Journal of Microbiology

Review

Fecal Microbiota Transplantation: Indications, Methods, and Challenges.: Jee Young Lee, Yehwon Kim, Jiyoun Kim, Jiyeun Kate Kim; J. Microbiol. 2024;62(12):1057-1074. Published online November 18, 2024; DOI: https://doi.org/10.1007/s12275-024-00184-3

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Over the past two decades, as the importance of gut microbiota to human health has become widely known, attempts have been made to treat diseases by correcting dysbiosis of gut microbiota through fecal microbiota transplantation (FMT). Apart from current knowledge of gut microbiota, FMT to treat disease has a long history, from the treatment of food poisoning in the fourth century to the treatment of Clostridioides difficile infections in the twentieth century. In 2013, FMT was recognized as a standard treatment for recurrent C. difficile because it consistently showed high efficacy. Though recurrent C. difficile is the only disease internationally recognized for FMT efficacy, FMT has been tested for other diseases and shown some promising preliminary results. Different FMT methods have been developed using various formulations and administration routes. Despite advances in FMT, some issues remain to be resolved, such as donor screening, manufacturing protocols, and unknown components in the fecal microbiota. In this review, we discuss the mechanisms, clinical indications, methods, and challenges of current FMT. We also discuss the development of alternative therapies to overcome the challenges of FMT.

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Transplantation of Fecal Flora from Patients with Atherosclerosis to Mice Can Increase Serum Low-Density Lipoprotein Cholesterol and Affect Intestinal Flora and Its Metabolites
Liang Feng, Jianting Feng, Li He, Fu Chen, Xin Feng, Suwen Wang
Applied Microbiology.2025; 5(1): 29. CrossRef

Journal Articles

Rhodobacteraceae are Prevalent and Ecologically Crucial Bacterial Members in Marine Biofloc Aquaculture: Meora Rajeev, Jang-Cheon Cho; J. Microbiol. 2024;62(11):985-997. Published online November 15, 2024; DOI: https://doi.org/10.1007/s12275-024-00187-0

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Abstract

Bioflocs are microbial aggregates primarily composed of heterotrophic bacteria that play essential ecological roles in maintaining animal health, gut microbiota, and water quality in biofloc aquaculture systems. Despite the global adoption of biofloc aquaculture for shrimp and fish cultivation, our understanding of biofloc microbiota-particularly the dominant bacterial members and their ecological functions-remains limited. In this study, we employed integrated metataxonomic and metagenomic approaches to demonstrate that the family Rhodobacteraceae of Alphaproteobacteria consistently dominates the biofloc microbiota and plays essential ecological roles. We first analyzed a comprehensive metataxonomic dataset consisting of 200 16S rRNA gene amplicons collected across three Asian countries: South Korea, China, and Vietnam. Taxonomic investigation identified Rhodobacteraceae as the dominant and consistent bacterial members across the datasets. The predominance of this taxon was further validated through metagenomics approaches, including read taxonomy and read recruitment analyses. To explore the ecological roles of Rhodobacteraceae, we applied genome-centric metagenomics, reconstructing 45 metagenome-assembled genomes. Functional annotation of these genomes revealed that dominant Rhodobacteraceae genera, such as Marivita, Ruegeria, Dinoroseobacter, and Aliiroseovarius, are involved in vital ecological processes, including complex carbohydrate degradation, aerobic denitrification, assimilatory nitrate reduction, ammonium assimilation, and sulfur oxidation. Overall, our study reveals that the common practice of carbohydrate addition in biofloc aquaculture systems fosters the growth of specific heterotrophic bacterial communities, particularly Rhodobacteraceae. These bacteria contribute to maintaining water quality by removing toxic nitrogen and sulfur compounds and enhance animal health by colonizing gut microbiota and exerting probiotic effects.

