvinylidene fluoride membrane filter (Viresolve NFP) has been optimized. The most critical factor affecting the filtration efficiency was operating pH and the optimum pH was 6 or 7. Flow rate increased with increasing operating pressure and temperature. Recovery yield in the optimized production-scale process was 96%. No substantial changes were observed in the physical and biochemical characteristics of the filtered factor IX in comparison with those before filtration. A 47-mm disk membrane filter was used to simulate the process performance of the production-scale cartridges and to test if it could remove several experimental model viruses for human pathogenic viruses, including human hepatitis A virus (HAV), porcine parvovirus (PPV), murine encephalomyocarditis virus (EMCV), human immunodeficiency virus type 1 (HIV), bovine viral diarrhea virus (BVDV), and bovine herpes virus (BHV). Nonenveloped viruses (HAV, PPV, and EMCV) as well as enveloped viruses (HIV, BVDV, and BHV) were completely removed during filtration. The log reduction factors achieved were >or=6.12 for HAV, >or=4.28 for PPV, >or=5.33 for EMCV, >or=5.51 for HIV, >or=5.17 for BVDV, and >or=5.75 for BHV. These results indicate that the virus filtration process successfully improved the viral safety of factor IX.
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July 2008

Healing of a porcine burn wound dressed with human and bovine amniotic membranes.

Wound Repair Regen 2008 Jul-Aug;16(4):520-8

Department of Plastic and Reconstructive Surgery, Dongsan Medical Center, Keimyung University, Daegu, South Korea.

The effects of amniotic membranes (AMs), either fresh human and bovine AMs or acellular bovine AMs, on wound healing were compared among the burn wounds of porcine skin. Six pigs were chosen for the study, and we created deep second-degree contact burns on them with a digitally controlled aluminum thermal block. Then we applied the dressings to some of the wounds using fresh human and bovine AMs, acellular bovine AMs, polyurethane foam, or no dressing. We evaluated the pigs for (1) the rate of epithelialization, (2) histological grading, and (3) infections. We found that the AM groups showed better wound-healing effects than did the polyurethane foam and no dressing groups, and these differences were statistically significant. However, the differences between the AM groups were not statistically significant. Wound cultures showed higher infection rates in the control and polyurethane foam groups compared with the other groups. Our study showed that fresh or acellular bovine AMs provided similar efficacy for wound healing as did the fresh human AMs.
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http://dx.doi.org/10.1111/j.1524-475X.2008.00399.xDOI Listing
September 2008

Dry-heat treatment process for enhancing viral safety of an antihemophilic factor VIII concentrate prepared from human plasma.

J Microbiol Biotechnol 2008 May;18(5):997-1003

Department of Biological Sciences, College of Life Science and Nanotechnology, Hannam University, Daejon 305-811, Korea.

Viral safety is a prerequisite for manufacturing clinical antihemophilic factor VIII concentrates from human plasma. With particular regard to the hepatitis A virus (HAV), a terminal dry-heat treatment (100 degrees for 30 min) process, following lyophilization, was developed to improve the virus safety of a solvent/detergent-treated antihemophilic factor VIII concentrate. The loss of factor VIII activity during dry-heat treatment was of about 5%. No substantial changes were observed in the physical and biochemical characteristics of the dry-heat-treated factor VIII compared with those of the factor VIII before dry-heat treatment. The dry-heat-treated factor VIII was stable for up to 24 months at 4oC. The dry-heat treatment after lyophilization was an effective process for inactivating viruses. The HAV, murine encephalomyocarditis virus (EMCV), and human immunodeficiency virus (HIV) were completely inactivated to below detectable levels within 10 min of the dry-heat treatment. Bovine herpes virus (BHV) and bovine viral diarrhea virus (BVDV) were potentially sensitive to the treatment. However porcine parvovirus (PPV) was slightly resistant to the treatment. The log reduction factors achieved during lyophilization and dry-heat treatment were > or =5.55 for HAV, > or =5.87 for EMCV, > or =5.15 for HIV, 6.13 for BHV, 4.46 for BVDV, and 1.90 for PPV. These results indicate that dry-heat treatment improves the virus safety of factor VIII concentrates, without destroying the activity. Moreover, the treatment represents an effective measure for the inactivation of non-lipid-enveloped viruses, in particular HAV, which is resistant to solvent/detergent treatment.
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May 2008

Polaribacter butkevichii sp. nov., a novel marine mesophilic bacterium of the family Flavobacteriaceae.

