Journal of Microbiology

Research Article

Dissimilatory nitrate reductions in soil Neobacillus and Bacillus strains under aerobic condition: Seohyun Ahn, Min Cho, Michael J. Sadowsky, Jeonghwan Jang; J. Microbiol. 2025;63(2):e2411019. Published online February 27, 2025; DOI: https://doi.org/10.71150/jm.2411019

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Abstract PDF Supplementary Material: Denitrification and dissimilatory nitrate reduction to ammonium (DNRA) were thought to be carried-out by anaerobic bacteria constrained to anoxic conditions as they use nitrate (NO₃^-) as a terminal electron acceptor instead of molecular O₂. Three soil bacilli, Neobacillus spp. strains PS2-9 and PS3-12 and Bacillus salipaludis PS3-36, were isolated from rice paddy field soil in Korea. The bacterial strains were selected as possible candidates performing aerobic denitrification and DNRA as they were observed to reduce NO₃^- and produce extracellular NH₄⁺ regardless of oxygen presence at the initial screening. Whole genome sequencing revealed that these strains possessed all the denitrification and DNRA functional genes in their genomes, including the nirK, nosZ, nirB, and nrfA genes, which were simultaneously cotranscribed under aerobic condition. The ratio between the assimilatory and dissimilatory NO₃^- reduction pathways depended on the availability of a nitrogen source for cell growth, other than NO₃^-. Based on the phenotypic and transcriptional analyses of the NO₃^- reductions, all three of the facultative anaerobic strains reduced NO₃^- likely in both assimilatory and dissimilatory pathways under both aerobic and anoxic conditions. To our knowledge, this is the first report that describes coexistence of NO₃^- assimilation, denitrification, and DNRA in a Bacillus or Neobacillus strain under aerobic condition. These strains may play a pivotal role in the soil nitrogen cycle.

Journal Articles

Functional Characterization of DNA N‑Glycosylase Ogg1 and Ntg1 in DNA Damage Stress of Cryptococcus neoformans: Kwang-Woo Jung , Sunhak Kwon , Jong-Hyun Jung , Sangyong Lim , Yong-Sun Bahn; J. Microbiol. 2023;61(11):981-992. Published online December 6, 2023; DOI: https://doi.org/10.1007/s12275-023-00092-y

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Abstract: Reactive oxygen species induce DNA strand breaks and DNA oxidation. DNA oxidation leads to DNA mismatches, resulting in mutations in the genome if not properly repaired. Homologous recombination (HR) and non-homologous end-joining (NHEJ) are required for DNA strand breaks, whereas the base excision repair system mainly repairs oxidized DNAs, such as 8-oxoguanine and thymine glycol, by cleaving the glycosidic bond, inserting correct nucleotides, and sealing the gap. Our previous studies revealed that the Rad53-Bdr1 pathway mainly controls DNA strand breaks through the regulation of HRand NHEJ-related genes. However, the functional roles of genes involved in the base excision repair system remain elusive in Cryptococcus neoformans. In the present study, we identified OGG1 and NTG1 genes in the base excision repair system of C. neoformans, which are involved in DNA oxidation repair. The expression of OGG1 was induced in a Hog1-dependent manner under oxidative stress. On the other hand, the expression of NTG1 was strongly induced by DNA damage stress in a Rad53-independent manner. We demonstrated that the deletion of NTG1, but not OGG1, resulted in elevated susceptibility to DNA damage agents and oxidative stress inducers. Notably, the ntg1Δ mutant showed growth defects upon antifungal drug treatment. Although deletion of OGG1 or NTG1 did not increase mutation rates, the mutation profile of each ogg1Δ and ntg1Δ mutant was different from that of the wild-type strain. Taken together, we found that DNA N-glycosylase Ntg1 is required for oxidative DNA damage stress and antifungal drug resistance in C. neoformans.

