Journal of Microbiology

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SimpleMicrobiome: An integrated web-based platform for streamlined microbiome data analysis and visualization: Seong-In Na, Juhee Kim, So-Yeon Kim, Jin Park, Yong-Joon Cho; Received June 11, 2026 Accepted August 4, 2026 Published online September 18, 2026; DOI: https://doi.org/10.71150/jm.2606011 [Epub ahead of print]

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Abstract PDF Supplementary Material: Microbiome studies require multiple analytical steps after initial sequence processing. These steps commonly include data harmonization, preprocessing, taxonomic profiling, diversity analysis, differential abundance testing, predictive modeling, network inference, and preparation of publication-ready outputs. Although robust packages are available for many of these tasks, routine use often depends on command-line workflows, repeated data reformatting, and method-specific scripting. These requirements can limit accessibility for experimental researchers and complicate consistent analysis across interdisciplinary teams. We developed SimpleMicrobiome, a web-based R Shiny platform that integrates established microbiome analysis methods into a single interactive downstream workflow. The application accepts standard abundance, taxonomy, and metadata tables, supports interactive preprocessing and sample filtering, and provides modules for taxa profile visualization, alpha and beta diversity analysis, ANCOM-BC2 and MaAsLin2 differential abundance testing, Random Forest modeling with SHAP-based interpretation, microbial association network inference using SparCC and SPIEC-EASI through NetCoMi, correlation heatmaps, and dbRDA/CAP-style association biplots. The platform is implemented as a modular Shiny application so that preprocessing choices are propagated across downstream analyses, results can be exported as figures and tables, and the same application can be run through the public server, source-code installation, or a Docker image.
SimpleMicrobiome consolidates major downstream microbiome analysis tasks in an accessible browser-based environment while retaining links to established analytical frameworks. The platform may reduce technical barriers for non-programming users, improve consistency across exploratory and reporting-oriented analyses, and support collaborative microbiome research. The public application is available at https://simplemicrobiome.mglab.org, the source code is available at https://github.com/yjcho2252/SimpleMicrobiome, and a Docker image for local deployment is available at https://hub.docker.com/r/mglab2252/simplemicrobiome.

Article

Development of an RT-LAMP−CRISPR/Cas12a assay for rapid and specific detection of Bandavirus dabieense: Bo Seung Song, Yun Hee Baek, Eun-Ha Kim, Hyeok-Il Kwon, Ah-Hyeon Kim, Si-Hyun Lee, Yu-Bin Son, Soo-Hyeon Kim, Min-Suk Song, Young Ki Choi, Su-Jin Park; J. Microbiol. 2025;63(11):e2506013. Published online November 30, 2025; DOI: https://doi.org/10.71150/jm.2506013

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Abstract PDF: Bandavirus dabieense, a single-stranded RNA virus, is the causative agent of severe fever with thrombocytopenia syndrome (SFTS), a disease associated with high fatality rates. Early and accurate diagnosis is essential for improving clinical outcomes, particularly given the limited therapeutic options and high mortality rates associated with SFTS. However, while highly sensitive, conventional diagnostic methods such as PCR and qRT-PCR require specialized laboratory facilities and trained personnel, making them impractical for rapid detection in resource-limited settings. To address these challenges, we developed a rapid and highly sensitive assay for Bandavirus dabieense detection by integrating reverse transcription loop-mediated isothermal amplification (RT-LAMP) with CRISPR/Cas12a technology. LAMP primers and guide RNA sequences were designed to target the L gene, ensuring broad detection across viral genotypes. The optimized assay demonstrated a detection limit of 5 RNA copies per reaction, showing more sensitivity than qRT-PCR, and exhibited 100% concordance with qRT-PCR results in clinical samples. Given its speed, accuracy, and field applicability, this LAMP-CRISPR/Cas12a-based assay represents a promising diagnostic tool for early SFTSV detection, particularly in resource-constrained environments where conventional molecular diagnostics are not readily available.

Erratum

Erratum: Unexpected Requirement of Small Amino Acids at Position 183 for DNA Binding in the Escherichia coli cAMP Receptor Protein: Marcus Carranza, Amanda Rea, Daisy Pacheco, Christian Montiel, Jin Park, Hwan Youn; J. Microbiol. 2024;62(12):1177-1177. Published online November 6, 2024; DOI: https://doi.org/10.1007/s12275-024-00189-y

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Article

Lipoteichoic Acid from Lacticaseibacillus rhamnosus GG as a Novel Intracanal Medicament Targeting Enterococcus faecalis Biofilm Formation: Ji-Young Yoon, Somin Park, Dongwook Lee, Ok-Jin Park, WooCheol Lee, Seung Hyun Han; J. Microbiol. 2024;62(10):897-905. Published online September 30, 2024; DOI: https://doi.org/10.1007/s12275-024-00165-6

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Abstract PDF

The demand for safe and effective endodontic medicaments to control Enterococcus faecalis biofilms, a contributor to apical periodontitis, is increasing. Recently, lipoteichoic acid (LTA) of family Lactobacillaceae has been shown to have anti-biofilm effects against various oral pathogens. Preliminary experiments showed that LTA purified from Lacticaseibacillus rhamnosus GG (Lgg.LTA) was the most effective against E. faecalis biofilms among LTAs from three Lactobacillaceae including L. rhamnosus GG, Lacticaseibacillus casei, and Lactobacillus acidophilus. Therefore, in this study, we investigated the potential of Lgg.LTA as an intracanal medicament in human root canals infected with E. faecalis. Twenty eight dentinal cylinders were prepared from extracted human teeth, where two-week-old E. faecalis biofilms were formed followed by intracanal treatment with sterile distilled water (SDW), N-2 methyl pyrrolidone (NMP), calcium hydroxide (CH), or Lgg.LTA. Bacteria and biofilms that formed in the root canals were analyzed by scanning electron microscopy and confocal laser scanning microscopy. The remaining E. faecalis cells in the root canals after intracanal medicament treatment were enumerated by culturing and counting. When applied to intracanal biofilms, Lgg.LTA effectively inhibited E. faecalis biofilm formation as much as CH, while SDW and NMP had little effect. Furthermore, Lgg.LTA reduced both live and dead bacteria within the dentinal tubules, indicating the possibility of minimal re-infection in the root canals. Collectively, intracanal application of Lgg.LTA effectively inhibited E. faecalis biofilm formation, implying that Lgg.LTA can be used as a novel endodontic medicament.

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Article

Unexpected Requirement of Small Amino Acids at Position 183 for DNA Binding in the Escherichia coli cAMP Receptor Protein: Marcus Carranza, Amanda Rea, Daisy Pacheco, Christian Montiel, Jin Park, Hwan Youn; J. Microbiol. 2024;62(10):871-882. Published online September 6, 2024; DOI: https://doi.org/10.1007/s12275-024-00169-2

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The Escherichia coli cAMP receptor protein (CRP) relies on the F-helix, the recognition helix of the helix-turn-helix motif, for DNA binding. The importance of the CRP F-helix in DNA binding is well-established, yet there is little information on the roles of its non-base-contacting residues. Here, we show that a CRP F-helix position occupied by a non-base-contacting residue Val183 bears an unexpected importance in DNA binding. Codon randomization and successive in vivo screening selected six amino acids (alanine, cysteine, glycine, serine, threonine, and valine) at CRP position 183 to be compatible with DNA binding. These amino acids are quite different in their amino acid properties (polar, non-polar, hydrophobicity), but one commonality is that they are all relatively small. Larger amino acid substitutions such as histidine, methionine, and tyrosine were made site-directedly and showed to have no detectable DNA binding, further supporting the requirement of small amino acids at CRP position 183. Bioinformatics analysis revealed that small amino acids (92.15% valine and 7.75% alanine) exclusively occupy the position analogous to CRP Val183 in 1,007 core CRP homologs, consistent with our mutant data. However, in extended CRP homologs comprising 3700 proteins, larger amino acids could also occupy the position analogous to CRP Val183 albeit with low occurrence. Another bioinformatics analysis suggested that large amino acids could be tolerated by compensatory small-sized amino acids at their neighboring positions. A full understanding of the unexpected requirement of small amino acids at CRP position 183 for DNA binding entails the verification of the hypothesized compensatory change(s) in CRP.

