Journal of Microbiology

Chi Nam Seong

12 Articles

Taxonomic hierarchy of the phylum Firmicutes and novel Firmicutes species originated from various environments in Korea: Chi Nam Seong , Joo Won Kang , Ji Hee Lee , So Yeon Seo , Jung Jae Woo , Chul Park , Kyung Sook Bae , Mi Sun Kim; J. Microbiol. 2018;56(1):1-10. Published online January 4, 2018; DOI: https://doi.org/10.1007/s12275-018-7318-x

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This study assessed the taxonomic hierarchy of the phylum Firmicutes as well as elucidated the isolation and classification states of novel Firmicutes species isolated from Korean territory. The hierarchical classification system of the phylum Firmicutes has been developed since 1872 when the genus Bacillus was first reported and has been generally adopted since 2001. However, this taxonomic hierarchy is still being modified. Until Feb. 2017, the phylum Firmicutes consisted of seven classes (Bacilli, Clostridia, Erysipelotrichia, Limnochordia, Negativicutes, Thermolithobacteria, and Tissierellia), 13 orders, 45 families, and 421 genera. Firmicutes species isolated from various environments in Korea have been reported from 2000, and 187 species have been approved as of Feb. 2017. All Firmicutes species were affiliated with three classes (Bacilli, Clostridia, and Erysipelotrichia), four orders (Bacillales, Lactobacillales, Clostridiales, and Erysipelotrichales), 17 families, and 54 genera. A total of 173 species belong to the class Bacilli, of which 151 species were affiliated with the order Bacillales and the remaining 22 species with the order Lactobacillales. Twelve species belonging to the class Clostridia were affiliated within only one order, Clostridiales. The most abundant family was Bacillaceae (67 species), followed by the family Paenibacillaceae (56 species). Thirteen novel genera were created using isolates from the Korean environment. A number of Firmicutes species were isolated from natural environments in Korean territory. In addition, a considerable number of species were isolated from artificial resources such as fermented foods. Most Firmicutes species, belonging to the families Bacillaceae, Planococcaceae, and Staphylococcaceae, isolated from Korean fermented foods and solar salterns were halophilic or halotolerant. Firmicutes species were isolated from the whole territory of Korea, especially large numbers from Provinces Gyeonggi, Chungnam, and Daejeon.

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Korean indigenous bacterial species with valid names belonging to the phylum Actinobacteria: Kyung Sook Bae , Mi Sun Kim , Ji Hee Lee , Joo Won Kang , Dae In Kim , Ji Hee Lee , Chi Nam Seong; J. Microbiol. 2016;54(12):789-795. Published online November 26, 2016; DOI: https://doi.org/10.1007/s12275-016-6446-4

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To understand the isolation and classification state of actinobacterial species with valid names for Korean indigenous isolates, isolation source, regional origin, and taxonomic affiliation of the isolates were studied. At the time of this writing, the phylum Actinobacteria consisted of only one class, Actinobacteria, including five subclasses, 10 orders, 56 families, and 330 genera. Moreover, new taxa of this phylum continue to be discovered. Korean actinobacterial species with a valid name has been reported from 1995 as Tsukamurella inchonensis isolated from a clinical specimen. In 1997, Streptomyces seoulensis was validated with the isolate from the natural Korean environment. Until Feb. 2016, 256 actinobacterial species with valid names originated from Korean territory were listed on LPSN. The species were affiliated with three subclasses (Acidimicrobidae, Actinobacteridae, and Rubrobacteridae), four orders (Acidimicrobiales, Actinomycetales, Bifidobacteriales, and Solirubrobacterales), 12 suborders, 36 families, and 93 genera. Most of the species belonged to the subclass Actinobacteridae, and almost of the members of this subclass were affiliated with the order Actinomycetales. A number of novel isolates belonged to the families Nocardioidaceae, Microbacteriaceae, Intrasporangiaceae, and Streptomycetaceae as well as the genera Nocardioides, Streptomyces, and Microbacterium. Twenty-six novel genera and one novel family, Motilibacteraceae, were created first with Korean indigenous isolates. Most of the Korean indigenous actionobacterial species were isolated from natural environments such as soil, seawater, tidal flat sediment, and fresh-water. A considerable number of species were isolated from artificial resources such as fermented foods, wastewater, compost, biofilm, and water-cooling systems or clinical specimens. Korean indigenous actinobacterial species were isolated from whole territory of Korea, and especially a large number of species were from Jeju, Gyeonggi, Jeonnam, Daejeon, and Chungnam. A large number of novel actinobacterial species continue to be discovered since the Korean government is encouraging the search for new bacterial species and researchers are endeavoring to find out novel strains from extreme or untapped environments.

