Publications by authors named "Seung Bum Kim"

120 Publications

sp. nov., isolated from soil.

Int J Syst Evol Microbiol 2021 Jul;71(7)

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

A Gram-stain-negative, oxidase-positive, catalase-positive, aerobic, orange-pigmented, rod-shaped and non-motile bacterium designated strain MMS17-SY002 was isolated from island soil. The isolate grew at 20-37 °C (optimum, 30 °C), at pH 6.0-9.5 (optimum, pH 7) and in the presence of 0.5-4.0 % (w/v) NaCl (optimum, 2.0 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain MMS17-SY002 was mostly related to the genus of the family and had highest sequence similarity of 96.82 % to A6B8 and EM44, but formed a distinct phylogenetic line within the genus. Chemotaxonomic analyses showed that menaquinone 6 was the predominant isoprenoid quinone, the major fatty acids were iso-C G and iso-C, and the diagnostic polar lipid was phosphatidylethanolamine. The genomic DNA G+C content was 42.4 mol%. Strain MMS17-SY002 could be distinguished from related species by the combination of trypsin, α-chymotrypsin, acid phosphatase, naphthol-AS-BI-phosphohydrolase, α-galactosidase, β-galactosidase and β-glucosidase activities. The orthologous average nucleotide identity between the genomes of strain MMS17-SY002 and and that between the strain and A6B8 were 73.26 and 73.33%, respectively, thus confirming the separation of the strain from related species at species level. Based on the phenotypic, phylogenetic, chemotaxonomic and genomic characterization, MMS17-SY002 should be recognized as a novel species of the genus , for which the name sp. nov. is proposed. The type strain is MMS17-SY002 (=KCTC 62790=JCM 32370).
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http://dx.doi.org/10.1099/ijsem.0.004887DOI Listing
July 2021

Heminiphilus faecis gen. nov., sp. nov., a member of the family Muribaculaceae, isolated from mouse faeces and emended description of the genus Muribaculum.

Antonie Van Leeuwenhoek 2021 Mar 10;114(3):275-286. Epub 2021 Feb 10.

Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.

The novel strain AM35 was isolated from the faeces of C57BL/6 mice. These cells are strictly anaerobic, gram negative, oxidase negative, catalase positive, rod-shaped and non-motile. The strain produced creamy yellowish colonies on brain heart infusion (BHI) agar with hemin. Growth was investigated at 30-41 °C in the presence of 0.5-1.5% (w/v) NaCl at pH 6.5-8.5. Taxonomic analysis based on 16S rRNA gene sequencing revealed that strain AM35 is affiliated with the family Muribaculaceae and closely related to the genus Muribaculum. The genomic DNA G + C content of strain AM35 was 47.8 mol%. We detected the whole-cell sugars ribose and galactose; meso-2,6-diaminopimelic acid was absent. The major fatty acids (> 10%) were anteiso-C and iso-C; the major polar lipid was phosphatidylethanolamine. The major respiratory quinones were MK-10 and MK-11. Based on our phylogenetic, phenotypic and chemotaxonomic analyses, strain AM35 represents a novel genus within the family Muribaculaceae, for which we propose the name Heminiphilus faecis gen. nov., sp. nov. The type strain of Heminiphilus faecis gen. nov., sp. nov. is AM35 (= KCTC 15907 = DSM 110151).
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http://dx.doi.org/10.1007/s10482-021-01521-xDOI Listing
March 2021

Genome Mining of the Genus for Biosynthetic and Biodegradation Potential.

Genes (Basel) 2020 10 3;11(10). Epub 2020 Oct 3.

Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon 34134, Korea.

The genus represents a group of acidophilic actinobacteria within the family , and currently encompasses 15 validly named species, which include five recent additions within the last two years. Considering the potential of the related genera within the family, namely and , these relatively new members of the family can also be a promising source for novel secondary metabolites. At present, 15 genome data for 11 species from this genus are available, which can provide valuable information on their biology including the potential for metabolite production as well as enzymatic activities in comparison to the neighboring taxa. In this study, the genome sequences of 11 species were subjected to the comparative analysis together with selected and genomes. This study represents the first comprehensive comparative genomic analysis of the genus . The results indicate that the genomes of contained various secondary metabolite (SM) producing biosynthetic gene clusters (BGCs), some of them exclusively identified in only. Several of these clusters may potentially code for SMs that may have a broad range of bioactivities, such as antibacterial, antifungal, antimalarial and antitumor activities. The biodegradation capabilities of were also explored by investigating the hydrolytic enzymes for complex carbohydrates. Although all genomes were enriched with carbohydrate-active enzymes (CAZymes), their numbers in the genomes of some strains such as Streptacidiphilus carbonis NBRC 100919 were higher as compared to well-known carbohydrate degrading organisms. These distinctive features of each species make them interesting candidates for future studies with respect to their potential for SM production and enzymatic activities.
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http://dx.doi.org/10.3390/genes11101166DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7601586PMC
October 2020

sp. nov., isolated from pine grove soil, exhibiting antimicrobial potential.

Int J Syst Evol Microbiol 2020 Oct 14;70(10):5567-5575. Epub 2020 Sep 14.

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

A polyphasic study was carried out to establish the taxonomic position of an acidophilic isolate designated MMS16-CNU292 (=JCM 32302) from pine grove soil, and provisionally assigned to the genus . On the basis of 16S rRNA gene sequence similarity, the strain formed a novel evolutionary lineage within and showed highest similarities to KCTC 9699 (98.75 %), IFO 15206 (98.74 %), NRRL B-1817 (98.61 %) and HKI 0315 (98.42 %), respectively. Strain MMS16-CNU292 possessed MK-9(H) and MK-9(H) as the major menaquinones, and a major amount of -diaminopimelic acid in the cell-wall peptidoglycan. The whole-cell hydrolysates were rich in galactose, glucose and mannose, and the polar lipids mainly consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylglycerol and phosphatidylinositol mannosides. The major fatty acids were anteiso-C-A, anteiso-C, and iso-C, and the DNA G+C content was 71.5 mol%. The strain exhibited antibacterial activity against a number of bacterial strains, and the activity was generally greater when grown in acidic conditions. The phylogenetic, chemotaxonomic and phenotypic properties enabled distinction of MMS16-CNU292 from related species, and thus the isolate should be recognized as a new species of the genus , for which the name sp. nov. (type strain=MMS16-CNU292=KCTC 49011=JCM 32302) is proposed.
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http://dx.doi.org/10.1099/ijsem.0.004450DOI Listing
October 2020

sp. nov., sp. nov. and sp. nov., isolated from soil.