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Adaptive evolution resulted in three subtypes of the Riemerella anatipestifer crpR1 gene
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Article

Lipocalin2 as a potential antibacterial drug against Acinetobacter baumannii infection: Daejin Lim , Su-Jin Park , Ha Young Kim , Minsang Shin , Miryoung Song; J. Microbiol. 2022;60(4):444-449. Published online March 28, 2022; DOI: https://doi.org/10.1007/s12275-022-2007-1

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Abstract PDF

Available antibiotics to treat Acinetobacter baumannii infection is limited due to increasing resistance and the emergence of multiple drug-resistant strains. Hence, discovering effective agents against A. baumannii to reduce the number of infectionrelated deaths is imperative. In search of novel and alternative antibiotics, the antibacterial function of lipocalin2 (Lcn2) was investigated to treat systemic infections of A. baumannii using a mouse neutropenia model. We observed a significant increase in serum Lcn2 levels upon bacterial injection into the mouse, and the administration of recombinant Lcn2 (rmLcn2) extended their survival. Such protective effects were also observed in rmLcn2-pretreated macrophages, where rmLcn2 reduced the survival of the pathogen inside the macrophages. The underlying molecular mechanism of Lcn2 protection was also investigated. We observed that pretreatment of the Raw- 264.7 macrophages with rmLcn2 markedly altered the expression of tonB3, which encodes a component of the transporter for ferrisiderophores in A. baumannii. However, the expression of katG, the gene encoding catalase, remained unaffected. These indicate that Lcn2-mediated defense against the pathogen is related to nutritional immunity rather than reactive oxygen species (ROS) production. Furthermore, the addition of rmLcn2 in infected mice diminished bacterial burden in multiple organs and enhanced the expression of tonB3 in the liver, spleen, and lungs of the infected mice. Increased survival rate due to rmLcn2 treatment declined when the infection model was established using lcn2-defective (lcn2-/-) mice, which indicated the necessity of endogenous Lcn2. Therefore, the antibacterial function of Lcn2 can be exploited to develop an alternative therapeutic agent against A. baumannii.

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Article

Differences in seroprevalence between epicenter and non-epicenter areas of the COVID-19 outbreak in South Korea: Hye Won Jeong , Hyun-Ha Chang , Eun Ji Kim , Yu Kyung Kim , Se-Mi Kim , Eun-Ha Kim , Young-Il Kim , Mark Anthony B. Casel , Seong-Gyu Kim , Rare Rollon , Seung-Gyu Jang , Kwang-Min Yu , Hee-Sung Kim , Hee Sue Park , Su-Jin Park , Yong-Dae Kim , Eung-Gook Kim , Young Ki Choi; J. Microbiol. 2021;59(5):530-533. Published online April 28, 2021; DOI: https://doi.org/10.1007/s12275-021-1095-7

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Abstract PDF

To compare the standardized severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) seroprevalence of high epicenter region with non-epicenter region, serological studies were performed with a total of 3,268 sera from Daegu City and 3,981 sera from Chungbuk Province. Indirect immunofluorescence assay (IFA) for SARS-CoV-2 IgG results showed a high seroprevalence rate in the Daegu City (epicenter) compared with a non-epicenter area (Chungbuk Province) (1.27% vs. 0.91%, P = 0.0358). It is noteworthy that the highest seroprevalence in Daegu City was found in elderly patients (70’s) whereas young adult patients (20’s) in Chungbuk Province showed the highest seroprevalence. Neutralizing antibody (NAb) titers were found in three samples from Daegu City (3/3, 268, 0.09%) while none of the samples from Chungbuk Province were NAb positive. These results demonstrated that even following the large outbreak, the seropositive rate of SARS-CoV-2 in the general population remained low in South Korea.

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Article

Development of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) thermal inactivation method with preservation of diagnostic sensitivity: Young-Il Kim , Mark Anthony B. Casel , Se-Mi Kim , Seong-Gyu Kim , Su-Jin Park , Eun-Ha Kim , Hye Won Jeong , Haryoung Poo , Young Ki Choi; J. Microbiol. 2020;58(10):886-891. Published online September 29, 2020; DOI: https://doi.org/10.1007/s12275-020-0335-6

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Abstract PDF

Various treatments and agents had been reported to inactivate RNA viruses. Of these, thermal inactivation is generally considered an effective and cheap method of sample preparation for downstream assays. The purpose of this study is to establish a safe inactivation method for SARS-CoV-2 without compromising the amount of amplifiable viral genome necessary for clinical diagnoses. In this study, we demonstrate the infectivity and genomic stability of SARSCoV- 2 by thermal inactivation at both 56°C and 65°C. The
results
substantiate that viable SARS-CoV-2 is readily inactivated when incubated at 56°C for 30 min or at 65°C for 10 min. qRT-PCR of specimens heat-inactivated at 56°C for 30 min or 65°C for 15 min revealed similar genomic RNA stability compared with non-heat inactivated specimens. Further, we demonstrate that 30 min of thermal inactivation at 56°C could inactivate viable viruses from clinical COVID-19 specimens without attenuating the qRT-PCR diagnostic sensitivity. Heat treatment of clinical specimens from COVID-19 patients at 56°C for 30 min or 65°C for 15 min could be a useful
method
for the inactivation of a highly contagious agent, SARS-CoV-2. Use of this method would reduce the potential for secondary infections in BSL2 conditions during diagnostic procedures. Importantly, infectious virus can be inactivated in clinical specimens without compromising the sensitivity of the diagnostic RT-PCR assay.

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Article

Propionate, together with triple antibiotics, inhibits the growth of Enterococci: Soyoung Jeong , Yunjae Lee , Cheol-Heui Yun , Ok-Jin Park , Seung Hyun Han; J. Microbiol. 2019;57(11):1019-1024. Published online October 28, 2019; DOI: https://doi.org/10.1007/s12275-019-9434-7

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Abstract PDF

Enterococci are Gram-positive facultative anaerobic bacteria that colonize the oral cavity and gastrointestinal tract. Enterococcal infections, mainly caused by Enterococcus faecalis and Enterococcus faecium, include apical periodontitis, endocarditis, and bloodstream infections. Recently, vancomycinresistant Enterococci are considered major pathogens that are common but difficult to treat, especially in nosocomial settings. Moreover, E. faecalis is closely associated with recurrent endodontic infections and failed endodontic treatment. In this study, we investigated the effects of short-chain fatty acids (SCFAs), acetate, propionate, and butyrate, which are metabolites fermented by gut microbiota, on the growth of Enterococci. Enterococci were cultured in the presence or absence of acetate, propionate, or butyrate, and the optical density at 600 nm was measured to determine bacterial growth. The minimum inhibitory concentration/minimum bactericidal concentration test was conducted. Bacteria were treated with a SCFA, together with clinically used endodontic treatment methods such as triple antibiotics (metronidazole, minocycline, and ciprofloxacin) and chlorhexidine gluconate (CHX) to determine the effects of combination treatment. Of the SCFAs, propionate had a bacteriostatic effect, inhibiting the growth of E. faecalis in a dose-dependent manner and also that of clinical strains of E. faecalis isolated from dental plaques. Meanwhile, acetate and butyrate had minimal effects on E. faecalis growth. Moreover, propionate inhibited the growth of other Enterococci including E. faecium. In addition, combination treatment of propionate and triple antibiotics led to further growth inhibition, whereas no cooperative effect was observed at propionate plus CHX. These results indicate that propionate attenuates the growth of Enterococci, suggesting propionate as a potential agent to control Enterococcal infections, especially when combined with triple antibiotics.

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Article

Efficacy of A/H1N1/2009 split inactivated influenza A vaccine (GC1115) in mice and ferrets: Hae Jung Han , Min-Suk Song , Su-Jin Park , Han Yeul Byun , Norbert John C. Robles , Suk-Hoon Ha , Young Ki Choi; J. Microbiol. 2019;57(2):163-169. Published online January 31, 2019; DOI: https://doi.org/10.1007/s12275-019-8504-1

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Abstract PDF

To evaluate the efficacy of a non-adjuvant A/H1N1/2009 influenza A vaccine (GC1115), we demonstrated the immunogenicity and protective efficacy of GC1115 in mouse and ferret models. The immunogenicity of GC1115 was confirmed after intramuscular administration of 1.875, 3.75, 7.5, and 15 μg hemagglutinin antigen (HA) in mice and 7.5, 15, and 30 μg HA in ferrets at 3-week intervals. A single immunization with GC1115 at HA doses > 7.5 μg induced detectable seroconversion in most mice, and all mice given a second dose exhibited high antibody responses in a dose-dependent manner. The mice in the mock (PBS) and 1.875 μg HA immunized groups succumbed by 13 days following A/California/ 04/09 infection, while all mice in groups given more than 3.75 μg HA were protected from lethal challenge with the A/California/04/09 virus. In ferrets, although immunization with even a single dose of 15 or 30 μg of HA induced detectable HI antibodies, all ferrets given two doses of vaccine seroconverted and exhibited HI titers greater than 80 units. Following challenge with A/California/04/09, the mock (PBS) immunized ferrets showed influenza-like clinical symptoms, such as increased numbers of coughs, elevated body temperature, and body weight loss, for 7 days, while GC1115- immunized ferrets showed attenuated clinical symptoms only for short time period (3–4 days). Further, GC1115-immunized ferrets displayed significantly lower viral titers in the upper respiratory tract (nasal cavity) than the mock vaccinated group in a dose-dependent manner. Taken together, this study demonstrates the immunogenicity and protective efficacy of GC1115 as a non-adjuvanted vaccine.