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Taxonomic hierarchy of the phylum Firmicutes and novel Firmicutes species originated from various environments in Korea
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Bhargavaea indica sp. nov., a Member of the Phylum Firmicutes, Isolated from Arabian Sea Sediment: Pankaj Verma , Chi Nam Seong , Prashant Kumar Pandey , Ramesh Ramchandra Bhonde , Cathrin Spröer , Manfred Rohde , Yogesh Shreepad Shouche; J. Microbiol. 2013;51(1):36-42. Published online March 2, 2013; DOI: https://doi.org/10.1007/s12275-013-2488-z

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A Gram-positive, aerobic, coccoid-rod shaped, non-motile, catalase- and oxidase-positive bacterium, designated strain KJW98T, was isolated from the marine sediment of Karwar jetty, west coast of India. The strain was β-haemolytic, nonendospore-forming and grew with 0–8.5% (w/v) NaCl, at 15–48°C and at pH 6.5–9.0, with optimum growth with 0.5% (w/v) NaCl, at 42°C and at pH 7.0–8.0. Phylogenetic analyses based on 16S rRNA and gyrB gene sequences showed that strain KJW98T forms a lineage within the genus Bhargavaea. The G+C content of the genomic DNA was 55 mol%. The DNA–DNA relatedness values of strain KJW98T with B. eijingensis DSM 19037T, B. cecembensis LMG 24411T and B. ginsengi DSM 19038T were 43.2, 39 and 26.5%, respectively. The major fatty acids were anteiso-C15:0 (37.7%), iso-C15:0 (19.7%), anteiso-C17:0 (17.0%) and iso-C16:0 (11.1%). The predominant menaquinone was MK-8 and the cell-wall peptidoglycan was of A4α type with L-lysine as the diagnostic diamino acid. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The phenotypic, genotypic and DNA–DNA relatedness data indicate that strain KJW98T should be distinguished from the members of the genus Bhargavaea, for which the name Bhargavaea indica sp. nov. is proposed with the type strain KJW98T (=KCTC 13583T =LMG 25219T).

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A metagenomic fosmid library was constructed using genomic DNA isolated from abalone intestine. Screening of a library of 3,840 clones revealed a 36 kb insert of a cellulase positive clone (pAM11E10). A shotgun clone library was constructed using the positive clone (pAM11E10) and further screening of 3,840 shotgun clones with an approximately 5 kb insert size using a Congo red overlay revealed only one cellulase positive clone (pAM11L9). The pAM11L9 consisted of a 5,293-bp DNA sequence and three open reading frames (ORFs). Among the three ORFs, cellulase activity was only shown in the recombinant protein (CelAM11) coded by ORF3, which showed 100% identity with outer membrane protein A from Vibrio alginolyticus 12G01, but no significant sequence homology to known cellulases. The expressed protein (CelAM11) has a molecular weight of approximately 37 kDa and the highest CMC hydrolysis activity was observed at pH 7.0 and 37°C. The carboxymethyl cellulase activity was determined by zymogram active staining and different degraded product profiles for CelAM11 were obtained when cellotetraose and cellopentaose were used as the substrates, while no substrate hydrolysis was observed on oligosaccharides such as cellobiose and cellotriose.

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Diversity of bacterial community in water layer of Woopo wetland was investigated. Cultivable bacterial strains were isolated by the standard dilution plating technique and culture-independent 16S rRNA gene clones were obtained directly from DNA extracts of a water sample. Amplified rDNA restriction analysis (ARDRA) was applied onto both of the isolates and 16S rRNA gene clones. Rarefaction curves, coverage rate and diversity indices of ARDRA patterns were calculated. Representative isolates and clones of all the single isolate/clone phylotype were partially sequenced and analyzed phylogenetically. Sixty-four and 125 phylotypes were obtained from 203 bacterial isolates and 235 culture-independent 16S rRNA gene clones, respectively. Bacterial isolates were composed of 4 phyla, of which Firmicutes (49.8%) and Actinobacteria (32.0%) were predominant. Isolates were affiliated with 58 species. Culture-independent 16S rRNA gene clones were composed of 8 phyla, of which Proteobacteria (62.2%), Actinobacteria (15.5%), and Bacteroidetes (13.7%) were predominant. Diversity of 16S rRNA gene clones originated from cultivation-independent DNA extracts was higher than that of isolated bacteria.