Int J Syst Evol Microbiol 2020 Apr 6;70(4):2682-2689. Epub 2020 Mar 6.

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

Three aerobic, rod-shaped actinobacterial strains, designated MMS17-SY117, MMS17-SY207-3 and MMS17-SY213, were isolated from soil and their taxonomic positions were analysed using a polyphasic approach. The isolates showed best growth at 30 °C, pH 7 and 0-1 % (w/v) NaCl. On the basis of 16S rRNA gene sequence similarity, the isolates were affiliated to the genus , and the closest species to MMS17-SY117, MMS17-SY207-3 and MMS17-SY213 were JC2056 (97.76%), IB-3 (97.41%) and RC825 (98.71%), respectively. Each isolate formed a distinct cluster within the clade in the phylogenetic tree. The orthologous average nucleotide identity and digital DNA-DNA hybridization values were in the range of 74.4-85.7 % and 16.6-39.2 %, respectively, with the type strains of related species. The major polar lipids in all three strains were phosphatidylinositol, phosphatidylglycerol and diphosphatidylglycerol. The predominant fatty acids were iso-C and C ω8. MK-8(H) was the major isoprenoid quinone and ll-DAP was the major diamino acid. Galactose, glucose and rhamnose were present in the whole-cell hydrolysate, and MMS17-SY213 also contained mannose and ribose. The DNA G+C contents of MMS17-SY117, MMS17-SY207-3 and MMS17-SY213 were 72.2, 70.4 and 71.5 mol%, respectively. The phylogenetic, phenotypic and chemotaxonomic data supported the classification of each strain as representing a new species of , for which the names sp. nov. (MMS17-SY117=KCTC 49175=JCM 32831), sp. nov. (MMS17-SY207-3=KCTC 49176=JCM 32832) and sp. nov. (MMS17-SY213=KCTC 49177=JCM 32833) are proposed accordingly.
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http://dx.doi.org/10.1099/ijsem.0.004095DOI Listing
April 2020

Genome-based analysis for the bioactive potential of Streptomyces yeochonensis CN732, an acidophilic filamentous soil actinobacterium.

BMC Genomics 2020 Feb 3;21(1):118. Epub 2020 Feb 3.

Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon, 34134, Republic of Korea.

Background: Acidophilic members of the genus Streptomyces can be a good source for novel secondary metabolites and degradative enzymes of biopolymers. In this study, a genome-based approach on Streptomyces yeochonensis CN732, a representative neutrotolerant acidophilic streptomycete, was employed to examine the biosynthetic as well as enzymatic potential, and also presence of any genetic tools for adaptation in acidic environment.

Results: A high quality draft genome (7.8 Mb) of S. yeochonensis CN732 was obtained with a G + C content of 73.53% and 6549 protein coding genes. The in silico analysis predicted presence of multiple biosynthetic gene clusters (BGCs), which showed similarity with those for antimicrobial, anticancer or antiparasitic compounds. However, the low levels of similarity with known BGCs for most cases suggested novelty of the metabolites from those predicted gene clusters. The production of various novel metabolites was also confirmed from the combined high performance liquid chromatography-mass spectrometry analysis. Through comparative genome analysis with related Streptomyces species, genes specific to strain CN732 and also those specific to neutrotolerant acidophilic species could be identified, which showed that genes for metabolism in diverse environment were enriched among acidophilic species. In addition, the presence of strain specific genes for carbohydrate active enzymes (CAZyme) along with many other singletons indicated uniqueness of the genetic makeup of strain CN732. The presence of cysteine transpeptidases (sortases) among the BGCs was also observed from this study, which implies their putative roles in the biosynthesis of secondary metabolites.

Conclusions: This study highlights the bioactive potential of strain CN732, an acidophilic streptomycete with regard to secondary metabolite production and biodegradation potential using genomics based approach. The comparative genome analysis revealed genes specific to CN732 and also those among acidophilic species, which could give some insights into the adaptation of microbial life in acidic environment.
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http://dx.doi.org/10.1186/s12864-020-6468-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6998099PMC
February 2020

sp. nov., isolated from an island soil.

Int J Syst Evol Microbiol 2020 Mar;70(3):2079-2083

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

A mycolic acid-containing actinobacterium designated strain MMS17-SY073 was isolated from island soil. The isolate showed best growth at 25 °C, pH 6, and 0 % (w/v) NaCl. The phylogenetic analysis based on 16S rRNA gene sequences indicated that strain MMS17-SY073 belongs to the genus , and is mostly related to the type strains of (98.5 % sequence similarity), (98.1%), and (97.8%). The genome-based comparisons showed a clear distinction between the strain and the two neighbouring species, and , with the average nucleotide identities (ANI) of 75.8 and 76.3 %, respectively. Notably, the genome of strain MMS17-SY073 was the largest in total stretch and gene counts among the complete genomes of , and contained a number of biosynthetic gene clusters for secondary metabolites, in particular those for non-ribosomal peptide synthetases. The major polar lipids were diphosphatidyl glycerol (DPG), phosphatidyl glycerol (PG), phosphatidyl ethanolamine (PE), phosphatidyl inositol (PI) and phosphatidyl inositol mannoside (PIM). The isoprenoid quinone was MK-9(H), and the main fatty acids were C (30.2%) and 10-methyl-C (33.7%). The whole cell hydrolysates contained galactose, arabinose, and -diaminopimelic acid. The DNA G+C content was 67.4 mol%. Based on phenotypic, chemotaxonomic and genetic analysis, strain MMS17-SY073 should be classified as a new species of the genus , for which the name sp. nov. is proposed (type strain=MMS17-SY073=KCTC 49257=JCM 33277).
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http://dx.doi.org/10.1099/ijsem.0.004023DOI Listing
March 2020

Genome based characterization of Kitasatospora sp. MMS16-BH015, a multiple heavy metal resistant soil actinobacterium with high antimicrobial potential.

Gene 2020 Apr 20;733:144379. Epub 2020 Jan 20.