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Lipoteichoic acids of lactobacilli inhibit Enterococcus faecalis biofilm formation and disrupt the preformed biofilm: Solmin Jung , Ok-Jin Park , A Reum Kim , Ki Bum Ahn , Dongwook Lee , Kee-Yeon Kum , Cheol-Heui Yun , Seung Hyun Han; J. Microbiol. 2019;57(4):310-315. Published online January 22, 2019; DOI: https://doi.org/10.1007/s12275-019-8538-4

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Enterococcus faecalis, a Gram-positive bacterium commonly isolated in patients with refractory apical periodontitis, invades dentin tubules easily and forms biofilms. Bacteria in biofilms, which contribute to recurrent and/or chronic inflammatory diseases, are more resistant to antimicrobial agents than planktonic cells and easily avoid phagocytosis. Although Lactobacillus plantarum lipoteichoic acid (Lp.LTA) is associated with biofilm formation, the effect of Lp.LTA on biofilm formation by E. faecalis is not clearly understood. In this study, we investigated whether Lp.LTA inhibits E. faecalis biofilm formation. The degree of biofilm formation was determined by using crystal violet assay and LIVE/DEAD bacteria staining. The quantification of bacterial growth was determined by measuring the optical density at 600 nm with a spectrophotometer. Formation of biofilms on human dentin slices was observed under a scanning electron microscope. E. faecalis biofilm formation was reduced by Lp.LTA treatment in a dose-dependent manner. Lp.LTA inhibited biofilm development of E. faecalis at the early stage without affecting bacterial growth. LTA from other Lactobacillus species such as Lactobacillus acidophilus, Lactobacillus casei, or Lactobacillus rhamnosus GG also inhibited E. faecalis biofilm formation. In particular, among LTAs from various lactobacilli, Lp.LTA showed the highest inhibitory effect on biofilms formed by E. faecalis. Interestingly, LTAs from lactobacilli could remove the biofilm preformed by E. faecalis. These inhibitory effects were also observed on the surface of human dentin slices. In conclusion, Lactobacillus species LTA inhibits biofilm formation caused by E. faecalis and it could be used as an anti-biofilm agent for prevention or treatment against E. faecalis-associated diseases.

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Article

Larkinella roseus sp. nov., a species of the family Cytophagaceae isolated from beach soil: Jae-Bong Lee , Sumin Hong , Seung-Yeol Lee , Su-Jin Park , Kyeung Il Park , Seok-Gwan Choi , Myung Kyum Kim , Leonid N. Ten , Hee-Young Jung; J. Microbiol. 2018;56(1):30-35. Published online January 4, 2018; DOI: https://doi.org/10.1007/s12275-018-7476-x

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Abstract PDF

The taxonomic position of bacterial strain, designated 15J16- 1T3AT, recovered from a soil sample was established using a polyphasic approach. Phylogenic analysis based on the 16S rRNA gene sequence showed that strain 15J16-1T3AT belonged to the family Cytophagaceae, phylum Bacteroidetes, and was most closely related to ‘Larkinella harenae’ 15J9-9 (95.9% similarity), Larkinella ripae 15J11-11T (95.6%), Larkinella bovis M2TB15T (94.7%), Larkinella arboricola Z0532T (93.9%), and Larkinella insperata LMG 22510T (93.5%). Cells were rod-shaped, Gram-stain-negative, aerobic, and nonmotile. The isolate grew on NA, R2A, TSA, but not on LB agar. The strain was able to grow at temperature range from 10°C to 30°C with an optimum at 25°C and pH 6–8. Menaquinone MK-7 was the predominant respiratory quinone. The major cellular fatty acids comprised C16:1 ω5c (48.6%) and C15:0 iso (24.1%). Phosphatidylethanolamine, phosphatidylserine, and an unidentified lipid were the major polar lipids. The G + C content of the genomic DNA was 49.5 mol%. Strain 15J16-1T3AT could be distinguished from its closest phylogenetic neighbors based on its phenotypic, genotypic, and chemotaxonomic features. Therefore, the isolate is considered to represent a novel species in the genus Larkinella, for which the name Larkinella roseus sp. nov. is proposed. The type strain is 15J16-1T3AT (= KCTC 52004T = JCM 31991T).

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Spirosoma migulaei sp. nov., isolated from soil: Joseph Okiria , Leonid N. Ten , Su-Jin Park , Seung-Yeol Lee , Dong Hoon Lee , In-Kyu Kang , Dae Sung Lee , Hee-Young Jung; J. Microbiol. 2017;55(12):927-932. Published online December 7, 2017; DOI: https://doi.org/10.1007/s12275-017-7377-4

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A Gram-stain-negative, non-motile, non-spore-forming, rodshaped, aerobic bacterium, designated 15J9-8T, was isolated from soil on Jeju Island, Republic of Korea. The isolate was able to grow between 10 and 30°C, pH 6.5–8.5, and in presence of 0–1% (w/v) NaCl. The results of comparative 16S rRNA gene sequence analysis indicated that strain 15J9-8T represented a member of the family Cytophagaceae, phylum Bacteroidetes, and was most closely related to Spirosoma aerophilum 5516J-17T (96.1% similarity), Spirosoma pulveris JSH5-14T (95.6%), and Spirosoma linguale DSM 74T (95.2%). The G + C content of the genomic DNA of the isolate was 47.0 mol%. Strain 15J9-8T contained summed feature 3 (C16:1 ω7c/C16:1 ω6c), C16:1 ω5c, and iso-C15:0 as the major fatty acids, phosphatidylethanolamine and an unidentified aminophospholipid as the main polar lipids, and menaquinone MK-7 as the predominant respiratory quinone. On the basis of its phenotypic and genotypic properties, and phylogenetic distinctiveness, strain 15J9-8T should be classified as a representative of a novel species of the genus Spirosoma, for which the name Spirosoma migulaei sp. nov. is proposed. The type strain is 15J9-8T (=KCTC 52028T =JCM 31996T).

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Spirosoma rhododendri sp. nov., isolated from a flower of royal azalea (Rhododendron schlippenbachii)
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Gly184 of the Escherichia coli cAMP receptor protein provides optimal context for both DNA binding and RNA polymerase interaction: Matt N. Hicks , Sanjiva Gunasekara , Jose Serate , Jin Park , Pegah Mosharaf , Yue Zhou , Jin-Won Lee , Hwan Youn; J. Microbiol. 2017;55(10):816-822. Published online September 28, 2017; DOI: https://doi.org/10.1007/s12275-017-7266-x

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The Escherichia coli cAMP receptor protein (CRP) utilizes the helix-turn-helix motif for DNA binding. The CRP’s recognition helix, termed F-helix, includes a stretch of six amino acids (Arg180, Glu181, Thr182, Val183, Gly184, and Arg185) for direct DNA contacts. Arg180, Glu181 and Arg185 are known as important residues for DNA binding and specificity, but little has been studied for the other residues. Here we show that Gly184 is another F-helix residue critical for the transcriptional activation function of CRP. First, glycine was repeatedly selected at CRP position 184 for its unique ability to provide wild type-level transcriptional activation activity. To dissect the glycine requirement, wild type CRP and mutants G184A, G184F, G184S, and G184Y were purified and their in vitro DNA-binding activity was measured. G184A and G184F displayed reduced DNA binding, which may explain their low transcriptional activation activity. However, G184S and G184Y displayed apparently normal DNA affinity. Therefore, an additional factor is needed to account for the diminished transcriptional activation function in G184S and G184Y, and the best explanation is perturbations in their interaction with RNA polymerase. The fact that glycine is the smallest amino acid could not fully warrant its suitability, as shown in this study. We hypothesize that Gly184 fulfills the dual functions of DNA binding and RNA polymerase interaction by conferring conformational flexibility to the F-helix.

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Spirosoma luteolum sp. nov. isolated from water: Jae-Jin Lee , Su-Jin Park , Yeon-Hee Lee , Seung-Yeol Lee , Sangkyu Park , Young-Je Cho , Myung Kyum Kim , Leonid N. Ten , Hee-Young Jung; J. Microbiol. 2017;55(4):247-252. Published online March 13, 2017; DOI: https://doi.org/10.1007/s12275-017-6455-y

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A novel Gram-negative and rod-shaped bacterial strain, de-signated as 16F6ET, was isolated from a water sample. Cells were yellowish in color and catalase- and oxidase-positive. The strain grew at 10–37°C (optimum at 25°C) but not at 4 and 42°C, and pH 5–7 (optimum at pH 7). It showed mod-erate resistance to gamma-ray irradiation. Comparative phy-logenetic analysis showed that strain 16F6ET belonged to the family Cytophagaceae of the class Cytophagia. Furthermore, this isolate showed relatively low 16S rRNA gene sequence similarities (90.7–93.1%) to the members of the genus Spiro-soma. The major fatty acids were summed feature 3 (C16:1 ω7c/C16:1 ω6c), C16:1 ω5c, C16:0 N alcohol, and C16:0. The polar lipid profile indicated presence of phosphatidylethanolamine, unknown aminophospholipids, an unknown amino lipid, unknown phospholipids, and unknown polar lipids. The pre-dominant isoprenoid quinone was MK-7. The genomic DNA G+C content of strain 16F6ET was 56.5 mol%. Phenotypic, phylogenetic, and chemotaxonomic properties indicated that isolate 16F6ET represents a novel species within the genus Spirosoma, for which the name Spirosoma luteolum sp. nov. is proposed. The type strain is 16F6ET (=KCTC 52199T =JCM 31411T).