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Ecological disposal of bauxite tailings and red mud: A sustainable strategy for bauxite industrial waste reuse
Xusheng Jiang, Xuehong Zhang, Xijun Liu, Hui Qiu, Mengting Lin, Guo Yu, Shouhui Zhang, Jie Liu
Resources, Conservation and Recycling.2025; 218: 108259. CrossRef
Variation of Microorganisms and Water Quality, and Their Impacts on the Production of Penaeus vannamei in Small-Scale Greenhouse Ponds
Siyu Wu, Haochang Su, Lei Su, Yucheng Cao, Guoliang Wen, Yu Xu, Bin Shen, Shanshan Wu, Yuting Su, Xiaojuan Hu
Microorganisms.2025; 13(3): 546. CrossRef

Description of Streptococcus dentalis sp. nov., Streptococcus gingivalis sp. nov., and Streptococcus lingualis sp. nov., Isolated from Human Oral Cavities: Beom-Jin Goo, Young-Sik Choi, Do-Hun Gim, Su-Won Jeong, Jee-Won Choi, Hojun Sung, Jae-Yun Lee, Jin-Woo Bae; J. Microbiol. 2024;62(11):973-983. Published online November 12, 2024; DOI: https://doi.org/10.1007/s12275-024-00178-1

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Abstract: We isolated three novel strains, S1^T, S2^T, and S5^T, from human oral cavities and identified them as distinct novel species. All these strains are facultatively anaerobic, Gram-stain-positive, and non-flagellated bacteria. Their optimal growth conditions for these strains were observed in Columbia broth (CB) at 37 °C, pH 7.0, and in the absence of NaCl. Phylogenetic analyses, employing the 16S rRNA gene and whole-genome sequencing, confirmed that all three strains belong to the genus Streptococcus. The 16S rRNA gene sequences of strains S1^T, S2^T, and S5^T showed the highest similarities to Streptococcus parasanguinis, 98.57%, 99.05%, and 99.05%, respectively, and the orthologous average nucleotide identity (OrthoANI) values between the three strains and S. parasanguinis were 93.82%, 93.67%, and 94.04%, respectively. The pairwise OrthoANI values between the novel strains were 94.37% (S1^T-S2^T), 95.03% (S2^T-S5^T), and 94.71% (S1^T-S5^T). All strains had C_20:1 ω9c and summed feature 8 (C_18:1 ω7c and/or C_18:1 ω6c) as major cellular fatty acids. Additionally, diphosphatidylglycerol (DPG) and hydroxyphosphatidylethanolamine (OH-PE) were identified as major polar lipids. Menaquinone was undetected in all strains. The results from the phylogenetic, phenotypic, chemotaxonomic, and genotypic analyses collectively indicated that strains S1^T, S2^T, and S5^T represent three distinct novel species within the genus Streptococcus, and we propose the names Streptococcus dentalis sp. nov. for strain S1^T (= KCTC 21234^T = JCM 36526^T), Streptococcus gingivalis sp. nov. for strain S2^T (= KCTC 21235^T = JCM 36527^T), and Streptococcus lingualis sp. nov. for strain S5^T (= KCTC 21236^T = JCM 36528^T).

The Impact of Makgeolli Consumption on Gut Microbiota: An Enterotype-Based Preliminary Study: Gyungcheon Kim, Seongok Kim, Hayan Jung, Seohyun Kang, Gwoncheol Park, Hakdong Shin; J. Microbiol. 2024;62(11):965-972. Published online October 16, 2024; DOI: https://doi.org/10.1007/s12275-024-00176-3

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Abstract

Makgeolli, a traditional Korean liquor, contains components such as lactic acid bacteria and dietary fiber, which can induce changes in the gut microbiome. Since variations in microbiome responses may exist between enterotypes-classifications based on the dominant bacterial populations in the gut-we hypothesized that the consumption of makgeolli leads to enterotype-dependent differences in gut microbial structures among healthy participants. This study aimed to determine the effect of makgeolli consumption on gut microbial structures by stratifying all participants into two enterotype groups: Bacteroides-dominant type (B-type, n = 7) and Prevotella-dominant type (P-type, n = 4). The B-type showed an increase in alpha diversity, while no significant difference was observed in the P-type following makgeolli consumption. The composition of gut microbiota significantly changed in the B-type, whereas no noticeable alteration was observed in the P-type after makgeolli consumption. Notably, Prevotella exhibited the most significant changes only in the P-type. In line with the increased abundance of Prevotella, the genes associated with carbohydrate metabolism, including pentose/glucuronate interconversions, fructose/mannose metabolism, starch/sucrose metabolism and amino sugar/nucleotide sugar metabolism were significantly enriched following makgeolli consumption in the P-type. These findings suggest that makgeolli consumption induces enterotype-dependent alterations in gut microbial composition and metabolic pathways, highlighting the potential for personalized dietary interventions.