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A non-motile and rod shaped bacterium, designated strain B1T, was isolated from forest soil at Mt. Baekwoon, Republic of Korea. Cells were Gram-negative, catalase-positive, and oxidase-negative. The major fatty acids were 9-octadecenoic acid (C18:1 ω9c; 42%) and hexadecanoic acid (C16:0; 25.9%) and summed feature 3 (comprising iso-C15:0 2-OH and/or C16:1 ω7c; 10.0%). The DNA G+C content was 44.1 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain B1T formed a lineage within the genus Acinetobacter and was closely related to A. baylyi DSM 14961T (98.6% sequence similarity), followed by A. baumannii DSM 30007T (97.4%), A. calcoaceticus DSM 30006T (97.0%), and 3 genomic species (96.8~7.6%). Phenotypic characteristics, gyrB gene sequence analysis and DNA-DNA relatedness data distinguished strain B1T from type strains of A. baylyi, A. baumannii, and A. calcoaceticus. On the basis of the evidence presented in this study, strain B1T represents a novel species of the genus Acinetobacter, for which the name Acinetobacter soli sp. nov. is proposed. The type strain is B1T (= KCTC 22184T= JCM 15062T).

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Li Yuan, Wei Zhi, Yangsheng Liu, Elizabeth Smiley, Daniel Gallagher, Xi Chen, Andrea M. Dietrich, Husen Zhang
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Utility of Whole-Genome Sequencing in Characterizing Acinetobacter Epidemiology and Analyzing Hospital Outbreaks
Margaret A. Fitzpatrick, Egon A. Ozer, Alan R. Hauser, B. A. Forbes
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Ömer Acer, Kemal Güven, Fatma Matpan Bekler, Reyhan Gül-Güven
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Seung Yeob Lee, Jong Hee Shin, Soo Hyun Kim, Myung Geun Shin, Soon Pal Suh, Dong Wook Ryang
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Jin-Gui Cao, Hu Zhang, Ya-Ping Xu, Zhong-Qiang Yan, Yun-Xi Liu
Diagnostic Microbiology and Infectious Disease.2015; 83(4): 407. CrossRef
Acinetobacter harbinensis sp. nov., isolated from river water
Weiguang Li, Duoying Zhang, Xiaofei Huang, Wen Qin
International Journal of Systematic and Evolutionary Microbiology .2014; 64(Pt_5): 1507. CrossRef
Acinetobacter gandensis sp. nov. isolated from horse and cattle
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International Journal of Systematic and Evolutionary Microbiology.2014; 64(Pt_12): 4007. CrossRef
Acinetobacter sp. isolates from emergency departments in two hospitals of South Korea
Ji-Young Choi, Eun Ah Ko, Ki Tae Kwon, Shinwon Lee, Choel In Kang, Doo-Ryeon Chung, Kyong Ran Peck, Jae-Hoon Song, Kwan Soo Ko
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Antimicrobial Agents and Chemotherapy.2014; 58(2): 936. CrossRef
NDM-1–producing Acinetobacter soli from Taiwan
Tsai-Ling Lauderdale, Ming-Chia Hsu, Jung-Jung Mu, Feng-Yee Chang, Jui-Fen Lai, Mei-Chen Tan, Hui-Yin Wang, Shan-Chwen Chang
Diagnostic Microbiology and Infectious Disease.2014; 80(2): 168. CrossRef
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Hiromitsu Kitanaka, Masa-aki Sasano, Satoru Yokoyama, Masahiro Suzuki, Wanchun Jin, Masami Inayoshi, Mitsuhiro Hori, Jun-ichi Wachino, Kouji Kimura, Keiko Yamada, Yoshichika Arakawa
Emerging Infectious Diseases.2014; 20(9): 1574. CrossRef
Acinetobacter apis sp. nov., isolated from the intestinal tract of a honey bee, Apis mellifera
Pil Soo Kim, Na-Ri Shin, Joon Yong Kim, Ji-Hyun Yun, Dong-Wook Hyun, Jin-Woo Bae
Journal of Microbiology.2014; 52(8): 639. CrossRef
Draft Genome Sequence of a Multidrug-Resistant bla NDM-1-Producing Acinetobacter soli Isolate in China
Yan Chen, Zhengsong Yan, Miaojuan Wang, Xia Zheng, Yun Lu, Shaohua Lin
Indian Journal of Microbiology.2014; 54(4): 474. CrossRef
Acinetobacter nectaris sp. nov. and Acinetobacter boissieri sp. nov., isolated from floral nectar of wild Mediterranean insect-pollinated plants
Sergio Álvarez-Pérez, Bart Lievens, Hans Jacquemyn, Carlos M. Herrera
International Journal of Systematic and Evolutionary Microbiology.2013; 63(Pt_4): 1532. CrossRef
Acinetobacter puyangensis sp. nov., isolated from the healthy and diseased part of Populus ×euramericana canker bark
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Journal of Virology.2012; 86(23): 13131. CrossRef
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Wei-Hua Zhao, Zhi-Qing Hu
Critical Reviews in Microbiology.2012; 38(1): 30. CrossRef
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List of new names and new combinations previously effectively, but not validly, published