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Isolation of Spirosoma foliorum sp. nov. from the fallen leaf of Acer palmatum by a novel cultivation technique
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Spirosoma rhododendri sp. nov., isolated from a flower of royal azalea (Rhododendron schlippenbachii)
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Spirosoma terrae sp. nov., Isolated from Soil from Jeju Island, Korea
Leonid N. Ten, Joseph Okiria, Jae-Jin Lee, Seung-Yeol Lee, Sangkyu Park, Dae Sung Lee, In-Kyu Kang, Myung Kyum Kim, Hee-Young Jung
Current Microbiology.2018; 75(4): 492. CrossRef
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Journal of Microbiology.2017; 55(12): 927. CrossRef
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Spirosoma daeguensis sp. nov., isolated from beach soil
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Article

Hymenobacter daeguensis sp. nov. isolated from river water: Leonid N. Ten , Yeon-Hee Lee , Jae-Jin Lee , Su-Jin Park , Seung-Yeol Lee , Sangkyu Park , Dae Sung Lee , In-Kyu Kang , Hee-Young Jung; J. Microbiol. 2017;55(4):253-259. Published online January 26, 2017; DOI: https://doi.org/10.1007/s12275-017-6524-2

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A Gram-stain-negative, non-motile, non-spore-forming, rod- shaped, aerobic bacterial strain, designated 16F3Y-2T, was isolated from the Han River, South Korea, and was charac-terized taxonomically using a polyphasic approach. Compa-rative 16S rRNA gene sequence analysis showed that strain 16F3Y-2T belonged to the family Cytophagaceae in the phy-lum Bacteroidetes and was most closely related to ‘Hymeno-bacter terrae’ DG7A (98.01%), H. soli PB17T (97.26%), H. glaciei VUG-A130T (96.78%), H. antarcticus VUG-A42aaT (96.72%), H. ruber PB156T (96.61%), and H. saemangeumensis GSR0100T (95.77%). The G+C content of the genomic DNA of strain 16F3Y-2T was 62.9 mol%. The isolate contained MK-7 as the predominant respiratory quinone, and summed fea-ture 3 (C16:1 ω7c/C16:1 ω6c; 35.5%), C15:0 iso (16.9%), C16:1 ω5c (10.9%), and C15:0 anteiso (9.9%) as major fatty acids. The ma-jor polar lipid was phosphatidylethanolamine. Phenotypic and chemotaxonomic data supported the affiliation of strain 16F3Y-2T with the genus Hymenobacter. However, strain 16F3Y-2T exhibited relatively low levels of DNA-DNA related-ness with 'H. terrae' KCTC 32554 (44.1%) and H. soli KCTC 12607T (24.3%), clearly indicating that the isolate constitutes a new genospecies. Strain 16F3Y-2T could be differentiated from its phylogenetic neighbors on the basis of several phe-notypic, genotypic, and chemotaxonomic features. Therefore, strain 16F3Y-2T represents a novel species in the genus Hy-menobacter, for which the name Hymenobacter daeguensis sp. nov. is proposed. The type strain is 16F3Y-2T (=KCTC 52537T =JCM 31654T).

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Article

Deinococcus sedimenti sp. nov. isolated from river sediment: Jae-Jin Lee , Yeon-Hee Lee , Su-Jin Park , Sangyong Lim , Sun-Wook Jeong , Seung-Yeol Lee , Sangkyu Park , Hyo-Won Choi , Myung Kyum Kim , Hee-Young Jung; J. Microbiol. 2016;54(12):802-808. Published online November 26, 2016; DOI: https://doi.org/10.1007/s12275-016-6361-8

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A novel Gram-positive, oval-shaped, non-motile bacterium designated strain 16F1LT was isolated from sediment collected from the Han River in Seoul, Republic of Korea. Based on the 16S rRNA gene sequence (1,448 bp), this strain was identified as a member of the genus Deinococcus that belongs to the class Deinococci. Similarities in the 16S rRNA gene sequence were shown with Deinococcus daejeonensis MJ27T (99.0%), D. grandis DSM 3963T (98.1%), D. radiotolerans C1T (97.5%), and D. caeni Ho-08T (97.2%). Strain 16F1LT was classified as a different genomic species from closely related Deinococcus members, based on less than 70% DNA-DNA relatedness. Genomic DNA G+C content of strain 16F1LT was 67.2 mol%. Strain 16F1LT was found to grow at temperatures of 10–37°C (optimum 25°C) and pH 7–8 (optimum pH 7) on R2A medium, and was catalase-positive and oxidase-negative. Strain 16F1LT showed resistance to gamma radiation (D10 > 2 kGy). In addition, this strain had the following chemotaxonomic characteristics: the major fatty acids were C15:1 ω6c and C16:1 ω7c; the polar lipid profile contained phosphoglycolipids, unknown aminophospholipids, an unknown aminoglycolipid, unknown aminolipids, an unknown glycolipid, an unknown phospholipid, and an unknown polar lipid; the major quinone was MK-8. Phylogenetic, genotypic, phenotypic, and chemotaxonomic characteristics indicated that strain 16F1LT represents a novel species within the genus Deinococcus, for which the name Deinococcus sedimenti sp. nov. is proposed. The type strain is 16F1LT (=KCTC 33796T =JCM 31405T).

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Deinococcus seoulensis sp. nov., a bacterium isolated from sediment at Han River in Seoul, Republic of Korea: Jae-Jin Lee , Yeon-Hee Lee , Su-Jin Park , Sangyong Lim , Sun-Wook Jeong , Seung-Yeol Lee , Young-Je Cho , Myung Kyum Kim , Hee-Young Jung; J. Microbiol. 2016;54(8):537-542. Published online August 2, 2016; DOI: https://doi.org/10.1007/s12275-016-6253-y

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Strain 16F1ET was isolated from a 3-kGy-irradiated sediment sample collected at Han River in Seoul, Republic of Korea. Cells of this strain were observed to be Gram-positive, pililike structure, and short rod shape, and colonies were red in color. The strain showed the highest degree of 16S rRNA gene sequence similarity to Deinococcus aquaticus PB314T (98.8%), Deinococcus depolymerans TDMA-24T (98.1%), Deinococcus caeni Ho-08T (98.0%), and Deinococcus grandis DSM 3963T (97.0%). 16S rRNA gene sequence analysis identified this strain as a member of the genus Deinococcus (Family: Deinococcaceae). The genomic DNA G+C content of strain 16F1ET was 66.9 mol%. The low levels of DNA-DNA hybridization (< 56.2%) with the species mentioned above identified strain 16F1ET as a novel Deinococcus species. Its oxidase and catalase activities as well as the production of acid from glucose were positive. Growth of the strain was observed at 10–37°C (optimum: 20–30°C) and pH 4–10 (optimum: pH 7–8). The cells tolerated less than 5% NaCl and had low resistance to gamma radiation (D10 < 4 kGy). Strain 16F1ET possessed the following chemotaxonomic characteristics: C16:0, C15:1 ω6c, and C16:1 ω7c as the major fatty acids; phosphoglycolipid as the predominant polar lipid; and menaquinone-8 as the predominant respiratory isoprenoid quinone. Based on the polyphasic evidence, as well as the phylogenetic, genotypic, phenotypic, and chemotaxonomic characterization results, strain 16F1ET (=KCTC 33793T =JCM 31404T) is proposed to represent the type strain of a novel species, Deinococcus seoulensis sp. nov.