Curr Microbiol 2005 Dec 15;51(6):408-12. Epub 2005 Oct 15.

Pacific Institute of Bioorganic Chemistry of the Far-Eastern Branch of the Russian Academy of Sciences, Pr. 100 Let Vladivostoku 159, Vladivostok 690022, Russia.

A novel heterotrophic, yellow pigmented, aerobic, Gram-negative, nonmotile, oxidase- and catalase-positive bacterium KMM 3,938(T) was isolated from sea water collected in the Sea of Japan, Russia. The strain grew at mesophilic temperature range, and required the presence of NaCl for growth. 16S rRNA gene sequence analysis revealed that strain KMM 3,938(T) is a member of the family Flavobacteriaceae. The predominant fatty acids were C13:0 iso, C14:0 iso, C15:0 iso, C15:0, C15:1Delta6, 3OH-C15:0:3 iso, and 3OH-C15:0. The G + C content of the DNA of KMM 3938(T) was 32.4 mol%. On the basis of phenotypic, chemotaxonomic, genotypic, and phylogenetic characteristics, the novel bacterium was assigned to the genus Polaribacter as Polaribacter butkevichii sp. nov. The type strain is KMM 3938(T )(= KCTC 12100(T) = CCUG 48005(T)).
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http://dx.doi.org/10.1007/s00284-005-0105-zDOI Listing
December 2005

Gramella echinicola gen. nov., sp. nov., a novel halophilic bacterium of the family Flavobacteriaceae isolated from the sea urchin Strongylocentrotus intermedius.

Int J Syst Evol Microbiol 2005 Jan;55(Pt 1):391-394

Department of Biological Sciences, Hannam University, 133 Ojung-Dong, Daeduk, Daejon 306-791, Republic of Korea.

A novel marine bacterium, strain KMM 6050T, was isolated from the sea urchin Strongylocentrotus intermedius, which inhabits the Sea of Japan. The strain studied was strictly aerobic, heterotrophic, yellow-orange-pigmented, motile by gliding, Gram-negative and oxidase-, catalase-, beta-galactosidase- and alkaline phosphatase-positive. The results of 16S rRNA gene sequence analysis showed that strain KMM 6050T occupies a distinct lineage within the family Flavobacteriaceae and is most closely related to the species Mesonia algae and Salegentibacter salegens (sequence similarity of 92.5-92.6 %). The DNA G+C content of KMM 6050T was 39.6 mol%. The major respiratory quinone was MK-6. The predominant fatty acids were i15 : 0, a15 : 0, 15 : 0, i16 : 1, i16 : 0, i16 : 0 3-OH and i17 : 0 3-OH. On the basis of phenotypic, chemotaxonomic, genotypic and phylogenetic characteristics, the novel bacterium has been assigned to the genus Gramella gen. nov., as Gramella echinicola sp. nov. The type strain is KMM 6050T (=KCTC 12278T=NBRC 100593T=LMG 22585T).
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http://dx.doi.org/10.1099/ijs.0.63314-0DOI Listing
January 2005

Salegentibacter mishustinae sp. nov., isolated from the sea urchin Strongylocentrotus intermedius.

Int J Syst Evol Microbiol 2005 Jan;55(Pt 1):235-238

Department of Biological Sciences, Hannam University, 133 Ojung Dong, Daeduk, Daejon 306-791, Republic of Korea.