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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Abstract

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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The assessment of host and bacterial proteins in sputum from active pulmonary tuberculosis: Hsin-Chih Lai , Yu-Tze Horng , Pen-Fang Yeh , Jann-Yuan Wang , Chin-Chung Shu , Jang-Jih Lu , Jen-Jyh Lee , Po-Chi Soo; J. Microbiol. 2016;54(11):761-767. Published online October 29, 2016; DOI: https://doi.org/10.1007/s12275-016-6201-x

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Abstract

Pulmonary tuberculosis (TB) is caused by Mycobacterium tuberculosis. The protein composition of sputum may reflect the immune status of the lung. This study aimed to evaluate the protein profiles in spontaneous sputum samples from patients with active pulmonary TB. Sputum samples were collected from patients with pulmonary TB and healthy controls. Western blotting was used to analyze the amount of interleukin 10 (IL-10), interferon-gamma (IFN-γ), IL-25, IL- 17, perforin-1, urease, albumin, transferrin, lactoferrin, adenosine deaminase (also known as adenosine aminohydrolase, or ADA), ADA-2, granzyme B, granulysin, and caspase- 1 in sputum. Results of detection of IL-10, IFN-γ, perforin- 1, urease, ADA2, and caspase-1, showed relatively high specificity in distinguishing patients with TB from healthy controls, although sensitivities varied from 13.3% to 66.1%. By defining a positive result as the detection of any two proteins in sputum samples, combined use of transferrin and urease as markers increased sensitivity to 73.2% and specificity to 71.1%. Furthermore, we observed that the concentration of transferrin was proportional to the number of acidfast bacilli detected in sputum specimens. Detection of sputum transferrin and urease was highly associated with pulmonary TB infection. In addition, a high concentration of transferrin detected in sputum might correlate with active TB infection. This data on sputum proteins in patients with TB may aid in the development of biomarkers to assess the severity of pulmonary TB.

Citations

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From simple to complex: Protein‐based biomarker discovery in tuberculosis
Zaynab Mousavian, Gunilla Källenius, Christopher Sundling
European Journal of Immunology.2023;[Epub] CrossRef
Interleukin 8 and Pentaxin (C-Reactive Protein) as Potential New Biomarkers of Bovine Tuberculosis
Xintao Gao, Xiaoyu Guo, Ming Li, Hong Jia, Weidong Lin, Lichun Fang, Yitong Jiang, Hongfei Zhu, Zhifang Zhang, Jiabo Ding, Ting Xin, Brad Fenwick
Journal of Clinical Microbiology.2019;[Epub] CrossRef

Research Support, Non-U.S. Gov'ts

Conditional probability analysis of multidrug resistance in Gram-negative bacilli isolated from tertiary medical institutions in South Korea during 1999–2009: Yong-Hak Kim; J. Microbiol. 2016;54(1):50-56. Published online January 5, 2016; DOI: https://doi.org/10.1007/s12275-016-5579-9

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Abstract

Multidrug resistance of Gram-negative bacilli is a major problem globally. However, little is known about the combined probability of resistance to various antibiotics. In this study, minimum inhibitory concentrations of widely used antibiotics were determined using clinical isolates of Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, and Acinetobacter baumannii, randomly chosen from strain collections created during 1999–2009 in tertiary medical institutions in Seoul, South Korea. To analyze combined efficacy of antibiotics against a subgroup of isolates, conditional probabilities were determined based on arbitrary, non-independent patterns of antimicrobial susceptibility and resistance. Multidrug resistance, defined as resistance to three or more classes of antibiotics, was observed in the following order: A. baumannii (96%), P. aeruginosa (65%), E. coli (52%), and K. pneumoniae (7%). A. baumannii strains resistant to gentamicin were found to be resistant to a number of antibiotics, except for colistin and polymyxin B. Resistance to gentamicin following exposure to this antibiotic was highly likely to lead to multidrug resistance in all four microbes. This study shows a causal relationship between gentamicin resistance and the prevalence of multidrug resistance in clinical isolates of Gramnegative bacilli in South Korea during 1999–2009 and suggests the importance of prudent use of gentamicin in hospitals.

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Analysis of Predictive Factors of Antibiotic Resistant Pseudomonas aeruginosa in Children with Acute Appendicitis
Mengqi Wan, Mengjie Yu, Juhua Xiao Jiangxi, Qiang Chen, Nuoya Li, Jun Lei, Weilong Chen, Shouhua Zhang, Qiang Tao
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International Journal of Colorectal Disease.2018; 33(4): 441. CrossRef
Abrupt Increase in Rate of Imipenem Resistance in Acinetobacter baumannii Complex Strains Isolated from General Hospitals in Korea and Correlation With Carbapenem Administration During 2002?2013
Young Ah Kim, Yoon Soo Park, Taemi Youk, Hyukmin Lee, Kyungwon Lee
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L. Dortet, R. Bonnin, A. Jousset, L. Gauthier, T. Naas
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Tae-Ok Kim, In-Seon Eom, Kwang-Ho Park, Kwon-Sam Park
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Paenibacillus swuensis sp. nov., a Bacterium Isolated from Soil: Jae-Jin Lee , Da-Hye Yang , Ye-Sil Ko , Jae-Kyoung Park , Eun-Young Im , Ju-Yeon Kim , Ka-Young Kwon , Yu-Jung Lee , Hyung-Mi Kim , Myung Kyum Kim; J. Microbiol. 2014;52(2):106-110. Published online February 1, 2014; DOI: https://doi.org/10.1007/s12275-014-3546-x