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Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology .2016; 66(11): 4299. CrossRef

Research Support, Non-U.S. Gov't

Molecular characterization of mammalian-adapted Korean-type avian H9N2 virus and evaluation of its virulence in mice: Kuk Jin Park , Min-Suk Song , Eun-Ha Kim , Hyeok-il Kwon , Yun Hee Baek , Eun-hye Choi , Su-Jin Park , Se Mi Kim , Young-il Kim , Won-Suk Choi , Dae-Won Yoo , Chul-Joong Kim , Young Ki Choi; J. Microbiol. 2015;53(8):570-577. Published online July 31, 2015; DOI: https://doi.org/10.1007/s12275-015-5329-4

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Avian influenza A virus (AIV) is commonly isolated from domestic poultry and wild migratory birds, and the H9N2 subtype is the most prevalent and the major cause of severe disease in poultry in Korea. In addition to the veterinary concerns regarding the H9N2 subtype, it is also considered to be the next potential human pandemic strain due to its rapid evolution and interspecies transmission. In this study, we utilize serial lung-to-lung passage of a low pathogenic avian influenza virus (LPAI) H9N2 (A/Ck/Korea/163/04, WT163) (Y439-lineage) in mice to increase pathogenicity and investigate the potential virulence marker. Mouse-adapted H9N2 virus obtained high virulence (100% mortality) in mice after 98 serial passages. Sequence results show that the mouse adaptation (ma163) possesses several mutations within seven gene segments (PB2, PA, HA, NP, NA, M, and NS) relative to the wild-type strain. The HA gene showed the most mutations (at least 11) with one resulting in the loss of an N-glycosylation site (at amino acid 166). Moreover, reverse genetic studies established that an E627K substitution in PB2 and the loss of the N-glycosylation site in the HA protein (aa166) are critical virulence markers in the mouse-adapted H9N2 virus. Thus, these results add to the increasing body of mutational analysis data defining the function of the viral polymerase and HA genes and their roles in mammalian host adaptation. To our knowledge, this is first report of the generation of a mammalian-adapted Korea H9N2 virus (Y493-lineages). Therefore, this study offers valuable insights into the molecular evolution of the LPAI Korean H9N2 in a new host and adds to the current knowledge of the molecular markers associated with increased virulence.

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Research Support, Non-U.S. Gov't

Anti-influenza Effect of Cordyceps militaris through Immunomodulation in a DBA/2 Mouse Model: Hwan Hee Lee , Heejin Park , Gi-Ho Sung , Kanghyo Lee , Taeho Lee , Ilseob Lee , Man-seong Park , Yong Woo Jung , Yu Su Shin , Hyojeung Kang , Hyosun Cho; J. Microbiol. 2014;52(8):696-701. Published online July 18, 2014; DOI: https://doi.org/10.1007/s12275-014-4300-0

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Abstract PDF

The immune-modulatory as well as anti-influenza effects of Cordyceps extract were investigated using a DBA/2 mouse model. Three different concentrations of Cordyceps extract, red ginseng extract, or drinking water were orally administered to mice for seven days, and then the mice were intranasally infected with 2009 pandemic influenza H1N1 virus. Body weight changes and survival rate were measured daily post-infection. Plasma IL-12, TNF-α, and the frequency of natural killer (NK) cells were measured on day 4 post-infection. The DBA/2 strain was highly susceptible to H1N1 virus infection. We also found that Cordyceps extract had an antiinfluenza effect that was associated with stable body weight and reduced mortality. The anti-viral effect of Cordyceps extract on influenza infection was mediated presumably by increased IL-12 expression and greater number of NK cells. However, high TNF-α expression after infection of H1N1 virus in mice not receiving treatment with Cordyceps extract suggested a two-sided effect of the extract on host immune regulation.

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Research Support, Non-U.S. Gov't

Alicyclobacillus tengchongensis sp. nov., a Thermo-Acidophilic Bacterium Isolated from Hot Spring Soil: Min Goo Kim , Jae-Chan Lee , Dong-Jin Park , Wen-Jun Li , Chang-Jin Kim Kim; J. Microbiol. 2014;52(10):884-889. Published online July 18, 2014; DOI: https://doi.org/10.1007/s12275-014-3625-z

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A thermo-acidophilic bacterium, designated strain ACK006T, was isolated from the soil of a hot spring at Tengchong in China. Cells were Gram-staining-positive, motile, catalasepositive and oxidase-negative, spore-forming rods. The isolate grew aerobically at 30–50°C (optimum at 45°C), pH 2.0–6.0 (optimum pH 3.2) and 0–5.0% (w/v) NaCl (optimum 1% NaCl). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain ACK006T belongs to the genus Alicyclobacillus with the sequence similarity of 92.3, 92.4, 92.5, and 92.8% to Alicyclobacillus cycloheptanicus SCHT, Alicyclobacillus ferrooxydans TC-34T, Alicyclobacillus contaminans 3-A191T and Alicyclobacillus disulfidooxidans SD-11T, respectively. Similarity to other species of the genus Alicyclobacillus was 90.3–92.8% and similarity to species of the genus Tumebacillus was 85.9–87.8%. The genomic DNA G+C content was 53.7 mol%. The predominant menaquinone was MK-7. Major fatty acids were ω-cycloheptane C18:0, iso-C17:0 and anteiso-C17:0. The cell-wall peptidoglycan was the A1γ type; containing meso-diaminopimelic acid as the diagnostic diamino acid. On the basis of polyphasic analysis from this study, strain ACK006T represents a novel species of the genus Alicyclobacillus for which the name Alicyclobacillus tengchongensis sp. nov. is proposed. The type strain is ACK006T (=KCTC 33022T =DSM 25924T).

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Research Support, Non-U.S. Gov't

Dyella jejuensis sp. nov., Isolated from Soil of Hallasan Mountain in Jeju Island: Min-Soo Kim , Dong-Wook Hyun , Joon Yong Kim , Soyeon Kim , Jin-Woo Bae , Eun-Jin Park; J. Microbiol. 2014;52(5):373-377. Published online May 9, 2014; DOI: https://doi.org/10.1007/s12275-014-3670-7

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A novel bacterium, designated JP1T, was isolated from soil of Hallasan Mountain in Jeju Island. The isolate was a Gram- negative, aerobic, motile and rod-shaped (0.2–0.4 × 1.2–2.0 μm) bacterium. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain JP1T was closely related to Dyella koreensis with 97.6% similarity. Growth of strain JP1T occurred at 10–37°C, pH 5–7 and 0–1% (w/v) NaCl. The genomic DNA G+C content of strain JP1T was 62.1 mol%. The major fatty acids were iso-C16:0, iso-C17:1 ω9c, and iso- C15:0. The predominant quinone was ubiquinone-8. The major polar lipids of strain JP1T were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, uniden-tified aminolipids and unidentified aminophospholipids. The DNA-DNA relatedness values between strain JP1T and pre-viously reported Dyella species were <10%. Based on pheno-typic, genotypic, and phylogenetic distinctness, strain JP1T represents a novel species in the genus Dyella, for which the name Dyella jejuensis sp. nov. is proposed. The type strain is JP1T (=KACC 17701T =JCM 19615T).

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Sequential Immunosuppressive Activities of Bacterial Secondary Metabolites from the Entomopahogenic Bacterium Xenorhabdus nematophila: Seonghyeon Eom , Youngjin Park , Yonggyun Kim; J. Microbiol. 2014;52(2):161-168. Published online February 1, 2014; DOI: https://doi.org/10.1007/s12275-014-3251-9

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The entomopathogenic bacterium Xenorhabdus nematophila secretes at least eight bacterial metabolites that play crucial roles suppressing target insect immune responses by inhibiting eicosanoid biosynthesis. We analyzed sequential changes in bacterial metabolite production during bacterial growth and analyzed their individual immunosuppressive activities against the insect host, Spodoptera exigua. X. nematophila exhibited a typical bacterial growth pattern in both insect host and culture medium, and eight metabolites were secreted at different time points. At the early growth phase (6–12 h), Ac-FGV and PHPP were detected in significant amounts in the culture broth. At this early phase, both Ac-FGV (18 μg/ml) and oxindole (110 μg/ml) levels significantly inhibited phenoloxidase and phospholipase A2 activities in S. exigua hemolymph. At the late growth phase (12–36 h), all eight metabolites were detected at significant levels (10–140 μg/ml) in the culture broth and were sufficient to induce hemocyte toxicity. These results suggest that X. nematophila sequentially produces immunosuppressive metabolites that might sequentially and cooperatively inhibit different steps of insect immune responses.

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Research Support, Non-U.S. Gov't

Next-Generation Sequencing-Based Transcriptome Analysis of L-Lysine-Producing Corynebacterium glutamicum ATCC 21300 Strain: Hong-Il Kim , Jae-Young Nam , Jae-Yong Cho , Chang-Soo Lee , Young-Jin Park; J. Microbiol. 2013;51(6):877-880. Published online December 19, 2013; DOI: https://doi.org/10.1007/s12275-013-3236-0

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In the present study, 151 genes showed a significant change in their expression levels in Corynebacterium glutamicum ATCC 21300 compared with those of C. glutamicum ATCC 13032. Of these 151 genes, 56 genes (2%) were up-regulated and 95 genes (3%) were down-regulated. RNA sequencing analysis also revealed that 11 genes, involved in the L-lysine biosynthetic pathway of C. glutamicum, were up- or downregulated compared with those of C. glutamicum ATCC 13032. Of the 151 genes, 10 genes were identified to have mutations including SNP (9 genes) and InDel (1 gene). This information will be useful for genome breeding of C. glutamicum to develop an industrial amino acid-producing strain with minimal mutation.