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY.2009; 59(7): 1555. CrossRef

InhA-Like Protease Secreted by Bacillus sp. S17110 Inhabited in Turban Shell: Sang Chul Jung , Hyoung-Rok Paik , Mi Sun Kim , Keun Sik Baik , Woo-Yiel Lee , Chi Nam Seong , Sang Ki Choi; J. Microbiol. 2007;45(5):402-408.; DOI: https://doi.org/2597 [pii]

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Abstract PDF: A strain producing a potent protease was isolated from turban shell. The strain was identified as Bacillus sp. S17110 based on phylogenetic analysis. The enzyme was purified from culture supernatant of Bacillus sp. S17110 to homogeneity by ammonium sulfate precipitation, SP-Sepharose, and DEAE-Sepharose anion exchange chromatography. Protease activity of the purified protein against casein was found to be stable at pH 7 to pH 10 and around 50°C. Approximately 70% of proteolytic activity of the enzyme was detected either in the presence of 100 mM SDS or Tween 20. The enzyme activity was enhanced in the presence of Ca2+, Zn2+, Mg2+, but was inhibited by EDTA, indicating that it requires metal for its activity. The purified enzyme was found to be a monomeric protein with a molecular mass of 75 kDa, as estimated by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and gel filtration chromatography. The purified enzyme was analyzed through peptide fingerprint mass spectra generated from matrix-assisted laser desorption ionization-time-of-flight-mass spectrometry (MALDI-TOF-MS) and a BLAST search, and identified as immune inhibitor A (inhA) deduced from nucleotide sequence of B. cereus G9241. Since InhA was identified as protease that cleave antibacterial proteins found in insect, inhA-like protease purified from Bacillus sp. S17110 might be pathogenic to sea invertebrates.

Production and Biological Activity of Laidlomycin, Anti-MRSA/VRE Antibiotic from Streptomyces sp. CS684: Jin Cheol Yoo , Jun Ho Kim , Jung Wan Ha , Nae Soo Park , Jae Kyung Sohng , June Woo Lee , Seong Chan Park , Mi Sun Kim , Chi Nam Seong; J. Microbiol. 2007;45(1):6-10.; DOI: https://doi.org/2499 [pii]

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Abstract PDF: Culture broth of a streptomycete isolate, Streptomyces sp. CS684 showed antibacterial activity on methicilin resistant Staphylococcus aureus (MRSA) and vancomycin resistant enterococci (VRE). Among purified substances from the organism, CSU-1, which is active against MRSA and VRE, is a C37H62O12Na (M+, 721.3875), and identified as laidlomycin. The anti-MRSA and anti-VRE activity of CSU-1 was stronger than oxacillin and vancomycin. Phylogenetic analysis showed that strain CS684 is very similar to Streptomyces ardus NRRL 2817T, whereas the ability of Streptomyces sp. CS684 to produce laidlomycin was shown to be unique.