Department of Microbiology and Molecular Biology, 99 Daehak-Ro, Yuseong, Daejeon 34134, Chungnam National University, Daejeon, Republic of Korea. Electronic address:

An actinobacterial strain designated Kitasatospora sp. MMS16-BH015, exhibiting high level of heavy metal resistance, was isolated from soil of an abandoned metal mining site, and its potential for metal resistance and secondary metabolite production was studied. The strain was resistant to multiple heavy metals including zinc (up to 100 mM), nickel (up to 2 mM) and copper (up to 0.8 mM), and also showed antimicrobial potential against a broad group of microorganisms, in particular filamentous fungi. The genome of strain MMS16-BH015 was 8.96 Mbp in size with a G + C content of 72.7%, and contained 7270 protein-coding genes and 107 tRNA/rRNA genes. The genome analysis revealed presence of at least 121 metal resistance related genes, which was prominently higher in strain MMS16-BH015 compared to other genomes of Kitasatospora. The genes included those for proteins representing various families involved in the transport of heavy metals, for example dipeptide transport ATP-binding proteins, high-affinity nickel transport proteins, and P-type heavy metal-transporting ATPases. Additionally, 43 biosynthetic gene clusters (BGCs) for secondary metabolites, enriched with those for non-ribosomal peptides, were detected in this multiple heavy metal resistant actinobacterium, which was again the highest among the compared genomes of Kitasatospora. The pan-genome analysis also identified higher numbers of unique genes related to secondary metabolite production and metal resistance mechanism in strain MMS16-BH015. A high level of correlation between the biosynthetic potential and heavy metal resistance could be observed, thus indicating that heavy metal resistant actinobacteria can be a promising source of bioactive compounds.
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http://dx.doi.org/10.1016/j.gene.2020.144379DOI Listing
April 2020

A comprehensive in silico analysis of sortase superfamily.

J Microbiol 2019 Jun 27;57(6):431-443. Epub 2019 May 27.

Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea.

Sortases are cysteine transpeptidases that assemble surface proteins and pili in their cell envelope. Encoded by all Gram-positive bacteria, few Gram-negative bacteria and archaea, sortases are currently divided into six classes (A-F). Due to the steep increase in bacterial genome data in recent years, the number of sortase homologues have also escalated rapidly. In this study, we used protein sequence similarity networks to explore the taxonomic diversity of sortases and also to evaluate the current classification of these enzymes. The resultant data suggest that sortase classes A, B, and D predominate in Firmicutes and classes E and F are enriched in Actinobacteria, whereas class C is distributed in both Firmicutes and Actinobacteria except Streptomyces family. Sortases were also observed in various Gram-negatives and euryarchaeota, which should be recognized as novel classes of sortases. Motif analysis around the catalytic cysteine was also performed and suggested that the residue at 2 position from cysteine may help distinguish various sortase classes. Moreover, the sequence analysis indicated that the catalytic arginine is highly conserved in almost all classes except sortase F in which arginine is replaced by asparagine in Actinobacteria. Additionally, class A sortases showed higher structural variation as compared to other sortases, whereas inter-class comparisons suggested structures of class C and D2 exhibited best similarities. A better understanding of the residues highlighted in this study should be helpful in elucidating their roles in substrate binding and the sortase function, and successively could help in the development of strong sortase inhibitors.
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http://dx.doi.org/10.1007/s12275-019-8545-5DOI Listing
June 2019

Streptomyces fodineus sp. nov., an actinobacterium with antifungal activity isolated from mine area soil.

Int J Syst Evol Microbiol 2019 May 21;69(5):1350-1354. Epub 2019 Mar 21.

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

A novel actinobacterial strain producing an antifungal substance was isolated from a sample of acidic mine area soil, and its taxonomic position was evaluated. The novel strain, designated TW1S1, formed white-grey aerial mycelium and yellow substrate mycelium on oatmeal agar. Growth occurred at 10-45 °C (optimum, 30 °C), pH 4-9 (pH 6-7) and in the presence of up to 8 % (w/v) NaCl. Melanin was produced on peptone-yeast extract-iron agar. Phylogenetic analysis based on its 16S rRNA gene sequence indicated that the novel strain should be assigned to the genus Streptomyces, and the closest species was Streptomyces puniciscabiei S77 with 99.1 % sequence similarity, which was followed by Streptomyces durhamensis NRRL B-3309 (99.0 %), Streptomyces filipinensis NBRC 12860 (98.9 %) and Streptomyces yaanensis Z4 (98.7 %). The chemotaxonomic properties were consistent with those of Streptomyces. ll-Diaminopimelic acid was the diagnostic diamino acid, and alanine, glutamic acid and glycine were present in the peptidoglycan. The cell-wall hydrolysate also contained galactose, glucose, mannose and ribose. The predominant isoprenoid quinones were MK-9(H4) and MK-9(H6), the major polar lipids were phosphatidylglycerol and an unidentified phospholipid, and the main fatty acids were iso-C16 : 0 and anteiso-C15 : 0. However, strain TW1S1 could be distinguished from its neighbouring species by its phenotypic properties. In addition, the genome-based comparison with the closest species indicated that strain TW1S1 should be recognized as a separate species. The phylogenetic, phenotypic and chemotaxonomic as well as genomic evidence supported that TW1S1 represents a novel species of Streptomyces, for which the name Streptomycesfodineus sp. nov. is proposed (type strain, TW1S1 = KCTC 49013 = JCM 32404).
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http://dx.doi.org/10.1099/ijsem.0.003353DOI Listing
May 2019

Mucibacter soli gen. nov., sp. nov., a new member of the family Chitinophagaceae producing mucin.

J Microbiol 2019 May 22;57(5):356-361. Epub 2019 Feb 22.

Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea.

A Gram-stain-negative, mucus-forming, motile by gliding, non-spore-forming and short rod-shaped bacterial strain designated R1-15 was isolated from soil and its taxonomic position was evaluated using a polyphasic approach. Strain R1-15 grew at 15-37°C (optimum, 30°C), at pH 6-7 (optimum, pH 6) and in the presence of 0-1% (w/v) NaCl (optimum, 0%) on 0.1X TSA. On the basis of 16S rRNA gene sequence similarity, the novel strain was assigned to the family Chitinophagaceae of the phylum Bacteroidetes, and its closest related taxa were species of the genera Taibaiella (88.76-90.02% sequence similarity), Lacibacter (89.24-90.00%), Chitinophaga (88.61-89.76%), and Terrimonas (89.04%). Flexirubin- type pigments were produced. The only isoprenoid quinone was MK-7, and the major polar lipid was phosphatidylethanolamine. Based on whole genome comparisons between the strain R1-15 and the type strains of relatives, the orthologous average nucleotide identity values were 66.9-67.0%. The DNA G + C content of strain R1-15 was 43.8 mol%. The combination of phylogenetic, chemotaxonomic and phenotypic data clearly supported separation of strain R1-15 from related taxa, and thus the name Mucibacter soli gen. nov., sp. nov. is proposed. The type strain is R1-15 (= KCTC 62274 = JCM 31190).
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http://dx.doi.org/10.1007/s12275-019-8512-1DOI Listing
May 2019

Acidiphilamides A-E, Modified Peptides as Autophagy Inhibitors from an Acidophilic Actinobacterium, Streptacidiphilus rugosus.