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Review of the Proteomics and Metabolic Properties of Corynebacterium glutamicum
Juhwan Park, Sooa Lim
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Jian Wang, Xuesong Wang, Qing Liang, Deheng Li, Dawei Li, Qunqun Guo
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RETRACTED ARTICLE: Comparative analysis of the Corynebacterium glutamicum transcriptome in response to changes in dissolved oxygen levels
Xiuxia Liu, Sun Yang, Fen Wang, Xiaofeng Dai, Yankun Yang, Zhonghu Bai
Journal of Industrial Microbiology and Biotechnology.2017; 44(2): 181. CrossRef
Transcriptome and Gene Ontology (GO) Enrichment Analysis Reveals Genes Involved in Biotin Metabolism That Affect l-Lysine Production in Corynebacterium glutamicum
Hong-Il Kim, Jong-Hyeon Kim, Young-Jin Park
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Research Support, Non-U.S. Gov't

Adjuvant Efficacy of mOMV against Avian Influenza Virus Infection in Mice: Byeong-Jae Lee , Sang-Ho Lee , Min-Suk Song , Philippe Noriel Q. Pascua , Hyeok-il Kwon , Su-Jin Park , Eun-Ha Kim , Arun Decano , Se Mi Kim , Gyo Jin Lim , Doo-Jin Kim , Kyu-Tae Chang , Sang-Hyun Kim , Young Ki Choi; J. Microbiol. 2013;51(5):682-688. Published online October 31, 2013; DOI: https://doi.org/10.1007/s12275-013-3411-3

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Highly pathogenic avian influenza H5N1 viruses are found chiefly in birds and have caused severe disease and death in infected humans. Development of influenza vaccines capable of inducing heterosubtypic immunity against a broad range of influenza viruses is the best option for the preparedness, since vaccination remains the principal method in controlling influenza viral infections. Here, a mOMV-adjuvanted recombinant H5N2 (rH5N2) whole virus antigen vaccine with A/Environment/Korea/W149/06(H5N1)-derived H5 HA and A/Chicken/Korea/ma116/04(H9N2)-derived N2 NA in the backbone of A/Puerto Rico/8/34(H1N1) was prepared and generated by reverse genetics. Groups of mice were vaccinated by a prime-boost regime with the rH5N2 vaccine (1.75 μg of HA with/without 10 μg mOMV or aluminum hydroxide adjuvant for comparison). At two weeks post-immunizations, vaccinated mice were challenged with lethal doses of 103.5 EID50/ml of H5N1 or H9N2 avian influenza viruses, and were monitored for 15 days. Both mOMV- and alum-adjuvant vaccine groups had high survival rates after H5N1 infection and low levels of body weight changes compared to control groups. Interestingly, the mOMV-adjuvanted group induced better cross-reactive antibody responses serologically and promoted cross-protectivity against H5N1 and H9N2 virus challenges. Our results suggest that mOMV could be used as a vaccine adjuvant in the development of effective vaccines used to control influenza A virus transmission.

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Evaluation of heterosubtypic cross-protection against highly pathogenic H5N1 by active infection with human seasonal influenza A virus or trivalent inactivated vaccine immunization in ferret models
Su-Jin Park, Eun-Ha Kim, Philippe Noriel Q. Pascua, Hyeok-Il Kwon, Gyo-Jin Lim, Arun Decano, Se Mi Kim, Man Ki Song, Eui-Cheol Shin, Young-Ki Choi
Journal of General Virology .2014; 95(4): 793. CrossRef
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Clinical and Experimental Vaccine Research.2014; 3(2): 194. CrossRef

Research Support, Non-U.S. Gov't

The Anti-influenza Virus Effect of Phellinus igniarius Extract: Sangmoo Lee , Jin Il Kim , Jun Heo , Ilseob Lee , Sehee Park , Min-Woong Hwang , Joon-Yong Bae , Mee Sook Park , Hyoung Jin Park , Man-Seong Park; J. Microbiol. 2013;51(5):676-681. Published online October 31, 2013; DOI: https://doi.org/10.1007/s12275-013-3384-2

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Herbal medicine has been used in the orient for thousands of years to treat large and small ailments, including microbial infections. Although there are treatments for influenza virus infection, there is no treatment for drug-resistant viruses. It is time that we explored and exploited the multicomponent nature of herbal extracts as multi-drug combination therapies. Here, we present data on the anti-influenza virus effect of a medicinal mushroom, Phellinus igniarius. The P. igniarius water extract was effective against influenza A and B viruses, including 2009 pandemic H1N1, human H3N2, avian H9N2, and oseltamivir-resistant H1N1 viruses. Virological assays revealed that the extract may interfere with one or more early events in the influenza virus replication cycle, including viral attachment to the target cell. Therefore, our results provide new insights into the use of P. igniarius as an anti-influenza medicine.

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The N3 Subdomain in A Domain of Fibronectin-Binding Protein B Isotype I Is an Independent Risk Determinant Predictive for Biofilm Formation of Staphylococcus aureus Clinical Isolates: An Sung Kwon , Dong Hoon Lim , Hyo Jung Shin , Geon Park , Jong H. Reu , Hyo Jin Park , Jungmin Kim , Yong Lim; J. Microbiol. 2013;51(4):499-505. Published online August 30, 2013; DOI: https://doi.org/10.1007/s12275-013-3319-y

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Fibronectin-binding proteins (FnBP), FnBPA and FnBPB, are purported to be involved in biofilm formation of Staphylococcus aureus. This study was performed to find which of three consecutive N subdomains of the A domain in the FnBP is the key domain in FnBP. A total of 465 clinical isolates of S. aureus were examined for the biofilm forming capacity and the presence of N subdomains of FnBP. In the biofilm-positive strains, N2 and N3 subdomains of FnBPA, and N1 and N3 subdomains of FnBPB were significantly more prevalent. Multivariate logistic regression analysis of 246 biofilm-positive and 123 biofilm-negative strains identified only the FnBPB-N3 subdomain as an independent risk determinant predictive for biofilm-positive strains of S. aureus (Odds ratio [OR], 13.174; P<0.001). We also attempted to delete each of the fnbA-N2 and -N3 and fnbB-N1 and -N3 from S. aureus strain 8325-4 and examined the biofilm forming capacity in the derivative mutants. In agreement with the results of the multivariate regression analysis, deletion of either the fnbA-N2 or -N3, or fnbB-N1 did not significantly diminish the capacity of strain 8325-4 to develop a biofilm, while deletion of the fnbB-N3 did. Therefore, it is suggested that the FnBPB-N3 subdomain of isotype I may be a key domain in FnBP which is responsible for the causing biofilm formation in S. aureus clinical isolates.

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The Microbial Population in the Air of Cultivation Facility of Oyster Mushrooms: Se Chul Chun , Yu Na Ahn , Sajid Mohamad Khan , Il Min Chung , Hyang Yoen Won , Chang Sung Jhune , Yool Jin Park; J. Microbiol. 2012;50(6):1053-1057. Published online December 30, 2012; DOI: https://doi.org/10.1007/s12275-012-2195-1

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The microbial population in the air of mushroom cultivation facility was studied to understand the population structure and size depending on the cultivation methods and regions. The air contents of ten farmers’ oyster mushroom cultivation facilities in Kyunggi province were sampled. The results indicated that there was no difference in population size depending on the regions of mushroom cultivation. In addition, the population size of bacteria in the growth room was bigger than that of the cooling room and outside of the mushroom house, but the fungal population was similar in size between cultivation stages. With regard to population structure, Pseudomonas and Penicillium species were most frequently isolated from the air of oyster mushroom cultivation facility.

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Next-Generation Sequencing-Based Genome-Wide Mutation Analysis of L-Lysine-Producing Corynebacterium glutamicum ATCC 21300 Strain: Chang-Soo Lee , Jae-Young Nam , Eun-Suk Son , O-chul Kwon , Woorijarang Han , Jae-Yong Cho , Young-Jin Park; J. Microbiol. 2012;50(5):860-863. Published online November 4, 2012; DOI: https://doi.org/10.1007/s12275-012-2109-2

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In order to identify single nucleotide polymorphism and insertion/deletion mutations, we performed whole-genome re-sequencing of the enhanced L-lysine-producing Corynebacterium glutamicum ATCC 21300 strain. In total, 142 single nucleotide polymorphisms and 477 insertion/deletion mutations were identified in the ATCC 21300 strain when compared to 3,434 predicted genes of the wild-type C. glutamicum ATCC 13032 strain. Among them, 110 transitions and 29 transversions of single nucleotide polymorphisms were found from genes of the ATCC 21300 strain. In addition, 11 genes, involved in the L-lysine biosynthetic pathway and central carbohydrate metabolism, contained mutations including single nucleotide polymorphisms and insertions/deletions. Interestingly, RT-PCR analysis of these 11 genes indicated that they were normally expressed in the ATCC 21300 strain. This information of genome-wide gene-associated variations will be useful for genome breeding of C. glutamicum in order to develop an industrial amino acidproducing strain with minimal mutation.

