Journal of Microbiology

Journal Articles

Isolation of a novel Lactiplantibacillus plantarum strain resistant to nitrite stress and its transcriptome analysis: Chae Young Kwon , Kyoung Jin Choi , Dongeun Yong , Ji-Eun Kim , Sang Sun Yoon; J. Microbiol. 2022;60(7):715-726. Published online July 4, 2022; DOI: https://doi.org/10.1007/s12275-022-2221-x

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Abstract: Nitric oxide (NO) is a reactive nitrogen species (RNS) that plays a vital role in regulating inflammatory processes. Under abnormal conditions, excessive NO levels can promote the oxidation of cellular components, which may cause or exacerbate diseases such as hypertension, cardiovascular dysfunction, and inflammatory bowel disease (IBD). Previous studies have shown that reducing NO levels in the lumen can attenuate the clinical symptoms of IBD. Thus, we aimed to identify bacteria that can reduce RNS and that can be used as valuable probiotics. In this study, we isolated bacteria resistant to nitrite stress from human feces and used 16S and whole-genome sequencing to identify them as Lactiplantibacillus plantarum LP7 (LP7). The ability to survive at high nitrite levels and to decrease them was greater in the LP7 strain than in the reference strain L. plantarum ATCC14917 (ATCC- 14917). To characterize the LP7 genome in more detail, we performed a comparative genome analysis. However, the unique genes that directly confer the ability to withstand nitrite stress were not present in the LP7 genome. Furthermore, we performed transcriptomic analysis of LP7 and ATCC14917 cells treated with nitrite. We found that the expression levels of genes involved in the cell division process were induced in LP7, which showed a more regular rod-shape than ATCC- 14917. This could explain why LP7 can survive better than ATCC14917 under nitrite stress. Based on its ability to survive better in nitrite stress and decrease nitrite concentration, we suggest that LP7 could be a valuable probiotic strain.

Complete genetic dissection and cell type-specific replication of old world alphaviruses, getah virus (GETV) and sagiyama virus (SAGV): Yiwen Zhang , Jinhan Yu , Lu Tan , Xingxing Wang , Runsheng Li , Dal Young Kim; J. Microbiol. 2021;59(11):1044-1055. Published online September 27, 2021; DOI: https://doi.org/10.1007/s12275-021-1361-8

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Getah virus (GETV), which was first isolated in Malaysia in 1955, and Sagiyama virus (SAGV), isolated in Japan in 1956, are members of the genus Alphavirus in the family Togaviridae. It is a consensus view that SAGV is a variant of GETV. In the present study, we determined the complete sequences of the prototype GETV MM2021 and SAGV M6-Mag132 genomic RNA extracted from plaque-purified viruses. The MM2021 genome was 11,692 nucleotides (nt) in length in the absence of 3􍿁􀁇poly(A) tail, and the length of M6-Mag132 genome was 11,698 nt. Through sequence alignment of MM2021 and M6-Mag132, we located all the amino acid differences between these two strains, which were scattered in all the encoded proteins. Subsequently, we validated the close evolutionary relationship between GETV and SAGV by constructing phylogenetic trees based on either complete genomes or structural genomes. We eventually analyzed the growth kinetics of GETV and SAGV as well as other representative alphaviruses in various mammalian and insect cell lines. It was shown that human-oriented cell lines such as HEK-293T and Hela cells were relatively resistant to GETV and SAGV infection due to absence of proviral factors or species-specific barrier. On the other hand, both GETV and SAGV replicated efficiently in non-human cell lines. Our results provide essential genetic information for future epidemiological surveillance on Alphaviruses and lay the foundation for developing effective interventions against GETV and SAGV.

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Novel Porcine Getah Virus from Diarrheal Piglets in Jiangxi Province, China: Prevalence, Genome Sequence, and Pathogenicity
Jianhui Lan, Mengtao Fang, Leilei Duan, Zhong Liu, Guanggao Wang, Qi Wu, Ke Fan, Dongyan Huang, Yu Ye, Gen Wan, Yuxin Tang, Deping Song
Animals.2024; 14(20): 2980. CrossRef
Characterization and arbovirus susceptibility of cultured CERNI cells derived from sika deer (Cervus nippon)
Makoto Takeishi, Shigeru Morikawa, Ryusei Kuwata, Mitsumori Kawaminami, Hiroshi Shimoda, Haruhiko Isawa, Ken Maeda, Yasuhiro Yoshikawa
In Vitro Cellular & Developmental Biology - Animal.2024; 60(8): 935. CrossRef
Getah Virus Infection Rapidly Causes Testicular Damage and Decreases Sperm Quality in Male Mice
Fengqing Li, Bing Zhang, Zhiwen Xu, Chaoyuan Jiang, Mincai Nei, Lei Xu, Jun Zhao, Huidan Deng, Xiangang Sun, Yuancheng Zhou, Ling Zhu
Frontiers in Veterinary Science.2022;[Epub] CrossRef

