Journal of Microbiology

Journal Articles

Hydroxychloroquine an Antimalarial Drug, Exhibits Potent Antifungal Efficacy Against Candida albicans Through Multitargeting.: Sargun Tushar Basrani, Tanjila Chandsaheb Gavandi, Shivani Balasaheb Patil, Nandkumar Subhash Kadam, Dhairyasheel Vasantrao Yadav, Sayali Ashok Chougule, Sankunny Mohan Karuppayil, Ashwini Khanderao Jadhav; J. Microbiol. 2024;62(5):381-391. Published online April 8, 2024; DOI: https://doi.org/10.1007/s12275-024-00111-6

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Abstract: Candida albicans is the primary etiological agent associated with candidiasis in humans. Unrestricted growth of C. albicans can progress to systemic infections in the worst situation. This study investigates the antifungal activity of Hydroxychloroquine (HCQ) and mode of action against C. albicans. HCQ inhibited the planktonic growth and yeast to hyphal form morphogenesis of C. albicans significantly at 0.5 mg/ml concentration. The minimum inhibitory concentrations (MIC(50)) of HCQ for C. albicans adhesion and biofilm formation on the polystyrene surface was at 2 mg/ml and 4 mg/ml respectively. Various methods, such as scanning electron microscopy, exploration of the ergosterol biosynthesis pathway, cell cycle analysis, and assessment of S oxygen species (ROS) generation, were employed to investigate HCQ exerting its antifungal effects. HCQ was observed to reduce ergosterol levels in the cell membranes of C. albicans in a dose-dependent manner. Furthermore, HCQ treatment caused a substantial arrest of the C. albicans cell cycle at the G0/G1 phase, which impeded normal cell growth. Gene expression analysis revealed upregulation of SOD2, SOD1, and CAT1 genes after HCQ treatment, while genes like HWP1, RAS1, TEC1, and CDC 35 were downregulated. The study also assessed the in vivo efficacy of HCQ in a mice model, revealing a reduction in the pathogenicity of C. albicans after HCQ treatment. These results indicate that HCQ holds for the development of novel antifungal therapies.

Biosynthesis of Chryseno[2,1,c]oxepin‑12‑Carboxylic Acid from Glycyrrhizic Acid in Aspergillus terreus TMZ05‑2, and Analysis of Its Anti‑inflammatory Activity: Liangliang Chen , Lin Zhao , Ju Han , Ping Xiao , Mingzhe Zhao , Sen Zhang , Jinao Duan; J. Microbiol. 2024;62(2):113-124. Published online February 27, 2024; DOI: https://doi.org/10.1007/s12275-024-00105-4

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Abstract: Glycyrrhizic acid, glycyrrhetinic acid, and their oxo, ester, lactone, and other derivatives, are known for their anti-inflammatory, anti-oxidant, and hypoglycemic pharmacological activities. In this study, chryseno[2,1-c]oxepin-12-carboxylic acid (MG) was first biosynthesized from glycyrrhizic acid through sequential hydrolysis, oxidation, and esterification using Aspergillus terreus TMZ05-2, providing a novel in vitro biosynthetic pathway for glycyrrhizic acid derivatives. Assessing the influence of fermentation conditions and variation of strains during culture under stress-induction strategies enhanced the final molar yield to 88.3% (5 g/L glycyrrhizic acid). CCK8 assays showed no cytotoxicity and good cell proliferation, and anti-inflammatory experiments demonstrated strong inhibition of NO release (36.3%, low-dose MG vs. model), transcriptional downregulation of classical effective cellular factors tumor necrosis factor-α (TNF-α; 72.2%, low-dose MG vs. model), interleukin-6 (IL-6; 58.3%, low-dose MG vs. model) and interleukin-1β (IL-1β; 76.4%, low-dose MG vs. model), and decreased abundance of P-IKK-α, P-IKB-α, and P-P65 proteins, thereby alleviating inflammatory responses through the NF-κB pathway in LPS-induced RAW264.7 cells. The findings provide a reference for the biosynthesis of lactone compounds from medicinal plants.