J Nat Prod 2019 02 8;82(2):341-348. Epub 2019 Feb 8.

Natural Products Research Institute, College of Pharmacy , Seoul National University , 1 Gwanak-ro , Gwanak-gu, Seoul 08826 , Republic of Korea.

Five new tripeptides, acidiphilamides A-E (1-5), were discovered along with two previously reported compounds, l-isoleucinamide (6) and l-valinamide (7), from Streptacidiphilus rugosus AM-16, an acidophilic actinobacterial strain isolated from acidic forest soil. The structures of 1-5 were elucidated as modified tripeptides bearing phenylalaninol or methioninol fragments with C-C acyl chains based mainly on NMR and mass spectroscopic data. The absolute configurations of the amine units were established by advanced Marfey's method and GITC (2,3,4,6-tetra- O-acetyl-β-d-glucopyranosyl isothiocyanate) derivatization followed by LC/MS analysis. Acidiphilamides A and B (1 and 2), the first secondary metabolites isolated from the rare actinobacterial genus Streptacidiphilus, significantly inhibited autophagic flux but not proteasome activity in HeLa cells. These compounds appeared to block mainly the autophagosome-lysosome fusion step in the late stage of cellular autophagy.
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http://dx.doi.org/10.1021/acs.jnatprod.8b00828DOI Listing
February 2019

Treatment Outcome and Renal Safety of 3-Year Tenofovir Disoproxil Fumarate Therapy in Chronic Hepatitis B Patients with Preserved Glomerular Filtration Rate.

Gut Liver 2019 01;13(1):93-103

Department of Internal Medicine, Research Institute of Clinical Medicine of Chonbuk National University-Biomedical Research Institute of Chonbuk National University Hospital, Chonbuk National University Medical School, Jeonju, Korea.

Background/aims: To investigate the treatment efficacy and renal safety of long-term tenofovir disoproxil fumarate (TDF) therapy in chronic hepatitis B (CHB) patients with preserved renal function.

Methods: The medical records of 919 CHB patients who were treated with TDF therapy were reviewed. All patients had preserved renal function with an estimated glomerular filtration rate (eGFR) of at least 60 mL/min/1.73 m².

Results: A total of 426 patients (184 treatment-naïve and 242 treatment-experienced) were included for analysis. A virologic response (VR) was defined as achieving an undetectable serum hepatitis B virus (HBV) DNA level, and the overall VR was 74.9%, 86.7%, and 89.4% at the 1, 2, and 3-year follow-ups, respectively. Achieving a VR was not influenced by previous treatment experience, TDF combination therapy, or antiviral resistance. In a multivariate analysis, being hepatitis B e antigen positive at baseline and having a serum HBV DNA level ≥2,000 IU/mL at 12 months were associated with lower VR rates during the long-term TDF therapy. The overall renal impairment was 2.9%, 1.8%, and 1.7% at the 1, 2, and 3-year follow-ups, respectively. With regard to renal safety, underlying diabetes mellitus (DM) and an initial eGFR of 60 to 89 mL/min/1.73 m² were significant independent predictors of renal impairment.

Conclusions: TDF therapy appears to be an effective treatment option for CHB patients with a preserved GFR. However, patients with underlying DM and initial mild renal dysfunction (eGFR, 60 to 89 mL/min/1.73 m²) have an increased risk of renal impairment.
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http://dx.doi.org/10.5009/gnl18183DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6347000PMC
January 2019

Streptacidiphilus pinicola sp. nov., isolated from pine grove soil.

Int J Syst Evol Microbiol 2018 Oct 13;68(9):3149-3155. Epub 2018 Aug 13.

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

A moderately acidophilic actinobacterial strain, designated MMS16-CNU450, was isolated from pine grove soil, and its taxonomic position was analysed using a polyphasic approach. The isolate showed best growth at 30 °C, pH 6 and 0.5 % (w/v) NaCl. On the basis of 16S rRNA gene sequence similarity, the isolate was assigned to the genus Streptacidiphilus, and the closest species were Streptacidiphilus rugosus AM-16 (sequence similarity, 98.61 %), Streptacidiphilus melanogenes NBRC 103184 (98.53 %), Streptacidiphilus jiangxiensis NBRC 100920 (98.19 %) and Streptacidiphilus anmyonensis NBRC 103185 (98.05 %). The isolate formed a distinct cluster of its own within the Streptacidiphilusclade in the phylogenetic tree. Based on whole-genome comparison between the strain MMS16-CNU450 and the type strains of related species, the orthologous average nucleotide identity and in silico DNA-DNA hybridization values were in the range of 77.9-87.0 and 22.3-32.7 %, respectively. The DNA G+C content of the isolate was 68.6 mol%. The phylogenetic, phenotypic, chemotaxonomic and genomic data supported the affiliation of the strain to Streptacidiphilus, and the name Streptacidiphilus pinicola sp. nov. (type strain, MMS16-CNU450=KCTC 49008=JCM 32300) is proposed accordingly.
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http://dx.doi.org/10.1099/ijsem.0.002957DOI Listing
October 2018

Assessing global surface water inundation dynamics using combined satellite information from SMAP, AMSR2 and Landsat.

Remote Sens Environ 2018 Aug 11;213:1-17. Epub 2018 May 11.

Numerical Terradynamic Simulation Group, W.A. Franke College of Forestry & Conservation, The University of Montana, Missoula, MT 59812, United States.

A method to assess global land surface water () inundation dynamics was developed by exploiting the enhanced sensitivity of L-band (1.4 GHz) passive microwave observations from the Soil Moisture Active Passive (SMAP) mission. The L-band ( ) retrievals were derived using SMAP H-polarization brightness temperature ( ) observations and predefined L-band reference microwave emissivities for water and land endmembers. Potential soil moisture and vegetation contributions to the microwave signal were represented from overlapping higher frequency observations from AMSR2. The resulting global record has high temporal sampling (1-3 days) and 36-km spatial resolution. The annual averages corresponded favourably (=0.85, <0.001) with a 250-m resolution static global water map (MOD44W) aggregated at the same spatial scale, while capturing significant inundation variations worldwide. The monthly averages also showed seasonal inundation changes consistent with river discharge records within six major US river basins. An uncertainty analysis indicated generally reliable performance for major land cover areas and under low to moderate vegetation cover, but with lower accuracy for detecting water bodies covered by dense vegetation. Finer resolution (30-m) results were obtained for three sub-regions in North America using an empirical downscaling approach and ancillary global Water Occurrence Dataset (WOD) derived from the historical Landsat record. The resulting 30-m retrievals showed favourable spatial accuracy for water (commission error 31.46%, omission error 30.20%) and land (commission error 0.87%, omission error 0.96%) classifications and seasonal wet and dry periods when compared to independent water maps derived from Landsat-8 imagery. The new algorithms and continuing SMAP and AMSR2 operations provide for near real-time, multi-scale monitoring of global surface water inundation dynamics and potential flood risk.
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http://dx.doi.org/10.1016/j.rse.2018.04.054DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6055934PMC
August 2018

Shewanella saliphila sp. nov., Shewanella ulleungensis sp. nov. and Shewanella litoralis sp. nov., isolated from coastal seawater.