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The prebiotic potential of dietary onion extracts: shaping gut microbial structures and promoting beneficial metabolites
Yebeen Yoo, Seongok Kim, WonJune Lee, Jinwoo Kim, Bokyung Son, Kwang Jun Lee, Hakdong Shin, Aviâja Lyberth Hauptmann
mSystems.2025;[Epub] CrossRef

The Gut Microbiota Mediates the Protective Effects of Spironolactone on Myocardial Infarction: Lu Li, Jian-Yong Sun, Yu-Lin Li, Shi-Wei Zhu, Sheng-Zhong Duan; J. Microbiol. 2024;62(10):883-895. Published online September 3, 2024; DOI: https://doi.org/10.1007/s12275-024-00164-7

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Abstract

Myocardial infarction (MI) is a type of cardiovascular disease that influences millions of human beings worldwide and has a great rate of mortality and morbidity. Spironolactone has been used as a critical drug for the treatment of cardiac failure and it ameliorates cardiac dysfunction post-MI. Despite these findings, whether there is a relationship between the therapeutic effects of spironolactone and the gut microorganism after MI has not been determined. In our research, we used male C57BL/6 J mice to explore whether the gut microbiota mediates the beneficial function of spironolactone after myocardial infarction. We demonstrated that deletion of the gut microbiota eliminated the beneficial function of spironolactone in MI mice, displaying exacerbated cardiac dysfunction, cardiac infarct size. In addition, the gut microbiota was altered by spironolactone after sham or MI operation in mice. We also used male C57BL/6 J mice to investigate the function of a probiotic in the myocardial infarction. In summary, our findings reveal a precious role of the gut flora in the therapeutic function of spironolactone on MI.

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The role of the gut microbiota in the onset and progression of heart failure: insights into epigenetic mechanisms and aging
Giulia Matacchione, Francesco Piacenza, Lorenzo Pimpini, Yuri Rosati, Serena Marcozzi
Clinical Epigenetics.2024;[Epub] CrossRef

Identification of avaC from Human Gut Microbial Isolates that Converts 5AVA to 2-Piperidone: Qiudi Zhou, Lihui Feng; J. Microbiol. 2024;62(5):367-379. Published online June 17, 2024; DOI: https://doi.org/10.1007/s12275-024-00141-0

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Abstract: 2-piperidone is a crucial industrial raw material of high-value nylon-5 and nylon-6,5. Currently, a major bottleneck in the biosynthesis of 2-piperidone is the identification of highly efficient 2-piperidone synthases. In this study, we aimed to identify specific strains among 51 human gut bacterial strains capable of producing 2-piperidone and to elucidate its synthetic mechanism. Our findings revealed that four gut bacterial strains, namely Collinsella aerofaciens LFYP39, Collinsella intestinalis LFYP54, Clostridium bolteae LFYP116, and Clostridium hathewayi LFYP18, could produce 2-piperidone from 5-aminovaleric acid (5AVA). Additionally, we observed that 2-piperidone could be synthesized from proline through cross-feeding between Clostridium difficile LFYP43 and one of the four 2-piperidone producing strains, respectively. To identify the enzyme responsible for catalyzing the conversion of 5AVA to 2-piperidone, we utilized a gain-of-function library and identified avaC (5-aminovaleric acid cyclase) in C. intestinalis LFYP54. Moreover, homologous genes of avaC were validated in the other three bacterial strains. Notably, avaC were found to be widely distributed among environmental bacteria. Overall, our research delineated the gut bacterial strains and genes involved in 2-piperidone production, holding promise for enhancing the efficiency of industrial biosynthesis of this compound.

Effects of Light and Dark Conditions on the Transcriptome of Aging Cultures of Candidatus Puniceispirillum marinum IMCC1322: Ji Hyen Lee, Hyun-Myung Oh; J. Microbiol. 2024;62(4):297-314. Published online April 25, 2024; DOI: https://doi.org/10.1007/s12275-024-00125-0