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Biological Control and Plant Growth Promoting Capacity of Rhizobacteria on Pepper under Greenhouse and Field Conditions: Mi-Seon Hahm , Marilyn Sumayo , Ye-Ji Hwang , Seon-Ae Jeon , Sung-Jin Park , Jai Youl Lee , Joon-Hyung Ahn , Byung-Soo Kim , Choong-Min Ryu , Sa-Youl Ghim; J. Microbiol. 2012;50(3):380-385. Published online June 30, 2012; DOI: https://doi.org/10.1007/s12275-012-1477-y

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Plant growth promoting rhizobacteria Ochrobactrum lupini KUDC1013 and Novosphingobium pentaromativorans KUDC1065 isolated from Dokdo Island, S. Korea are capable of eliciting induced systemic resistance (ISR) in pepper against bacterial spot disease. The present study aimed to determine whether plant growth-promoting rhizobacteria (PGPR) strains including strain KUDC1013, strain KUDC1065, and Paenibacillus polymyxa E681 either singly or in combinations were evaluated to have the capacity for potential biological control and plant growth promotion effect in the field trials. Under greenhouse conditions, the induced systemic resistance (ISR) effect of treatment with strains KUDC1013 and KUDC1065 differed according to pepper growth stages. Drenching of 3-week-old pepper seedlings with the KUDC-1013 strain significantly reduced the disease symptoms. In contrast, treatment with the KUDC1065 strain significantly protected 5-week-old pepper seedlings. Under field conditions, peppers treated with PGPR mixtures containing E681 and KUDC1013, either in a two-way combination, were showed greater effect on plant growth than those treated with an individual treatment. Collectively, the application of mixtures of PGPR strains on pepper might be considered as a potential biological control under greenhouse and field conditions.

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Research Support, Non-U.S. Gov't

Oceanobacillus kimchii sp. nov. Isolated from a Traditional Korean Fermented Food: Tae Woong Whon , Mi-Ja Jung , Seong Woon Roh , Young-Do Nam , Eun-Jin Park , Kee-Sun Shin , Jin-Woo Bae; J. Microbiol. 2010;48(6):862-866. Published online January 9, 2011; DOI: https://doi.org/10.1007/s12275-010-0214-7

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Abstract PDF

A moderate halophile, strain X50T, was isolated from mustard kimchi, a traditional Korean fermented food. The organism grew under conditions ranging from 0-15.0% (w/v) NaCl (optimum: 3.0%), pH 7.0-10.0 (optimum: pH 9.0) and 15-45°C (optimum: 37°C). The morphological, physiological, and biochemical features and the 16S rRNA gene sequences of strain X50T were characterized. Colonies of the isolate were creamcolored and the cells were rod-shaped. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain X50T belongs to the genus Oceanobacillus and is closely related phylogenetically to the type strain O. iheyensis HTE831T (98.9%) and O. oncorhynchi subsp. oncorhynchi R-2T (97.0%). The cellular fatty acid profiles predominately included anteiso-C15:0 and iso-C15:0. The G+C content of the genomic DNA of the isolate was 37.9 mol% and the major isoprenoid quinone was MK-7. Analysis of the 16S rRNA gene sequences, DNA-DNA relatedness and physiological and biochemical tests indicated genotypic and phenotypic differences among strain X50T and reference species in the genus Oceanobacillus. Therefore, strain X50T was proposed as a novel species and named Oceanobacillus kimchii. The type strain of the new species is X50T (=JCM 16803T =KACC 14914T =DSM 23341T).

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Research Support, Non-U.S. Gov't

Inhibitory Effect of the Essential Oil from Chamaecyparis obtusa on the Growth of Food-Borne Pathogens: Mi-Jin Park , Won-Sil Choi , Ha-Young Kang , Ki-Seob Gwak , Geun-Shik Lee , Eui-Bae Jeung , In-Gyu Choi; J. Microbiol. 2010;48(4):496-501. Published online August 20, 2010; DOI: https://doi.org/10.1007/s12275-010-9327-2

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Abstract PDF

In this study, the antibacterial activity of essential oil from Chamaecyparis obtusa (Sieb. et Zucc) leaves and twigs was investigated. The test strains were Klebsiella pneumoniae, Listeria monocytogenes, Salmonella typhimurium, Staphylococcus aureus, Escherichia coli, Legionella pneumophila, and Methicilline-resistant Staphylococcus aureus. Antibacterial activity was estimated by measuring bacterial growth inhibition. Histopathological examination was also performed. C. obtusa oil distinctly inhibited the growth of all test strains and exhibited the strongest antibacterial activity against L. monocytogenes. It was chromatographically divided into several fractions. The fractions were further tested against antibacterial activity and their chemical compositions were analyzed. The fraction containing terpinen-4-ol (TA) showed high antibacterial activity toward all strains tested. Tests with authentic samples showed that TA played a major role in the antibacterial activity of C. obtusa oil, and in a mice test, the oil actively minimized inflammation by S. aureus.

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Research Support, Non-U.S. Gov't

Application of Quantitative Real-Time PCR for Enumeration of Total Bacterial, Archaeal, and Yeast Populations in Kimchi: Eun-Jin Park , Ho-Won Chang , Kyoung-Ho Kim , Young-Do Nam , Seong Woon Roh , Jin-Woo Bae; J. Microbiol. 2009;47(6):682-685. Published online February 4, 2010; DOI: https://doi.org/10.1007/s12275-009-0297-1

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Abstract PDF

Kimchi is a Korean traditional fermented food made of brined vegetables, with a variety of spices. Various microorganisms are associated with the kimchi fermentation process. This study was undertaken in order to apply quantitative real-time PCR targeting the 16S and 26S rRNA genes for the investigation of dynamics of bacterial, archaeal, and yeast communities during fermentation of various types of kimchi. Although the total bacterial and archaeal rRNA gene copy numbers increased during kimchi fermentation, the number of yeasts was not significantly altered. In 1 ng of bulk DNA, the mean number of rRNA gene copies for all strains of bacteria was 5.45×106 which was 360 and 50 times greater than those for archaea and yeast, respectively. The total gene copy number for each group of microorganisms differed among the different types of kimchi, although the relative ratios among them were similar. The common dominance of bacteria in the whole microbial communities of various types of kimchi suggests that bacteria play a principal role in the kimchi fermentation process.

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Journal of Food Science.2015;[Epub] CrossRef
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Man Lu, Xingxing Wang, Guowei Sun, Bing Qin, Jinzhou Xiao, Shuling Yan, Yingjie Pan, Yongjie Wang, Cecile Fairhead
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Research Support, Non-U.S. Gov't

Virgibacillus xinjiangensis sp. nov., Isolated from a Salt Lake of Xin-jiang Province in China: Che Ok Jeon , Jeong Myeong Kim , Dong-Jin Park , Li-Hua Xu , Cheng-Lin Jiang , Chang-Jin Kim; J. Microbiol. 2009;47(6):705-709. Published online February 4, 2010; DOI: https://doi.org/10.1007/s12275-009-0107-9

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A strictly aerobic Gram-positive, moderately halophilic spore forming bacterium, designated strain SL6-1T, was isolated from a salt lake in Xin-jiang province, China. Growth of strain SL6-1T was observed at NaCl concentrations of 0~20% (w/v) (the optimum being 5~7%, w/v). The peptidoglycan type of strain SL6-1T was A1γ-meso-diaminopimelic acid and its major cellular fatty acids were iso-C14:0 and iso-C16:0 and anteiso-C15:0. The major respiratory isoprenoid quinone was MK-7 and the G+C content of the genomic DNA was 44.5 mol%. The major cellular phospholipids were phosphatidylglycerol and diphosphatidylglycerol. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SL6-1T formed a phylogenetic lineage within the genus Virgibacillus. Based on 16S rRNA gene sequence similarity, the strain was most closely related to Virgibacillus olivae E308T, Virgibacillus kekensis YIM kkny16T, Virgibacillus marismortui DSM 12325T with 97.1%, 97.1%, and 97.0% gene sequence similarities, respectively and the sequence similarities to other related taxa were less than 96.7%. The DNA relatedness values between strain SL6-1T and V. olivae E308T, V. kekensis YIM kkny16T, V. marismortui DSM 12325T were 16.7%, 51.0%, and 22.8%, respectively. On the basis of physiological, biochemical and phylogenetic properties, strain SL6-1T represents a novel species, for which the name Virgibacillus xinjiangensis sp. nov. is proposed. The type strain is SL6-1T (=KCTC 13128T =DSM 19031T).