Review

Raloxifene as a treatment option for viral infections: Subin Hong , JuOae Chang , Kwiwan Jeong , Wonsik Lee; J. Microbiol. 2021;59(2):124-131. Published online February 1, 2021; DOI: https://doi.org/10.1007/s12275-021-0617-7

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Abstract

Severe acute respiratory syndrome coronavirus 2 (SARSCoV- 2) has caused corona virus disease 2019 (COVID-19) pandemic and led to mass casualty. Even though much effort has been put into development of vaccine and treatment
methods
to combat COVID-19, no safe and efficient cure has been discovered. Drug repurposing or drug repositioning which is a process of investigating pre-existing drug candidates for novel applications outside their original medical indication can speed up the drug development process. Raloxifene is a selective estrogen receptor modulator (SERM) that has been approved by FDA in 1997 for treatment and prevention of postmenopausal osteoporosis and cancer. Recently, raloxifene demonstrates efficacy in treating viral infections by Ebola, influenza A, and hepatitis C viruses and shows potential for drug repurposing for the treatment of SARS-CoV-2 infection. This review will provide an overview of raloxifene’s mechanism of action as a SERM and present proposed mechanisms of action in treatment of viral infections.

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Veronica Cocetta, Manuel Zorzi, Stefano Bejor, Maria Candida Cesta, Maria De Pizzol, Jean-Philippe Theurillat, Marcello Allegretti, Andrea Alimonti, Monica Montopoli, Massimo Rugge
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A real‑world pharmacovigilance study of raloxifene based on the FDA adverse event reporting system (FAERS)
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Mohammad Abavisani, Alireza Khoshrou, Souzan Eshaghian, Sercan Karav, Amirhossein Sahebkar
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Agnidipta Das, Kanamarlapudi Joshna Lavanya, Nandini, Kamalpreet Kaur, Vikas Jaitak
Current Medicinal Chemistry.2023; 30(29): 3287. CrossRef
Rapid discovery and classification of inhibitors of coronavirus infection by pseudovirus screen and amplified luminescence proximity homogeneous assay
Kwiwan Jeong, JuOae Chang, Sun-mi Park, Jinhee Kim, Sangeun Jeon, Dong Hwan Kim, Young-Eui Kim, Joo Chan Lee, Somyoung Im, Yejin Jo, Ji-Young Min, Hanbyeul Lee, Minjoo Yeom, Sang-Hyuk Seok, Da In On, Hyuna Noh, Jun-Won Yun, Jun Won Park, Daesub Song, Je K
Antiviral Research.2023; 209: 105473. CrossRef
Synthesis of raloxifene-like quinoxaline derivatives by intramolecular electrophilic cyclization with disulfides
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The potential renoprotective effect of Raloxifene in renal ischemia-reperfusion injury in a male rat model
Raghad Abdul Hameed Ali, Murooj Altimimi, Najah Rayish Hadi
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Multimodal representation learning for predicting molecule–disease relations
Jun Wen, Xiang Zhang, Everett Rush, Vidul A Panickan, Xingyu Li, Tianrun Cai, Doudou Zhou, Yuk-Lam Ho, Lauren Costa, Edmon Begoli, Chuan Hong, J Michael Gaziano, Kelly Cho, Junwei Lu, Katherine P Liao, Marinka Zitnik, Tianxi Cai, Zhiyong Lu
Bioinformatics.2023;[Epub] CrossRef
A Systematic Review of Molecular Pathway Analysis of Drugs for Potential Use in Liver Cancer Treatment
Ruchi Jakhmola Mani, Mridul Anand, Kritie Agarwal, Avi Tiwari, Qazi Amanur Rahman Hashmi, Tumul Vikram Singh, Potshangbam Nongdam, Deepshikha Pande Katare, Angamba Meetei Potshangabam
Drugs and Drug Candidates.2023; 2(2): 210. CrossRef
A phase 2 randomized, double-blinded, placebo-controlled, multicenter trial evaluating the efficacy and safety of raloxifene for patients with mild to moderate COVID-19
Emanuele Nicastri, Franco Marinangeli, Emanuele Pivetta, Elena Torri, Francesco Reggiani, Giuseppe Fiorentino, Laura Scorzolini, Serena Vettori, Carolina Marsiglia, Elizabeth Marie Gavioli, Andrea R. Beccari, Giuseppe Terpolilli, Maria De Pizzol, Giovanni
eClinicalMedicine.2022; 48: 101450. CrossRef
Repurposing the estrogen receptor modulator raloxifene to treat SARS-CoV-2 infection
Marcello Allegretti, Maria Candida Cesta, Mara Zippoli, Andrea Beccari, Carmine Talarico, Flavio Mantelli, Enrico M. Bucci, Laura Scorzolini, Emanuele Nicastri
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The SARS-CoV-2 spike protein binds and modulates estrogen receptors
Oscar Solis, Andrea R. Beccari, Daniela Iaconis, Carmine Talarico, Camilo A. Ruiz-Bedoya, Jerome C. Nwachukwu, Annamaria Cimini, Vanessa Castelli, Riccardo Bertini, Monica Montopoli, Veronica Cocetta, Stefano Borocci, Ingrid G. Prandi, Kelly Flavahan, Mel
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Characterization of raloxifene as a potential pharmacological agent against SARS-CoV-2 and its variants
Daniela Iaconis, Licia Bordi, Giulia Matusali, Carmine Talarico, Candida Manelfi, Maria Candida Cesta, Mara Zippoli, Francesca Caccuri, Antonella Bugatti, Alberto Zani, Federica Filippini, Laura Scorzolini, Marco Gobbi, Marten Beeg, Arianna Piotti, Monica
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Inhibition of KIF20A suppresses the replication of influenza A virus by inhibiting viral entry
Hoyeon Jeon, Younghyun Lim, In-Gu Lee, Dong-In Kim, Keun Pil Kim, So-Hee Hong, Jeongkyu Kim, Youn-Sang Jung, Young-Jin Seo
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JuOae Chang, Jihoon Kim, Wonsik Lee
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Aurosikha Das, Soumendra Rana
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Sara J Cromer, Elaine W Yu
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Journal Article