Review

Searching for a Reliable Viral Indicator of Faecal Pollution in Aquatic Environments: Felana Harilanto Andrianjakarivony , Yvan Bettarel , Christelle Desnues; J. Microbiol. 2023;61(6):589-602. Published online June 1, 2023; DOI: https://doi.org/10.1007/s12275-023-00052-6

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Abstract: The disposal of sewage in significant quantities poses a health hazard to aquatic ecosystems. These effluents can contain a wide range of pathogens, making faecal contamination a leading source of waterborne diseases around the world. Yet monitoring bacteria or viruses in aquatic environments is time consuming and expensive. The standard indicators of faecal pollution all have limitations, including difficulty in determining the source due to lack of host specificity, poor connection with the presence of non-bacterial pathogens, or low environmental persistence. Innovative monitoring techniques are sorely needed to provide more accurate and targeted solutions. Viruses are a promising alternative to faecal indicator bacteria for monitoring, as they are more persistent in ambient water, more abundant in faeces, and are extremely host-specific. Given the range of viruses found in diverse contexts, it is not easy to find one “ideal” viral indicator of faecal pollution; however, several are of interest. In parallel, the ongoing development of molecular techniques coupled with metagenomics and bioinformatics should enable improved ways to detect faecal contamination using viruses. This review examines the evolution of faecal contamination monitoring with the following aims (i) to identify the characteristics of the main viral indicators of faecal contamination, including human enteric viruses, bacteriophages, CRESS and plant viruses, (ii) to assess how these have been used to monitor water pollution in recent years, (iii) to evaluate the reliability of recent detection methods of such viruses, and (iv) to tentatively determine which viruses may be most effective as markers of faecal pollution.

Journal Articles

Potential Use of Mycobacterium paragordonae for Antimycobacterial Drug Screening Systems: Ga-Yeong Cha , Hyejun Seo , Jaehun Oh , Byoung-Jun Kim , Bum-Joon Kim; J. Microbiol. 2023;61(1):121-129. Published online January 31, 2023; DOI: https://doi.org/10.1007/s12275-022-00009-1

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Abstract: Our recent genome-based study indicated that Mycobacterium paragordonae (Mpg) has evolved to become more adapted to an intracellular lifestyle within free-living environmental amoeba and its enhanced intracellular survival within Acanthamoeba castellanii was also proved. Here, we sought to investigate potential use of Mpg for antimycobacterial drug screening systems. Our data showed that Mpg is more susceptible to various antibiotics compared to the close species M. marinum (Mmar) and M. gordonae, further supporting its intracellular lifestyle in environments, which would explain its protection from environmental insults. In addition, we developed two bacterial whole-cell-based drug screening systems using a recombinant Mpg stain harboring a luciferase reporter vector (rMpg-LuxG13): one for direct application to rMpg-LuxG13 and the other for drug screening via the interaction of rMpg-LuxG13 with A. castellanii. Direct application to rMpg-LuxG13 showed lower inhibitory concentration 50 ( IC50) values of rifampin, isoniazid, clarithromycin, and ciprofloxacin against Mpg compared to Mmar. Application of drug screening system via the interaction of rMpg-LuxG13 with A. castellanii also exhibited lower IC50 values for rifampin against Mpg compared to Mmar. In conclusion, our data indicate that Mpg is more susceptible to various antibiotics than other strains. In addition, our data also demonstrate the feasibility of two whole cellbased drug screening systems using rMpg-LuxG13 strain for the discovery of novel anti-mycobacterial drugs.

Coumarin-based combined computational study to design novel drugs against Candida albicans: Akhilesh Kumar Maurya , Nidhi Mishra; J. Microbiol. 2022;60(12):1201-1207. Published online November 10, 2022; DOI: https://doi.org/10.1007/s12275-022-2279-5

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Abstract: Candida species cause the most prevalent fungal illness, candidiasis. Candida albicans is known to cause bloodstream infections. This species is a commensal bacterium, but it can cause hospital–acquired diseases, particularly in COVID-19 patients with impaired immune systems. Candida infections have increased in patients with acute respiratory distress syndrome. Coumarins are both naturally occurring and synthetically produced. In this study, the biological activity of 40 coumarin derivatives was used to create a three-dimensional quantitative structure activity relationship (3D-QSAR) model. The training and test minimum inhibitory concentration values of C. albicans active compounds were split, and a regression model based on statistical data was established. This model served as a foundation for the creation of coumarin derivative QSARs. This is a unique way to create new therapeutic compounds for various ailments. We constructed novel structural coumarin derivatives using the derived QSAR model, and the models were confirmed using molecular docking and molecular dynamics simulation.