Int J Syst Evol Microbiol 2018 Sep 20;68(9):2960-2966. Epub 2018 Jul 20.

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

Three Gram-negative, non-spore-forming, rod-shaped and motile bacterial strains, designated MMS16-UL250, MMS16-UL253 and MMS16-UL482, were isolated from coastal seawater and subjected to taxonomic characterization. All isolates grew at 4-30 °C (optimum, 25 °C), at pH 6-10 (pH 7) and in the presence of up to 8 % NaCl (2.5-4.5 %). The 16S rRNA gene sequence similarities between the three isolates and Shewanella algicola St-6, the closest species, were 98.1-99.2 %, and those among the isolates were 98.5-99.0 %. In the phylogenetic tree, MMS16-UL250 formed a cluster with S. algicola St-6, but the DNA-DNA relatedness between the two strains was 28.8±1.5 %, thus confirming their separation at species level. The other two strains formed separate phylogenetic lines respectively. The main quinones for all strains were Q-7, Q-8, MK-7 and MMK-7, which is typical for Shewanella. The major polar lipids of all strains were phosphatidylglycerol and phosphatidylethanolamine, and the common major fatty acid was a summed feature consisting of C16 : 1ω7c and/or C16 : 1ω6c while the proportions varied among the three strains. The DNA G+C contents of the strains also varied between 42.1 and 43.7 mol%. Phenotypic properties distinguished each strain from S. algicola as well as from one another. Based on the polyphasic analysis, each strain is considered to represent a novel species of Shewanella, for which the names Shewanellasaliphila sp. nov. (type strain, MMS16-UL250=KCTC 62131=JCM 32304), Shewanella ulleungensis sp. nov. (type strain, MMS16-UL253=KCTC 62130=JCM 32305) and Shewanella litoralis sp. nov. (type strain, MMS16-UL482=KCTC 62129=JCM 32306) are proposed.
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http://dx.doi.org/10.1099/ijsem.0.002929DOI Listing
September 2018

Pseudogracilibacillus endophyticus sp. nov., a moderately thermophilic and halophilic species isolated from plant root.

Int J Syst Evol Microbiol 2018 Jan 10;68(1):165-169. Epub 2017 Nov 10.

Department of Microbiology and Molecular Biology, Chungnam National University, 99 Daehak-Ro, Yuseong, Daejeon 34134, Republic of Korea.

A Gram-stain-positive strain, designated DT7-02, was isolated from the surface-sterilized root of Oenotherabiennis (evening primrose) and subjected to taxonomic characterization. Cells of DT7-02 were slender rod-shaped, motile by means of flagella, and oxidase- and catalase-positive. The colonies were circular, pinkish-yellow, opaque, glistering and 1-2 mm in diameter. The strain was moderately thermophilic and halophilic, as growth occurred at 20-44 °C (optimum 40 °C), pH 7-10 (optimum pH 8-9) and in the presence of 0-8 % of NaCl (optimum 4 %) in tryptic soy broth. The analysis of 16S rRNA gene sequences indicated that the strain represented a member of the genus Pseudogracilibacillus of the family Bacillaceae, and the sequence similarity was 96.5 % with Pseudogracilibacillus auburnensis P-207 and 95.9 % with Pseudogracilibacillus marinus NIOT-bflm-S4. Other related taxa were Ornithinibacillus contaminans DSM 22953 and Sinibacillus soli KCTC 33117, with 16S rRNA gene sequence similarities of 95.4 and 94.3 %, respectively. The major cellular fatty acids of DT7-02 were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The DNA G+C content was 35.1 mol%, and the respiratory quinone was MK-7. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine. The combination of chemotaxonomic properties enabled differentiation of DT7-02 from the other two species of the genus Pseudogracilibacillus. The results of phylogenetic, phenotypic and chemotaxonomic analyses demonstrate that strain DT7-02 (=KCTC 33854=JCM 31192) merits recognition as representing a novel species of the genus Pseudogracilibacillus, for which the name Pseudogracilibacillusendophyticus sp. nov. is proposed.
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http://dx.doi.org/10.1099/ijsem.0.002475DOI Listing
January 2018

Flavobacterium commune sp. nov., isolated from freshwater and emended description of Flavobacterium seoulense.

Int J Syst Evol Microbiol 2018 Jan 7;68(1):93-98. Epub 2017 Nov 7.

Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon, Republic of Korea.

A Gram-stain-negative, yellow, facultatively-anaerobic, short, rod-shaped, non-spore-forming bacterium, designated PK15, was isolated from freshwater. Growth was observed at 4-40 °C (optimum, 30 °C), pH 6-9 (optimum, 8), and in the presence of 0-0.8 % (w/v) NaCl (optimum, 0.4 %). Strain PK15 exhibited both catalase and oxidase activities and was able to reduce nitrate. On the basis of 16S rRNA gene sequence similarities, strain PK15 was shown to belong to the genus Flavobacterium with close similarities to Flavobacterium palustre S44 (97.9 %) and Flavobacterium seoulense EM1321 (97.7 %). Menaquinone-6 (MK-6) was the major respiratory quinone, while the G+C content of the genomic DNA was 35.5 (±0.9) mol%. The major polar lipids were phosphatidylethanolamine, three unidentified aminolipids, one unidentified aminophospholipid and three unidentified polar lipids. The predominant cellular fatty acids (≥10 %) were anteiso-C15 : 0 (17.3 %), a summed feature comprising C16 : 1ω7c and/or C16 : 1ω6c (15.1 %) and iso-C15 : 0 (10.0 %). Chemotaxonomic data supported the affiliation of strain PK15 to the genus Flavobacterium. The results of physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain PK15 from strains of closely related species. It was, therefore, evident that PK15 represents a novel species of the genus Flavobacterium, for which the name Flavobacterium commune sp. nov. is proposed with strain PK15 (=KCTC 52562=JCM 32115) as the type strain. Based on the results of the chemotaxonomic characterization in the present study, an emended description of Flavobacterium seoulense is also proposed.
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http://dx.doi.org/10.1099/ijsem.0.002463DOI Listing
January 2018

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

Flavobacterium fluminis sp. nov. to accommodate an aerobic, halotolerant and gliding flavobacterium isolated from freshwater.