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Abstract: To elucidate the function of proteorhodopsin in Candidatus Puniceispirillum marinum strain IMCC1322, a cultivated representative of SAR116, we produced RNA-seq data under laboratory conditions. We examined the transcriptomes of six different cultures, including sets of expression changes under constant dark (DD), constant light (LL), and diel-cycled (LD; 14 h light: 10 h dark) conditions at the exponential and stationary/death phases. Prepared mRNA extracted from the six samples was analyzed on the Solexa Genome Analyzer with 36 cycles. Differentially expressed genes on the IMCC1322 genome were distinguished as four clusters by K-mean clustering and each CDS (n = 2546) was annotated based on the KEGG BRITE hierarchy. Cluster 0 (n = 1573) covered most constitutive genes including proteorhodopsin, retinoids, and glycolysis/TCA cycle. Cluster 1 genes (n = 754) were upregulated in stationary/death phase under constant dark conditions and included genes associated with bacterial defense, membrane transporters, nitrogen metabolism, and senescence signaling. Cluster 2 genes (n = 197) demonstrated upregulation in exponential phase cultures and included genes involved in genes for oxidative phosphorylation, translation factors, and transcription machinery. Cluster 3 (n = 22) contained light-stimulated upregulated genes expressed under stationary/phases. Stringent response genes belonged to cluster 2, but affected genes spanned various cellular processes such as amino acids, nucleotides, translation, transcription, glycolysis, fatty acids, and cell wall components. The coordinated expression of antagonistic stringent genes, including mazG, ppx/gppA, and spoT/relA may provide insight into the controlled cultural response observed between constant light and constant dark conditions in IMCC1322 cultures, regardless of cell numbers and biomass.

Reviews

Balancing Act of the Intestinal Antimicrobial Proteins on Gut Microbiota and Health: Ye Eun Ra, Ye‑Ji Bang; J. Microbiol. 2024;62(3):167-179. Published online April 17, 2024; DOI: https://doi.org/10.1007/s12275-024-00122-3

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Abstract

The human gut houses a diverse and dynamic microbiome critical for digestion, metabolism, and immune development, exerting profound efects on human health. However, these microorganisms pose a potential threat by breaching the gut barrier, entering host tissues, and triggering infections, uncontrolled infammation, and even sepsis. The intestinal epithelial cells form the primary defense, acting as a frontline barrier against microbial invasion. Antimicrobial proteins (AMPs), produced by these cells, serve as innate immune efectors that regulate the gut microbiome by directly killing or inhibiting microbes. Abnormal AMP production, whether insufcient or excessive, can disturb the microbiome equilibrium, contributing to various intestinal diseases. This review delves into the complex interactions between AMPs and the gut microbiota and sheds light on the role of AMPs in governing host-microbiota interactions. We discuss the function and mechanisms of action of AMPs, their regulation by the gut microbiota, microbial evasion strategies, and the consequences of AMP dysregulation in disease. Understanding these complex interactions between AMPs and the gut microbiota is crucial for developing strategies to enhance immune responses and combat infections within the gut microbiota. Ongoing research continues to uncover novel aspects of this intricate relationship, deepening our understanding of the factors shaping gut health. This knowledge has the potential to revolutionize therapeutic interventions, ofering enhanced treatments for a wide range of gut-related diseases.

Citations

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Host-directed therapies modulating innate immunity against infection in hematologic malignancies
Qiong Wang, Kristján Hermannsson, Egill Másson, Peter Bergman, Guðmundur Hrafn Guðmundsson
Blood Reviews.2025; 70: 101255. CrossRef
Comparison of naturalization mouse model setups uncover distinct effects on intestinal mucosa depending on microbial experience
Henriette Arnesen, Signe Birkeland, Harriet Stendahl, Klaus Neuhaus, David Masopust, Preben Boysen, Harald Carlsen
Discovery Immunology.2025;[Epub] CrossRef
Oral administration of LEAP2 enhances immunity against Edwardsiella tarda through regulation of gut bacterial community and metabolite in mudskipper
Ting-Fang Zhu, Hai-Peng Guo, Li Nie, Jiong Chen
Fish & Shellfish Immunology.2025; 158: 110128. CrossRef
Pharmacology of Intestinal Inflammation and Repair
Céline Deraison, Nathalie Vergnolle
Annual Review of Pharmacology and Toxicology .2025; 65(1): 301. CrossRef
Macrophages and Gut Barrier Function: Guardians of Gastrointestinal Health in Post-Inflammatory and Post-Infection Responses
Edward Xiangtai Meng, George Nicholas Verne, Qiqi Zhou
International Journal of Molecular Sciences.2024; 25(17): 9422. CrossRef
Progress in the Identification and Design of Novel Antimicrobial Peptides Against Pathogenic Microorganisms
Shengwei Sun
Probiotics and Antimicrobial Proteins.2024;[Epub] CrossRef
Host-Associated Microbiome
Woo Jun Sul
Journal of Microbiology.2024; 62(3): 135. CrossRef
Gut Microbiota as Emerging Players in the Development of Alcohol-Related Liver Disease
Wei Li, Wenkang Gao, Shengqi Yan, Ling Yang, Qingjing Zhu, Huikuan Chu
Biomedicines.2024; 13(1): 74. CrossRef