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Abstract

Strain DY6T, a Gram-positive endospore-forming motile rodshaped bacterium, was isolated from soil in South Korea and characterized to determine its taxonomic position. Phylogenetic analyses based on the 16S rRNA gene sequence of strain DY6T revealed that strain DY6T belongs to the genus Paenibacillus in the family Paenibacillaceae in the class Bacilli. The highest degree of sequence similarities of strain DY6T were found with Paenibacillus gansuensis B518T (97.9%), P. chitinolyticus IFO 15660T (95.3%), P. chinjuensis WN9T (94.7%), and P. rigui WPCB173T (94.7%). Chemotaxonomic data revealed that the predominant fatty acids were anteiso-C15:0 (38.7%) and C16:0 (18.0%). A complex polar lipid profile consisted of major amounts of diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylglycerol. The predominant respiratory quinone was MK-7. Based on these phylogenetic, chemotaxonomic, and phenotypic data, strain DY6T (=KCTC 33026T =JCM 18491T) should be classified as a type strain of a novel species, for which the name Paenibacillus swuensis sp. nov. is proposed.

Citations

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Paenibacillus arcticus sp. nov., isolated from Arctic soil
In-Tae Cha, Eui-Sang Cho, Yesol Yoo, Yoon Ji Seok, Inhye Park, Hee Seon Lim, Jung-Min Park, Seong Woon Roh, Young-Do Nam, Hak-Jong Choi, Yoo Kyung Lee, Myung-Ji Seo
International Journal of Systematic and Evolutionary Microbiology.2017; 67(11): 4385. CrossRef
Paenibacillus albidus sp. nov., isolated from grassland soil
Junli Zhuang, Di Xin, Yu-Qin Zhang, Jingnan Guo, Jianli Zhang
International Journal of Systematic and Evolutionary Microbiology.2017; 67(11): 4685. CrossRef
Complete genome sequence of Paenibacillus swuensis DY6T, a bacterium isolated from gamma-ray irradiated soil
Myung Kyum Kim, Seung-Yeol Lee, Hee-Young Jung, Sathiyaraj Srinivasan
The Korean Journal of Microbiology.2016; 52(4): 500. CrossRef
Paenibacillus baekrokdamisoli sp. nov., isolated from soil of crater lake
Keun Chul Lee, Kwang Kyu Kim, Jong-Shik Kim, Dae-Shin Kim, Suk-Hyung Ko, Seung-Hoon Yang, Jung-Sook Lee
International Journal of Systematic and Evolutionary Microbiology.2016; 66(5): 1937. CrossRef
List of new names and new combinations previously effectively, but not validly, published
A. Oren, G. M. Garrity
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY.2015; 65(Pt 3): 741. CrossRef

Journal Articles

Macrolide Resistance and In Vitro Selection of Resistance to Antibiotics in Lactobacillus Isolates: Lorenzo Drago , Roberto Mattina , Lucia Nicola , Valentina Rodighiero , Elena De Vecchi; J. Microbiol. 2011;49(4):651-656. Published online September 2, 2011; DOI: https://doi.org/10.1007/s12275-011-0470-1

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Abstract: Spreading of resistance to antibiotics is of great concern due to the increasing rate of isolation of multiresistant pathogens. Since commensal bacteria may transfer determinants of resistance to pathogens, studies on development of resistance should include also lactobacilli. Resistance to macrolides, penicillins and tetracycline was determined in 40 isolates of Lactobacillus acidophilus, Lactobacillus plantarum, Lactobacillus crispatus, and Lactobacillus casei isolated from faeces of apparently healthy volunteers. Frequency of mutation and changes in susceptibility after serial exposure to these antibiotics at concentrations of 4× and 8× MIC were evaluated in susceptible isolates. Acquired resistance was defined as an increment in MIC values of at least four times in respect to the pre-selection values. Resistance to macrolides and/or tetracycline was identified in 14 and 4 isolates, respectively. ermB gene and A2058G mutation in 23S rRNA were detected in macrolide resistant isolates. Frequencies of mutation of susceptible isolates (n=26) were lower for ampicillin and erythromycin than for tetracycline. Serial exposure to antibiotics led to selection of resistant mutants. However, acquired resistance was rather unstable and was lost after subcultures in antibiotic-free medium in most mutants. Resistance to erythromycin was associated to a A2058G mutation in 23S rRNA. In conclusion,
results
indicate that resistance to macrolides and tetracycline is present among intestinal lactobacilli. Decrease in susceptibility following serial exposure to antibiotics might occur in lactobacilli, in a strain- and antibiotic- dependent way. Since lactobacilli are often used as probiotics, their ability to acquire resistance should be evaluated for isolates candidate to be included in probiotics based products.