Rasiella rasia gen. nov. sp. nov. within the family Flavobacteriaceae isolated from seawater recirculating aquaculture system: Seong-Jin Kim , Young-Sam Kim , Sang-Eon Kim , Hyun-Kyoung Jung , Jeeeun Park , Min-Ju Yu , Kyoung-Ho Kim; J. Microbiol. 2022;60(11):1070-1076. Published online October 17, 2022; DOI: https://doi.org/10.1007/s12275-022-2099-7

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Abstract: A novel bacterium designated RR4-40T was isolated from a biofilter of seawater recirculating aquaculture system in Busan, South Korea. Cells are strictly aerobic, Gram-negative, irregular short rod, non-motile, and oxidase- and catalase-negative. Growth was observed at 15–30°C, 0.5–6% NaCl (w/v), and pH 5.0–9.5. The strain grew optimally at 28°C, 3% salinity (w/v), and pH 8.5. The phylogenetic analysis based on 16S rRNA gene sequences showed that strain RR4-40T was most closely related to Marinirhabdus gelatinilytica NH83T (94.16% of 16S rRNA gene similarity) and formed a cluster with genera within the family Flavobacteriaceae. The values of the average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and average amino acid identity (AAI) between genomes of strain RR4-40T and M. gelatinilytica NH83T were 72.91, 18.2, and 76.84%, respectively, and the values against the strains in the other genera were lower than those. The major fatty acids were iso-C15:0 (31.34%), iso-C17:0 3-OH (13.65%), iso-C16:0 3-OH (10.61%), and iso-C15:1 G (10.38%). The polar lipids comprised phosphatidylglycerol, diphosphatidylglycerol, aminophospholipid, aminolipid, glycolipid, and sphingolipid. The major respiratory quinone was menaquinone-6 (MK-6) and the DNA G + C content of strain RR4-40T was 37.4 mol%. According to the polyphasic analysis, strain RR4-40T is considered to represent a novel genus within the family Flavobacteriaceae, for which the name Rasiella rasia gen. nov, sp. nov. is proposed. The type strain is RR4-40T (= KCTC 52650T = MCCC 1K04210T).

Sulforaphane kills Mycobacterium tuberculosis H37Ra and Mycobacterium smegmatis mc2155 through a reactive oxygen species dependent mechanism: Yongjie Zhao , Shengwen Shang , Ya Song , Tianyue Li , Mingliang Han , Yuexuan Qin , Meili Wei , Jun Xi , Bikui Tang; J. Microbiol. 2022;60(11):1095-1105. Published online September 1, 2022; DOI: https://doi.org/10.1007/s12275-022-2284-8

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Abstract: Mycobacterium tuberculosis (M. tuberculosis) is a highly pathogenic intracellular pathogen that causes tuberculosis (TB), the leading cause of mortality from single infections. Redox homeostasis plays a very important role in the resistance of M. tuberculosis to antibiotic damage and various environmental stresses. The antioxidant sulforaphane (SFN) has been reported to exhibit anticancer activity and inhibit the growth of a variety of bacteria and fungi. Nonetheless, it remains unclear whether SFN exhibits anti-mycobacterial activity. Our
results
showed that the SFN against M. tuberculosis H37Ra exhibited bactericidal activity in a time and dose-dependent manner. The anti-tubercular activity of SFN was significantly correlated with bacterial reactive oxygen species (ROS) levels. In addition, SFN promoted the bactericidal effect of macrophages on intracellular bacteria in a dose-dependent manner, mediated by increasing intracellular mitochondrial ROS levels and decreasing cytoplasmic ROS levels. Taken together, our data revealed the previously unrecognized antimicrobial functions of SFN. Future studies focusing on the mechanism of SFN in macrophages against M. tuberculosis are essential for developing new host-directed therapeutic approaches against TB.