Genetic variation and phylogenetic relationships of the ectomycorrhizal Floccularia luteovirens on the Qinghai-Tibet Plateau: Rui Xing , Qing-bo Gao , Fa-qi Zhang , Peng-cheng Fu , Jiu-li Wang , Hui-ying Yan , Shi-long -Chen; J. Microbiol. 2017;55(8):600-606. Published online July 4, 2017; DOI: https://doi.org/10.1007/s12275-017-7101-4

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Abstract

Floccularia luteovirens, as an ectomycorrhizal fungus, is widely distributed in the Qinghai-Tibet Plateau. As an edible fungus, it is famous for its unique flavor. Former studies mainly focus on the chemical composition and genetic structure of this species. However, the phylogenetic relationship between genotypes remains unknown. In this study, the genetic variation and phylogenetic relationship between the genotypes of F. luteovirens in Qinghai-Tibet Plateau was estimated through the analysis on two protein-coding genes (rpb1 and ef-1α) from 398 individuals collected from 24 wild populations. The sample covered the entire range of this species during all the growth seasons from 2011 to 2015. 13 genotypes were detected and moderate genetic diversity was revealed. Based on the results of network analysis, the maximum likelihood (ML), maximum parsimony (MP), and Bayesian inference (BI) analyses, the genotypes H-1, H-4, H-6, H-8, H-10, and H-11 were grouped into one clade. Additionally, a relatively higher genotype diversity (average h value is 0.722) and unique genotypes in the northeast edge of Qinghai- Tibet plateau have been found, combined with the results of mismatch analysis and neutrality tests indicated that Southeast Qinghai-Tibet plateau was a refuge for F. luteovirens during the historical geological or climatic events (uplifting of the Qinghai-Tibet Plateau or Last Glacial Maximum). Furthermore, the present distribution of the species on the Qinghai-Tibet plateau has resulted from the recent population expansion. Our findings provide a foundation for the future study of the evolutionary history and the speciation of this species.

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Diversity and Multigene Phylogeny of the Genus Floccularia (Agaricales, Basidiomycota)
Zai-Wei Ge, Hua Qu, Malka Saba, Tian Gao, Martin Ryberg
Journal of Fungi.2025; 11(1): 74. CrossRef
Metabolomic Profiling of Floccularia luteovirens from Different Geographical Regions Proposes a Novel Perspective on Their Antioxidative Activities
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Selection and validation of reference genes for normalization of gene expression in Floccularia luteovirens
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Fungal Biology.2024; 128(1): 1596. CrossRef
Study on Enzyme Activity and Metabolomics during Culture of Liquid Spawn of Floccularia luteovirens
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Yanqing Ni, Luping Cao, Wensheng Li, Qin Zhang, Rencai Feng, Zhiqiang Zhao, Xu Zhao
Journal of Fungi.2023; 9(11): 1071. CrossRef
Polysaccharides of Floccularia luteovirens Alleviate Oxidative Damage and Inflammatory Parameters of Diabetic Nephropathy in db/db Mice
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Frontiers in Bioscience-Landmark.2023;[Epub] CrossRef
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The Genomic and Transcriptomic Analyses of Floccularia luteovirens, a Rare Edible Fungus in the Qinghai–Tibet Plateau, Provide Insights into the Taxonomy Placement and Fruiting Body Formation
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