Skin Deep: The Potential of Microbiome Cosmetics: Ju Hee Han, Hei Sung Kim; J. Microbiol. 2024;62(3):181-199. Published online April 16, 2024; DOI: https://doi.org/10.1007/s12275-024-00128-x

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Abstract

The interplay between the skin microbiome and its host is a complex facet of dermatological health and has become a critical focus in the development of microbiome cosmetics. The skin microbiome, comprising various microorganisms, is essential from birth, develops over the lifespan, and performs vital roles in protecting our body against pathogens, training the immune system, and facilitating the breakdown of organic matter. Dysbiosis, an imbalance of these microorganisms, has been implicated in a number of skin conditions such as acne, atopic dermatitis, and skin cancer. Recent scientific findings have spurred cosmetic companies to develop products that preserve and enhance the skin's microbial diversity balance. These products may incorporate elements like prebiotics, probiotics, and postbiotics, which are beneficial for the skin microbiome. Beyond topical products, there's increasing interest in ingestible beauty supplements (i.e. oral probiotics), highlighting the connection between the gut and skin. This review examines the influence of the microbiome on skin health and the emerging trends of microbiome skincare products.

Citations

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Influence of Cosmetic Skincare Products with pH < 5 on the Skin Microbiome: A Randomized Clinical Evaluation
Ciska Janssens-Böcker, Claudia Doberenz, Marta Monteiro, Marta de Oliveira Ferreira
Dermatology and Therapy.2025; 15(1): 141. CrossRef
Host-Associated Microbiome
Woo Jun Sul
Journal of Microbiology.2024; 62(3): 135. CrossRef
Skin Microbiome and Acne: Microbial Imbalances and Impact – Interview with Three Key Opinion Leaders
Brigitte Scott
EMJ Dermatology.2024; : 83. CrossRef
Cosmeceuticals: A Review of Clinical Studies Claiming to Contain Specific, Well-Characterized Strains of Probiotics or Postbiotics
Ioannis M. Theodorou, Dorothea Kapoukranidou, Markos Theodorou, Joulia K. Tsetis, Alexandra Eleftheria Menni, Georgios Tzikos, Stella Bareka, Anne Shrewsbury, George Stavrou, Katerina Kotzampassi
Nutrients.2024; 16(15): 2526. CrossRef
Effect of Staphylococcus aureus colonization and immune defects on the pathogenesis of atopic dermatitis
Evrim Özdemіr, Lütfiye Öksüz
Archives of Microbiology.2024;[Epub] CrossRef
A New Generation of Postbiotics for Skin and Scalp: In Situ Production of Lipid Metabolites by Malassezia
Martin Patrick Pagac, Mathias Gempeler, Remo Campiche
Microorganisms.2024; 12(8): 1711. CrossRef
Antimelanogenic and Antioxidant Effects of Postbioics of Lactobacillus Strains in α-MSH-Induced B16F10 Melanoma Cells via CREB/MITF and MAPKs Signaling Pathway
Hye-Won Lee, Yu-Rim Lee, Kyung-Min Park, Na-Kyoung Lee, Hyun-Dong Paik
Journal of Microbiology and Biotechnology.2024; 34(11): 2279. CrossRef
Evaluation of the Effects of Age, Sex, and Dexpanthenol-Containing Skin Care on the Facial and Body Skin Microbiome
Zainab Qaizar, Raffaella de Salvo, Gregor Bieri, Katrin Unbereit, Shannon Montgomery, Erwan Peltier
Cosmetics.2024; 11(6): 213. CrossRef

MAPK Cascades in Plant Microbiota Structure and Functioning: Thijs Van Gerrewey, Hoo Sun Chung; J. Microbiol. 2024;62(3):231-248. Published online April 8, 2024; DOI: https://doi.org/10.1007/s12275-024-00114-3

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Abstract

Mitogen-activated protein kinase (MAPK) cascades are highly conserved signaling modules that coordinate diverse biological processes such as plant innate immunity and development. Recently, MAPK cascades have emerged as pivotal regulators of the plant holobiont, infuencing the assembly of normal plant microbiota, essential for maintaining optimal plant growth and health. In this review, we provide an overview of current knowledge on MAPK cascades, from upstream perception of microbial stimuli to downstream host responses. Synthesizing recent fndings, we explore the intricate connections between MAPK signaling and the assembly and functioning of plant microbiota. Additionally, the role of MAPK activation in orchestrating dynamic changes in root exudation to shape microbiota composition is discussed. Finally, our review concludes by emphasizing the necessity for more sophisticated techniques to accurately decipher the role of MAPK signaling in establishing the plant holobiont relationship.