Crystal structure of the phage-encoded N-acetyltransferase in complex with acetyl-CoA, revealing a novel dimeric arrangement: Nayeon Ki , Inseong Jo , Yongseong Hyun , Jinwook Lee , Nam-Chul Ha , Hyun-Myung Oh; J. Microbiol. 2022;60(7):746-755. Published online July 4, 2022; DOI: https://doi.org/10.1007/s12275-022-2030-2

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Abstract: Bacteriophages employ diverse mechanisms to facilitate the proliferation of bacteriophages. The Salmonella-infecting phage SPN3US contains a putative N-acetyltransferase, which is widely found in bacteriophages. However, due to low sequence similarity to the N-acetyltransferases from bacteria and eukaryotic cells, the structure and function of phage-encoded acetyltransferases are mainly unknown. This study determines the crystal structure of the putative N-acetyltransferase of SPN3US in complex with acetyl-CoA. The crystal structure showed a novel homodimeric arrangement stabilized by exchanging the C-terminal α-helix within the dimer. The following biochemical analyses suggested that the phageencoded acetyltransferase might have a very narrow substrate specificity. Further studies are required to reveal the biochemical activity, which would help elucidate the interaction between the phage and host bacteria in controlling pathogenic bacteria.

Review

Overview of bioinformatic methods for analysis of antibiotic resistome from genome and metagenome data: Kihyun Lee , Dae-Wi Kim , Chang-Jun Cha; J. Microbiol. 2021;59(3):270-280. Published online February 23, 2021; DOI: https://doi.org/10.1007/s12275-021-0652-4

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16 Citations

Abstract: Whole genome and metagenome sequencing are powerful approaches that enable comprehensive cataloging and profiling of antibiotic resistance genes at scales ranging from a single clinical isolate to ecosystems. Recent studies deal with genomic and metagenomic data sets at larger scales; therefore, designing computational workflows that provide high efficiency and accuracy is becoming more important. In this review, we summarize the computational workflows used in the research field of antibiotic resistome based on genome or metagenome sequencing. We introduce workflows, software tools, and data resources that have been successfully employed in this rapidly developing field. The workflow described in this review can be used to list the known antibiotic resistance genes from genomes and metagenomes, quantitatively profile them, and investigate the epidemiological and evolutionary contexts behind their emergence and transmission. We also discuss how novel antibiotic resistance genes can be discovered and how the association between the resistome and mobilome can be explored.

Fibroblast Growth Factor 11 Inhibits Hepatitis B Virus Gene Expression Through FXRα Suppression: Mi So Seong , Jeong Ah Jang , Ye Rim Jeong , Ye Bin Kim , Yi Yi Kyaw , Hee Jeong Kong , Jung-Hyun Lee , JaeHun Cheong; J. Microbiol. 2023;61(7): 693-702.; DOI: https://doi.org/10.1007/s12275-023-00065-1

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Abstract: Fibroblast growth factor 11 (FGF11) is a member of the intracellular FGF family, which shows different signal transmission compared with other FGF superfamily members. The molecular function of FGF11 is not clearly understood. In this study, we identified the inhibitory effect of FGF11 on hepatitis B virus (HBV) gene expression through transcriptional suppression. FGF11 decreased the mRNA and protein expression of HBV genes in liver cells. While the nuclear receptor FXRα1 increased HBV promoter transactivation, FGF11 decreased the FXRα-mediated gene induction of the HBV promoter by the FXRα agonist. Reduced endogenous levels of FXRα by siRNA and the dominant negative mutant protein (aa 1–187 without ligand binding domain) of FXRα expression indicated that HBV gene suppression by FGF11 is dependent on FXRα inhibition. In addition, FGF11 interacts with FXRα protein and reduces FXRα protein stability. These results indicate that FGF11 inhibits HBV replicative expression through the liver cell-specific transcription factor, FXRα, and suppresses HBV promoter activity. Our findings may contribute to the establishment of better regimens for the treatment of chronic HBV infections by including FGF11 to alter the bile acid mediated FXR pathway.

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