Int J Syst Evol Microbiol 2017 Aug 4;67(8):3117-3121. Epub 2017 Aug 4.

Department of Microbiology and Molecular Biology, Chungnam National University, 99 Daehak-Ro, Yuseong, Daejeon 34134, Republic of Korea.

A Gram-stain-negative, aerobic, oxidase-positive, catalase-positive and rod-shaped bacterium designated strain 3R17T was isolated from freshwater. Strain 3R17T produced bright-yellow, circular, convex and smooth colonies on R2A agar, tryptic soy agar, potato dextrose agar, nutrient agar and brain-heart infusion agar media. The strain was motile by gliding. The strain grew at 4-30 °C (optimum, 25 °C), at pH 6-9 (optimum, pH 7) and in the presence of up to 3 % NaCl (optimum, 0 %) on R2A agar. The 16S rRNA gene sequence analysis indicated that 3R17T represents a member of the genus Flavobacterium and is most closely related to Flavobacterium resistens BD-b365T, with a sequence similarity of 97.78 %, but the strain formed a distinct phylogenetic lineage of its own. Fatty acid analysis indicated that a summed feature comprising C16 : 1ω7c and/or C16 : 1ω6c, iso-C15 : 0, iso-C15 : 1G, anteiso-C15 : 0, C16 : 0, iso-C17 : 0 3-OH and iso-C15 : 0 3-OH were the major components (>5 %). Strain 3R17T contained phosphatidylethanolamine (PE) and several unidentified aminolipids as main polar lipids, and MK-6 as the predominant isoprenoid quinone. Flexirubin pigments were not produced. The DNA G+C content was 35.4 mol%. The combination of physiological and chemotaxonomic properties distinguished 3R17T from related species of the genus Flavobacterium. On the basis of polyphasic taxonomy, 3R17T evidently represents a novel species within the genus Flavobacterium, for which the name Flavobacterium fluminis sp. nov. is proposed. The type strain is 3R17T (=KCTC 42062T=JCM 30338T).
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http://dx.doi.org/10.1099/ijsem.0.002135DOI Listing
August 2017

Flavobacterium keumense sp. nov., isolated from freshwater.

Int J Syst Evol Microbiol 2017 Jul 3;67(7):2166-2170. Epub 2017 Jul 3.

Department of Microbiology and Molecular Biology, Chungnam National University, 99 Daehak-Ro, Yuseong, Daejeon 34134, Republic of Korea.

A yellow-pigmented, oxidase-positive, catalase-negative, Gram-stain-negative, rod-shaped, aerobic and non-motile bacterial strain designated K3R-10T was isolated from a freshwater source. The strain grew over a temperature range from 4 to 35 °C (optimum, 30 °C), pH range pH 6-8 (optimum, pH 7) and in the presence of 0-0.5 % NaCl (optimum, 0 %). Phylogenetic analysis based on 16S rRNA gene sequence revealed that strain K3R-10T belonged to the genus Flavobacterium and shared close similarities with Flavobacterium succinicans LMG 10402T (97.0 %), Flavobacterium chungangense LMG 26729T (96.4 %), Flavobacterium branchiophilum IFO 15030T (96.4 %) and Flavobacteriumpiscis412R-09T (96.3 %), but formed a distinct phylogenetic line of its own in the phylogenetic trees. The polar lipids consisted of phosphatidylethanolamine, an unidentified aminolipid and three unidentified phospholipids. The DNA G+C content was 35.4 mol%, MK-6 was the major isoprenoid quinone, and homospermidine was the predominant polyamine. The predominant cellular fatty acids were iso-C15 : 0 3-OH, iso-C15 : 0, a summed feature comprising C16 : 1ω7c and/or C16 : 1ω6c and iso-C15 : 1 G. The absence of aminophospholipid, acid production from carbohydrates, DNA G+C content and colony morphology differentiated strain K3R-10T from related species of the genus Flavobacterium. Thus, on the basis of phenotypic, chemotaxonomic and phylogenetic features, strain K3R-10T evidently represents a novel species in the genus Flavobacterium, for which the name Flavobacterium keumense sp. nov. is proposed. The type strain is K3R-10T (=JCM 31220T=KCTC 52563T).
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http://dx.doi.org/10.1099/ijsem.0.001920DOI Listing
July 2017

Surface Soil Moisture Retrieval Using the L-Band Synthetic Aperture Radar Onboard the Soil Moisture Active-Passive Satellite and Evaluation at Core Validation Sites.

IEEE Trans Geosci Remote Sens 2017 Jan;Volume 55(Iss 4):1897-1914

Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109 USA.

This paper evaluates the retrieval of soil moisture in the top 5-cm layer at 3-km spatial resolution using L-band dual-copolarized Soil Moisture Active-Passive (SMAP) synthetic aperture radar (SAR) data that mapped the globe every three days from mid-April to early July, 2015. Surface soil moisture retrievals using radar observations have been challenging in the past due to complicating factors of surface roughness and vegetation scattering. Here, physically based forward models of radar scattering for individual vegetation types are inverted using a time-series approach to retrieve soil moisture while correcting for the effects of static roughness and dynamic vegetation. Compared with the past studies in homogeneous field scales, this paper performs a stringent test with the satellite data in the presence of terrain slope, subpixel heterogeneity, and vegetation growth. The retrieval process also addresses any deficiencies in the forward model by removing any time-averaged bias between model and observations and by adjusting the strength of vegetation contributions. The retrievals are assessed at 14 core validation sites representing a wide range of global soil and vegetation conditions over grass, pasture, shrub, woody savanna, corn, wheat, and soybean fields. The predictions of the forward models used agree with SMAP measurements to within 0.5 dB unbiased-root-mean-square error (ubRMSE) and -0.05 dB (bias) for both copolarizations. Soil moisture retrievals have an accuracy of 0.052 m/m ubRMSE, -0.015 m/m bias, and a correlation of 0.50, compared to measurements, thus meeting the accuracy target of 0.06 m/m ubRMSE. The successful retrieval demonstrates the feasibility of a physically based time series retrieval with L-band SAR data for characterizing soil moisture over diverse conditions of soil moisture, surface roughness, and vegetation.
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http://dx.doi.org/10.1109/TGRS.2016.2631126DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6839717PMC
January 2017

Taibaiella soli sp. nov., isolated from pine forest soil.