A bacterial strain, designated KMM 6049T, was isolated from the sea urchin Strongylocentrotus intermedius inhabiting the Sea of Japan. The bacterium studied was strictly aerobic, heterotrophic, yellow-pigmented, non-motile, Gram-negative and oxidase-, catalase-, beta-galactosidase- and alkaline phosphatase-positive. 16S rRNA gene sequence analysis indicated that strain KMM 3524T was closely related to Salegentibacter holothuriorum and Salegentibacter salegens (sharing 97.7 and 98 % sequence similarity, respectively). DNA-DNA relatedness levels between strains KMM 6049T and S. holothuriorum KMM 3524T and S. salegens DSM 5424T were 24 and 45 %, respectively, indicating that KMM 6049T belongs to a novel species of the genus Salegentibacter, for which the name Salegentibacter mishustinae sp. nov. is proposed. The type strain is KMM 6049T (=KCTC 12263T=LMG 22584T=NBRC 100592T).
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http://dx.doi.org/10.1099/ijs.0.63297-0DOI Listing
January 2005

Pibocella ponti gen. nov., sp. nov., a novel marine bacterium of the family Flavobacteriaceae isolated from the green alga Acrosiphonia sonderi.

Int J Syst Evol Microbiol 2005 Jan;55(Pt 1):177-181

Department of Biological Sciences, Hannam University, 133 Ojung Dong, Daejon 306-791, Republic of Korea.

A marine, heterotrophic, Gram-negative, aerobic, yellow-pigmented, bacterium that was motile by gliding, isolated from the green alga Acrosiphonia sonderi, was studied by polyphasic taxonomic methods. 16S rRNA gene sequence analysis indicated that strain KMM 6031T formed a distinct lineage within the family Flavobacteriaceae. On the basis of phenotypic, chemotaxonomic, genotypic and phylogenetic analyses, the novel bacterium was classified as Pibocella ponti gen. nov., sp. nov. The type strain is KMM 6031T (=KCTC 12262T=NBRC 100591T=LMG 22573T).
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http://dx.doi.org/10.1099/ijs.0.63251-0DOI Listing
January 2005

Characterization of binding and phagocytosis of oxidatively damaged erythrocyte to macrophage.

Korean J Intern Med 2002 Dec;17(4):220-6

Division of Cardiology, Department of Internal Medicine, College of Medicine, Chung-Ang University, Seoul, Korea.

Background: Scavenger receptors are thought to be involved in the recognition of oxidized low-density lipoprotein (oxLDL) and oxidized erythrocyte (oxRBC). However, there are controversies about the kind of receptors and ligands related to the binding. Macrophages lacking class A scavenger receptor show identical binding of oxRBC with wild-type ones.

Methods: RBCs were oxidized with ascorbic acid and CuSO4. Lipid oxidation was measured indirectly by measuring TBARS semiquantitatively. The binding and phagocytosis were measured by counting the number of oxRBC bound or taken up after incubation at 4 degrees C or 37 degrees C for 60 minutes to 100 macrophages differentiated from human monocytic leukemia cell line.

Results: The degree of oxidation and the binding of oxRBCs were dependent on the concentration of CuSO4. The binding and phagocytosis of oxRBC were inhibited by 99% with oxLDL. Fucoidan, competing class A scavenger receptor, inhibited the binding by more than 90%. The binding of oxRBC was higher at 37 degrees C than at 4 degrees C by 3 times. The binding of oxRBCs was maximal at pH 6.5 and higher than at physiologic pH by 2.8 times. At pH 8.5 and 9.5, binding decreased by 67 and 88%, respectively.

Conclusion: OxRBCs might bind and be taken up to macrophages not mainly through class A nor B scavenger receptors, but through other scavenger receptors and/or pathways. These processes are dynamic and ionic strength might be involved.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4531690PMC
http://dx.doi.org/10.3904/kjim.2002.17.4.220DOI Listing
December 2002