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Virgibacillus kimchii sp. nov., a halophilic bacterium isolated from kimchi
Young Joon Oh, Ja-Young Jang, Seul Ki Lim, Min-Sung Kwon, Jieun Lee, NamHee Kim, Mi-Young Shin, Hyo Kyeong Park, Myung-Ji Seo, Hak-Jong Choi
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Xijie Yin, Yanliu Yang, Shuang Wang, Gaiyun Zhang
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Virgibacillus natechei sp. nov., A Moderately Halophilic Bacterium Isolated from Sediment of a Saline Lake in Southwest of Algeria
Meriam Amziane, Farida Metiaz, Amel Darenfed-Bouanane, Zahia Djenane, Okba Selama, Ahmed Abderrahmani, Jean-Luc Cayol, Marie-Laure Fardeau
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Soo-Young Lee, Chul-Hyung Kang, Tae-Kwang Oh, Jung-Hoon Yoon
International Journal of Systematic and Evolutionary Microbiology .2012; 62(2): 347. CrossRef
Virgibacillus alimentarius sp. nov., isolated from a traditional Korean food
Jandi Kim, Mi-Ja Jung, Seong Woon Roh, Young-Do Nam, Kee-Sun Shin, Jin-Woo Bae
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Impact of ionic liquids on extreme microbial biotypes from soil
Francisco J. Deive, Ana Rodríguez, Adélia Varela, Cátia Rodrígues, Maria C. Leitão, Jos A. M. P. Houbraken, Ana B. Pereiro, María A. Longo, M. Ángeles Sanromán, Robert A. Samson, Luís Paulo N. Rebelo, Cristina Silva Pereira
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Analysis of a Novel Class 1 Integron Containing Metallo-β-Lactamase Gene VIM-2 in Pseudomonas aeruginosa: Jae Hoon Jeong , Kyeong Seob Shin , Jang Won Lee , Eun Jin Park , Seung-Yeol Son; J. Microbiol. 2009;47(6):753-759. Published online February 4, 2010; DOI: https://doi.org/10.1007/s12275-008-0272-2

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Carbapenems such as imipenem are stable to most β-lactamases. Recently, increased numbers of carbapenemase producing Gram-negative bacterial strains have been isolated because of the increased use of cabapenems. In this respect, control of these infectious carbapenemase producing Gram-negative bacteria and understanding their resistance mechanism are becoming more important. These carbapenem-hydrolyzing β-lactamase genes have been reported to exist mostly as gene cassettes in an integron. This implies that antibiotic resistance genes may be transferred to other bacteria via the integron. In the present study, we identified and analyzed an integron containing VIM-2 type metallo-β-lactamase gene in a carbapenemase producing Pseudomonas aeruginosa. In addition, the possibility of resistance spread by integron located in a plasmid was tested. Among glucose non-fermenting Gram-negative bacilli with reduced imipenem susceptibility (MIC≥8 μg/ml) isolated from Korean patients, P. aeruginosa 1082 showed resistance to most β-lactams, cephalosporin, and aminoglycoside. We found that P. aeruginosa 1082 was inhibited by EDTA in EDTA double disk synergy test which means that this strain produces metallo-β-lactamase. Class 1 integron containing blaVIM-2 (carbapenem resistance gene), qacF (quaternary ammonium compound resistance gene), aacA4 (aminoglycoside resistance gene), catB3 (chloramphenicol resistance gene), blaOXA-30 (extended-spectrum β-lactam resistance gene), and aadA1 (aminoglycoside resistance gene) gene cassettes was detected in P. aeruginosa 1082. The size of the integron was 5,246 bp and the structure and arrangement of the integron was a novel one in comparison with other integrons found in other P. aeruginosa. The integron could be transferred to Escherichia coli JM109 from P. aeruginosa 1082 possibly via self-transferable plasmid DNA. The integron and a blaVIM-2 gene were detected in the plasmid DNA of the transconjugants whose imipenem resistance was slightly increased as a result of accepting the integron from the donor strain.

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Functional Analysis of pilQ Gene in Xanthomanas oryzae pv. oryzae, Bacterial Blight Pathogen of Rice: Seon-Hwa Lim , Byoung-Ho So , Ji-Chun Wang , Eun-Seong Song , Young-Jin Park , Byoung-Moo Lee , Hee-Wan Kang; J. Microbiol. 2008;46(2):214-220. Published online June 11, 2008; DOI: https://doi.org/10.1007/s12275-007-0173-9

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Bacterial blight (BB) of rice, caused by Xanthomonas oryzae pv. oryzae (Xoo), is the most devastating bacterial disease in rice. A virulence-attenuated mutant strain HNU89K9 of X. oryzae pv. oryzae (KACC10331), with a transposon insertion in the pilQ gene was used for this study. The pilQ was involved in the gene cluster pilMNOPQ of the Xoo genome. Growth rate of the pilQ mutant was similar to that of wild-type. At level of amino acids, PilQ of Xoo showed that a high sequence identities more than 94% and 70% to Xanthomonas species and to Xyllela fastidiosa, respectively but a low sequence homology less than 30% to other bacterial species. The twitching motility forming a marginal fringe on PSA media was observed on colony of the wild-type strain KACC10331, but not in mutant HNU89K9. Wild-type Xoo cells formed a biofilm on the surface of the PVC plastic test tube, while the mutant strain HNU89K9 did not form a biofilm. The results suggest that the pilQ gene of X. oryzae pv. oryzae plays a critical role in pathogenicity, twitching motility, and biofilm formation.

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Antifungal Activities of the Essential Oils in Syzygium aromaticum (L.) Merr. Et Perry and Leptospermum petersonii Bailey and their Constituents against Various Dermatophytes: Mi-Jin Park , Ki-Seob Gwak , In Yang , Won-Sil Choi , Hyun-Jin Jo , Je-Won Chang , Eui-Bae Jeung , In-Gyu Choi; J. Microbiol. 2007;45(5):460-465.; DOI: https://doi.org/2589 [pii]

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Abstract PDF: This study was carried out in order to investigate the potential of using plant oils derived from Leptospermum petersonii Bailey and Syzygium aromaticum L. Merr. Et Perry as natural antifungal agents. The antifungal effects of essential oils at concentrations of 0.05, 0.1, 0.15, and 0.2 mg/ml on the dermatophytes Microsporum canis (KCTC 6591), Trichophyton mentagrophytes (KCTC 6077), Trichophyton rubrum (KCCM 60443), Epidermophyton floccosum (KCCM 11667), and Microsporum gypseum were evaluated using the agar diffusion method. The major constituents of the active fraction against the dermatophytes were identified by gas chromatography-mass spectrometry and high-performance liquid chromatography analysis. The antifungal activities of S. aromaticum oil (clove oil) against the dermatophytes tested were highest at a concentration of 0.2 mg/ml, with an effectiveness of more than 60%. Hyphal growth was completely inhibited in T. mentagrophytes, T. rubrum, and M. gypseum by treatment with clove oil at a concentration of 0.2 mg/ml. Eugenol was the most effective antifungal constituent of clove oil against the dermatophytes T. mentagrophytes and M. canis. Morphological changes in the hyphae of T. mentagrophytes, such as damage to the cell wall and cell membrane and the expansion of the endoplasmic reticulum, after treatment with 0.11 mg/ml eugenol were observed by transmission electron microscopy (TEM). At a concentration of 0.2 mg/ml, L. petersonii oil (LPO) was more than 90% effective against all of the dermatophytes tested, with the exception of T. rubrum. Geranial was determined to be the most active antifungal constituent of L. petersonii oil. Taken together, the results of this study demonstrate that clove and tea tree oils exhibited significant antifungal activities against the dermatophytes tested in this study.

Research Support, Non-U.S. Gov't

Application of Bovine Viral Diarrhoea Virus as an Internal Control in Nucleic Acid Amplification Tests for Hepatitis C Virus RNA in Plasma-Derived Products: Si Hyung Yoo , Seung Hee Hong , Sa Rah Jung , Su Jin Park , Nam Kyung Lee , Soon Nam Kim , Sang Mo Kang , Hong Ki Min , Sue Nie Park , Seung Hwa Hong; J. Microbiol. 2006;44(1):72-76.; DOI: https://doi.org/2334 [pii]

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Abstract PDF: Plasma-derived products are produced from plasma via fractionation and chromatography techniques, but can also be produced by other methods. In the performance of nucleic acid amplification tests (NAT) with plasma-derived products, it is necessary to include an internal control for the monitoring of all procedures. In order to avoid false negative results, we confirmed the usefulness of the bovine viral diarrhoea virus (BVDV) for use as an internal control in the detection of hepatitis C virus (HCV) RNA in plasma-derived products. These products, which were spiked with BVDV, were extracted and then NAT was performed. Specificity and sensitivity were determined via the adjustment of primer concentrations and annealing temperatures. BVDV detection allows for validation in the extraction, reverse transcription, and amplification techniques used for HCV detection in plasma-derived products.

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