Int J Syst Evol Microbiol 2016 Aug 24;66(8):3230-3234. Epub 2016 May 24.

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

A Gram-stain-negative, motile by gliding, non-spore-forming and oval-shaped bacterial strain designated T1-10T was isolated from pine forest soil, and its taxonomic position was investigated using a polyphasic approach. Growth occurred at 10-37 °C (optimum, 30 °C), at pH 6-7 and in the presence of 0-1 % (w/v) (optimum, 0 %) NaCl. Flexirubin-type pigments were produced. On the basis of 16S rRNA gene sequence similarity, strain T1-10T was assigned to the genus Taibaiella of the phylum Bacteroidetes, and the most closely related species was Taibaiella koreensis THG-DT86T with 97.11 % sequence similarity, but the strain formed an independent lineage in the phylogenetic tree. The genomic DNA G+C content of strain T1-10T was 42.5 mol%. The main cellular fatty acids were iso-C15 : 1 G, iso-C15 : 0 and iso-C17 : 0 3-OH. The only isoprenoid quinone detected in the strain was MK-7, and the major polyamine was homospermidine. The major polar lipids were phosphatidylethanolamine and unidentified aminophospholipids. Strain T1-10T could be distinguished from related species by physiological and biochemical properties. Phenotypic and phylogenetic data supported that strain T1-10T represents a novel species of the genus Taibaiella, for which the name Taibaiella soli sp. nov. is proposed (type strain T1-10T=KCTC 42277T=JCM 31014T).
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http://dx.doi.org/10.1099/ijsem.0.001172DOI Listing
August 2016

Humibacter soli sp. nov., isolated from soil.

Int J Syst Evol Microbiol 2016 Jul 15;66(7):2509-2514. Epub 2016 Apr 15.

Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon, South Korea.

A novel actinobacterial strain, designated R1-20, was isolated during a study of the bacterial diversity of the soil at a white heron nesting site. The isolate was non-motile, Gram-stain-positive and short rod-shaped. Colonies were dull white and convex with entire margin during the early stages of growth, and gradually became yellow. 16S rRNA gene sequence analysis indicated that the isolate belongs to the genus Humibacter of the family Microbacteriaceae, as sequence similarity with its nearest neighbours was 97.16 % with Humibacter antriD7-27and 96.44 % with Humibacter albusDSM 18994. However, the combination of cultural and physiological as well as chemotaxonomic properties clearly distinguished strain R1-20 from other Humibacter species. The DNA G+C content of strain R1-20 was 65.5 mol%, and the major respiratory isoprenoid quinone was menaquinone MK-11. The acyl group of the peptidoglycan was of acetyl type, and the diagnostic diamino acid was 2,4-diaminobutyric acid. Glutamic acid, alanine and glycine were also present in the cell wall. The major fatty acids of strain R1-20 were anteiso-C17 : 0, iso-C16 : 0 and anteiso-C15 : 0. On the basis of phylogenetic, phenotypic and chemotaxonomic analysis, strain R1-20 merits recognition as a representative of a novel species of the genus Humibacter, for which the name Humibacter soli sp. nov. is proposed. The type strain is R1-20 (=KCTC 39614=JCM 31015).
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http://dx.doi.org/10.1099/ijsem.0.001081DOI Listing
July 2016

Allohumibacter endophyticus gen. nov., sp. nov., isolated from the root of wild Artemisia princeps (mugwort).

Int J Syst Evol Microbiol 2016 Apr 2;66(4):1823-1827. Epub 2016 Feb 2.

Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon 305-764, Republic of Korea.

A novel actinobacterium designated strain MWE-A11T was isolated from the root of wild Artemisia princeps (mugwort). The isolate was aerobic, Gram-stain-positive and short rod-shaped, and the colonies were yellow and circular with entire margin. Strain MWE-A11T grew at 15-37 °C and pH 6.0-8.0. The predominant isoprenoid quinones were MK-11 and MK-10. The predominant fatty acids were anteiso-C15:0 and iso-C16:0, and the DNA G+C content was 68.8 mol%. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid. The peptidoglycan contained 2,4-diaminobutyric acid as the diagnostic diamino acid, and the acyl type was glycolyl. Phylogenetic analyses based on 16S rRNA gene sequence comparisons indicated that strain MWE-A11T was affiliated with the family Microbacteriaceae, and was most closely related to the type strains of Humibacter antri (96.4% 16S rRNA gene sequence similarity), Herbiconiux moechotypicola (96.3%), Leifsonia soli (96.3%), Leifsonia lichenia (96.2%), Leifsonia xyli subsp. cynodontis (96.1%), Microbacterium testaceum (96.0%) and Humibacter albus (96.0%). However, the combination of chemotaxonomic properties clearly distinguished strain MWE-A11T from the related taxa at genus level. Accordingly, Allohumibacter endophyticus gen. nov., sp. nov. is proposed to accommodate a new member of the family Microbacteriaceae. The type strain of the type species is MWE-A11T (=JCM 19371T=KCTC 29232T).
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http://dx.doi.org/10.1099/ijsem.0.000948DOI Listing
April 2016

Amylibacter ulvae sp. nov., a new alphaproteobacterium isolated from the Pacific green alga Ulva fenestrata.

Arch Microbiol 2016 Apr 13;198(3):251-6. Epub 2016 Jan 13.

Department of Microbiology and Molecular Biology, School of Bioscience and Biotechnology, Chungnam National University, 220 Gung-dong, Yuseong, Daejeon, 305-764, Republic of Korea.

A strictly aerobic, Gram-stain-negative, rod-shaped and non-motile bacterium, designated strain 6Alg 255(T), was isolated from the green alga Ulva fenestrata. Phylogenetic analysis based on 16S rRNA gene sequencing revealed that the novel strain affiliated to the family Rhodobacteraceae of the class Alphaproteobacteria being most closely related to Amylibacter marinus LMG 28364(T) with 16S rRNA gene sequence similarity of 97.2 %. Strain 6Alg 255(T) grew with 0.5-6.0 % NaCl and at 4-33 °C, hydrolysed aesculin, casein, gelatin and urea. The DNA G + C content was 50.4 mol%. The prevalent fatty acids were C18:1 ω7c and C16:0. The polar lipid profile was characterized by the presence of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and unidentified aminolipid. The major respiratory quinone was Q-10. The significant molecular distinctiveness between the novel isolate and its nearest neighbour was strongly supported by the differences in physiological and biochemical tests. Therefore, strain 6Alg 255(T) represents a novel species of the genus Amylibacter, for which the name Amylibacter ulvae sp. nov. is proposed. The type strain is 6Alg 255(T) (=KCTC 32465(T) = KMM 6515(T)).
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http://dx.doi.org/10.1007/s00203-015-1185-1DOI Listing
April 2016

Antibiotic resistance among aquatic bacteria in natural freshwater environments of Korea.