Phylogenetic Diversity of Acidophilic Sporoactinobacteria Isolated from Various Soils: Sung-Heun Cho , Ji-Hye Han , Chi Nam Seong , Seung Bum Kim; J. Microbiol. 2006;44(6):600-606.; DOI: https://doi.org/2468 [pii]

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Abstract PDF: Spore forming actinobacteria (sporoactinobacteria) isolated from soils with an acidic pH in Pinus thunbergii forests and coal mine waste were subjected to taxonomic characterization. For the isolation of acidophilic actinobacteria, acidified starch casein agar (pH adjusted to 4-5) was used. The numbers of actinobacteria growing in acidic media were between 3.2 × 104 and 8.0 × 106 CFU/g soil. Forty three acidophilic actinobacterial strains were isolated and their 16S rDNA sequences were determined. The isolates were divided into eight distinctive phylogenetic clusters within the variation encompassed by the family Streptomycetaceae. Four clusters among them were assigned to the genus Streptacidiphilus, whereas the remaining four were assigned to Streptomyces. The clusters belonging to either Streptomyces or Streptacidiphilus did not form monophyletic clade. The growth pH profiles indicated that the representative isolates grew best between pH 5 and 6. It is evident from this study that acidity has played a critical role in the differentiation of the family Streptomycetaceae, and also that different mechanisms might have resulted in the evolution of two groups, Streptacidiphilus (strict acidophiles) and neutrotolerant acidophilic Streptomyces. The effect of geographic separation was clearly seen among the Streptacidiphilus isolates, which may be a key factor in speciation of the genus.

Tsukamurella sunchonensis sp. nov., a Bacterium Associated with Foam in Activated Sludge: Chi Nam Seong , Young Sook Kim , Keun Shik Baik , Sang Ki Choi , Min Bae Kim; J. Microbiol. 2003;41(2):83-88.

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Abstract PDF: aeration basin of an activated sludge process, was clarified by phenotypic, chemotaxonomic and phylogenetic analyses. The strain possesses wall chemotype IV, MK-9(H_0 ), as the major menaquinone, and contains saturated, monounsaturated and 10-methyl branched fatty acids. The G+C content of its DNA is 68.1 mol%. Phenotypic data and DNA relatedness to known species indicate that the strain SCNU5^T represents a new species within the genus Tsukamurella, for which we propose the name Tsukamurella sunchonensis sp. nov. The type strain of T. sunchonensis is SCNU5^T (=KCTC 9827^T ).

Prevalence and Antibiotic Susceptibility of Vancomycin-Resistant Enterococci in Chicken Intestines and Fecal Samples from Healthy Young Children and Intensive Care Unit Patients: Shin Moo Kim , Eun Sook Shim , Chi Nam Seong; J. Microbiol. 2001;39(2):116-120.

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Abstract PDF: The prevalence, resistance genotype and antibiotic susceptibility of vancomycin-resistant enterococci (VRE) were determined. Prevalence of VRE in chickens, healthy children and intensive care unit (ICU) patients was 43.0%, 12.7% and 24.1%, respectively. Forty out of 56 isolates from chicken intestines were identified as Enterococcus faecium, and 12 were E. faecalis. All the isolates contained the vanA gene. Nine out of 13 VRE isolates from patients and two out of 21 from healthy young children were identified as E. faecium. The resistance types of E. faecium, E. gallinarium and E. casseliflavus were VanA, VanC1, and VanC2, respectively. The mimimum inhibitory concentrations (MICs) of E. faecium, E. gallinarium, and E. casseliflavus to vancomycin were 512, 8 and 4 g/ml, respectively. Specifically, E. faecium isolates were resistant to most of antibiotics except ampicillin and gentamicin. This is the first report of high VanA type VRE prevalence in nonhospitalized young children in Korea.

An Improved Selective Isolation of Rare Actinomycetes from Forest Soil: Chi Nam Seong , Ji Heok Choi , Keun-Shik Baik; J. Microbiol. 2001;39(1):17-23.

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Abstract PDF: Various pretreatment procedures and selective media were applied to assess the optimal conditions for the isolation of rare actinomycetes from soil. Pretreatment of wet-heating for 15 min at 70oC and phenol treatment of soil suspension were the most effective methods for the isolation of those microorganisms. Hair hydrolysate vitamin agar (HHVA) was the most suitable medium for the recovery of rare actinomycetes. Thirty-five rare actinomycete strains were chosen using selective isolation approaches, then morphological and chemical properties of the isolates were determined. The isolates belonged to one of the following genus, Micromonospora, Microbispora, Actinoplanes and Streptosporangium.

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