Induction of Cytokines and Nitric Oxide in Murine Macrophages Stimulated with Enzymatically Digested Lactobacillus Strains: Dong Woon Kim , Sung Back Cho , Cheol Heui Yun , Ha Yeon Jeong , Wan Tae Chung , Chang Weon Choi , Hyun Jeong Lee , In Sik Nam , Guk Hyun Suh , Sang Suk Lee , Byong Seak Lee; J. Microbiol. 2007;45(5):373-378.; DOI: https://doi.org/2601 [pii]

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Abstract: Based on observations that lactic acid bacteria have the ability to activate macrophages, we assessed the potential effects of eight different Lactobacillus strains treated with gastrointestinal enzymes on the production of nitric oxide and various cytokines in macrophages. RAW 264.7 murine macrophage cells were cultured with either precipitates or supernatants of Lactobacillus strains digested with pepsin followed by pancreatin. The increased production of nitric oxide and interleukin (IL)-1β, IL-6, IL-12 and tumour necrosis factor (TNF)-α were observed when cultured with precipitates, and this effect was largely strain-dependent. In contrast, the exposure of RAW 264.7 cells to supernatants produced weaker or nearly undetectable effects in comparison to the effects of exposure to precipitates. The induction of nitric oxide appeared to be unaffected. These results demonstrate that nitric oxide and cytokines were effectively induced when the bacterial precipitate was treated with macrophages. The results of the present study also indicate that Lactobacillus strains treated with digestive enzymes are capable of stimulating the production of nitric oxide and cytokines in macrophages, which may modulate the gastrointestinal immune function of the host when it is given as a feed additive.

Infectious RNA viruses in the edible mushroom pleurotus spp: Park, Jeong Soo , Kim, Young Ho; J. Microbiol. 1996;34(1):61-67.

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Abstract: Double-stranded RNA (dsRNA) viruses and single-stranded RNA(ssRNA) viruses were detected in a strain of Pleurotus mushroom cultivated in a farm. Those fungal viruses were purified in the pH 6.0 or pH 7.2 using CsCI or Cs₂SO₄buoyant density centrifugation. Each viral particles were not completely separated at any trials. However, mushroom bacili-form virus contains a single major nucleic acid with 0.7 Kb ssRNA, which might code for 20 Kd viral capsid protein. The dsRNAs are encapsidatred into spherical-form viruses, whereas ssRNA viral genomes are encapsidated into two different sizes of bacili-form particles. A healthy-looking mushroom also contained some spherical-form viruses with dsRNAs. Laboratory strains of Pleurotus ostreatus and a cultivated strain of P. sajor-caju did not show any viral particles. Mushrooms with specific disease symptoms. however, contained at least four different sizes of spherical-form viruses. Thus, we concluded that a bacilli-form virus case a severe disease symptoms of abnormal on mushroom development.

Antibacterial Activities of Lactobacillus crispatus ATCC 33820 and Lactobacillus gasseri ATCC 33323: Jin-Woo Kim , S.N. Rajagopal; J. Microbiol. 2001;39(2):146-148.

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Abstract: Lactobacillus crispatus ATCC 33820 and L. gasseri ATCC 33323 were grown in MRS broth (pH 6.5) at 37 C for 24 h and the antibacterial activities of cell free culture supernatants were determined by the agar well diffusion method. The culture supernatants were inhibitory to Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Bacillus subtilis, Staphylococcus aureus, Enterococcus faecalis, Pediococcus acidilacticii, and Lactobacillus helveticus. The supernatants did not show any lysozyme activity. Addition of catalase did not affect the antibacterial activities of the supernatants. The antibacterial substances were heat stable (100 C for 60 min) and sensitive to proteases.

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