J Water Health 2015 Dec;13(4):1085-97

Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, 99 Daehak-Ro, Yuseong, Daejeon 305-764, Republic of Korea E-mail:

The taxonomic diversity and antibiotic resistance among freshwater bacterial communities in the major water bodies of Korea was examined using 437 penicillin-resistant, and 110 tetracycline-resistant bacterial isolates. Based on 16S rRNA gene sequence analysis, most isolates were assigned to Proteobacteria, which was then followed by Bacteroidetes. Strains of Aeromonas were found as the most abundant penicillin-resistant populations, whereas those affiliated to diverse species including enteric groups were found as the most abundant tetracycline-resistant populations. Most strains exhibited multiple antibiotic resistance, and all tested strains were resistant to penicillin and hygromycin. High levels of resistance were observed for antibiotics acting on cell wall synthesis, whereas low levels were for those acting on DNA replication or transcription in general. It is apparent from this study that penicillin resistance is widespread among environmental bacteria, although the antibiotic has been generally non-detectable in the environment. It is also likely from the taxonomic composition of the resistant communities that various sources including terrestrial animals and humans may contribute to antibiotic resistance in the freshwater environment.
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http://dx.doi.org/10.2166/wh.2015.032DOI Listing
December 2015

Flavobacterium paronense sp. nov., isolated from freshwater of an artificial vegetated island.

Int J Syst Evol Microbiol 2016 Jan 30;66(1):365-370. Epub 2015 Oct 30.

Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, 449-791, Republic of Korea.

A Gram-stain-negative, motile by gliding, yellow-pigmented bacterial strain, designated KNUS1T, was isolated from Lake Paro in Korea. The phylogenetic tree based on 16S rRNA gene sequences showed that strain KNUS1T formed a distinct lineage within the genus Flavobacterium. Strain KNUS1T was closely related to Flavobacterium cheonhonense ARSA-15T (96.8 %16S rRNA gene sequence similarity), Flavobacterium pectinovorum DSM 6368T (96.3 %) and Flavobacterium dankookense ARSA-19T (96.1 %). The major fatty acids of strain KNUS1T were iso-C15 : 0 and iso-C15 : 1 G. The major polyamine was sym-homospermidine. The major polar lipids of strain KNUS1T were phosphatidylethanolamine, five unidentified aminolipids and three unidentified polar lipids. The major respiratory'quinone was menaquinone 6 (MK-6). The DNA G+C content of strain KNUS1T was 34.2 mol%. On the basis of the evidence presented in this study, strain KNUS1T represents a novel species of the genus Flavobacterium, for which the name Flavobacterium paronense sp. nov. is proposed. The type strain is KNUS1T ( = KACC 17692T = CECT 8460T).
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http://dx.doi.org/10.1099/ijsem.0.000727DOI Listing
January 2016

Fluviicoccus keumensis gen. nov., sp. nov., isolated from freshwater.

Int J Syst Evol Microbiol 2016 Jan 22;66(1):201-205. Epub 2015 Oct 22.

Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, 220 Gung-Dong, Yuseong, Daejeon 34134, Republic of Korea.

A Gram-stain-negative, non-spore-forming and coccus-shaped bacterial strain, designated 4DR5T, was isolated from freshwater and its taxonomic position was investigated using a polyphasic approach. Growth occurred at 10-40 °C (optimum 30 °C), at pH 6-9 (optimum pH 7) and in the presence of 0-0.4 % (w/v) NaCl (optimum 0 %) on R2A agar. On the basis of 16S rRNA gene sequence similarity, strain 4DR5T was assigned to the family Moraxellaceae of the class Gammaproteobacteria, and its closest related taxa were species of the genera Perlucidibaca (93.67 % sequence similarity), Agitococcus (93.07 %), Paraperlucidibaca (92.31-92.38 %), Alkanindiges (91.79 %) and Acinetobacter (90.24-91.23 %). The predominant isoprenoid quinone detected in strain 4DR5T was Q-10. The major cellular fatty acids were a summed feature consisting of C16 : 1ω7c and/or C16 : 1ω6c, one consisting of C18 : 1ω7c and/or C18 : 1ω6c, and C16 : 0. The major polar lipid was phosphatidylethanolamine. The genomic DNA G+C content of the strain was 61.2 mol%. The phylogenetic, chemotaxonomic and biochemical data not only supported the affiliation of strain 4DR5T to the family Moraxellaceae, but also separated it from other established genera within the family. Therefore, the novel isolate evidently represents a novel species of a new genus of Moraxellaceae, for which the name Fluviicoccus keumensis gen. nov., sp. nov. is proposed. The type strain of Fluviicoccus keumensis is 4DR5T ( = KCTC 32475T = JCM 19370T).
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http://dx.doi.org/10.1099/ijsem.0.000694DOI Listing
January 2016

High-level production of violacein by the newly isolated Duganella violaceinigra str. NI28 and its impact on Staphylococcus aureus.

Sci Rep 2015 Oct 22;5:15598. Epub 2015 Oct 22.

School of Life Sciences, Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, S. Korea.

A violacein-producing bacterial strain was isolated and identified as a relative of Duganella violaceinigra YIM 31327 based upon phylogenetic analyses using the 16S rRNA, gyrB and vioA gene sequences and a fatty acid methyl ester (FAME) analysis. This new strain was designated D. violaceinigra str. NI28. Although these two strains appear related based upon these analyses, the new isolate was phenotypically different from the type strain as it grew 25% faster on nutrient media and produced 45-fold more violacein. When compared with several other violacein producing strains, including Janthinobacterium lividum, D. violaceinigra str. NI28 was the best violacein producer. For instance, the crude violacein yield with D. violaceinigra str. NI28 was 6.0 mg/OD at 24 hours, a value that was more than two-fold higher than all the other strains. Finally, the antibacterial activity of D. violaceinigra str. NI28 crude violacein was assayed using several multidrug resistant Staphylococcus aureus. Addition of 30 μM crude violacein led to a 96% loss in the initial S. aureus population while the minimum inhibitory concentration was 1.8 μM. Consequently, this novel isolate represents a phenotypic variant of D. violaceinigra capable of producing much greater quantities of crude violacein, an antibiotic effective against multidrug resistant S. aureus.
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http://dx.doi.org/10.1038/srep15598DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4614999PMC
October 2015
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