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Lipid transfer protein VAS inhibits the hypersensitive response via reactive oxygen species signaling in Nicotiana benthamiana
Rina Koyama, Akira Suzuki, Kouhei Ohnishi, Yasufumi Hikichi, Akinori Kiba, Stefanie Ranf
Journal of Experimental Botany.2025; 76(4): 1285. CrossRef
Short-Term Fertilization with the Nitrogen-Fixing Bacterium (NFB) Kosakonia radicincitans GXGL-4A Agent Can Modify the Transcriptome Expression Profiling of Cucumber (Cucumis sativus L.) Root
Baoyun Feng, Erxing Wang, Yating Zhang, Lurong Xu, Yanwen Xue, Yunpeng Chen
Microorganisms.2025; 13(3): 506. CrossRef
Pharmacological effects and the related mechanism of scutellarin on inflammation-related diseases: a review
Yang Zhou, Chenlin Gu, Yan Zhu, Yuting Zhu, Yutong Chen, Li Shi, Yang Yang, Xin Lu, Hanqing Pang
Frontiers in Pharmacology.2024;[Epub] CrossRef
Rice E3 ubiquitin ligases: From key modulators of host immunity to potential breeding applications
Yuqing Yan, Hui Wang, Yan Bi, Fengming Song
Plant Communications.2024; 5(12): 101128. CrossRef
Host-Associated Microbiome
Woo Jun Sul
Journal of Microbiology.2024; 62(3): 135. CrossRef
The microbiome orchestrates contaminant low-dose phytostimulation
Evgenios Agathokleous, Edward J. Calabrese, Stavros D. Veresoglou
Trends in Plant Science.2024;[Epub] CrossRef

Journal Article

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.

Review

Genomic Evolution and Recombination Dynamics of Human Adenovirus D Species: Insights from Comprehensive Bioinformatic Analysis: Anyeseu Park, Chanhee Lee, Jeong Yoon Lee; J. Microbiol. 2024;62(5):393-407. Published online March 7, 2024; DOI: https://doi.org/10.1007/s12275-024-00112-5

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Abstract

Human adenoviruses (HAdVs) can infect various epithelial mucosal cells, ultimately causing different symptoms in infected organ systems. With more than 110 types classified into seven species (A-G), HAdV-D species possess the highest number of viruses and are the fastest proliferating. The emergence of new adenovirus types and increased diversity are driven by homologous recombination (HR) between viral genes, primarily in structural elements such as the penton base, hexon and fiber proteins, and the E1 and E3 regions. A comprehensive analysis of the HAdV genome provides valuable insights into the evolution of human adenoviruses and identifies genes that display high variation across the entire genome to determine recombination patterns. Hypervariable regions within genetic sequences correlate with functional characteristics, thus allowing for adaptation to new environments and hosts. Proteotyping of newly emerging and already established adenoviruses allows for prediction of the characteristics of novel viruses. HAdV-D species evolved in a direction that increased diversity through gene recombination. Bioinformatics analysis across the genome, particularly in highly variable regions, allows for the verification or re-evaluation of recombination patterns in both newly introduced and pre-existing viruses, ultimately aiding in tracing various biological traits such as virus tropism and pathogenesis. Our research does not only assist in predicting the emergence of new adenoviruses but also offers critical guidance in regard to identifying potential regulatory factors of homologous recombination hotspots.

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In Silico Intensive Analysis for the E4 Gene Evolution of Human Adenovirus Species D
Chanhee Lee, Anyeseu Park, Jeong Yoon Lee
Journal of Microbiology.2024; 62(5): 409. CrossRef

Journal Articles

Effects of Feather Hydrolysates Generated by Probiotic Bacillus licheniformis WHU on Gut Microbiota of Broiler and Common carp: Kamin Ke, Yingjie Sun, Tingting He, Wenbo Liu, Yijiao Wen, Siyuan Liu, Qin Wang, Xiaowei Gao; J. Microbiol. 2024;62(6):473-487. Published online February 29, 2024; DOI: https://doi.org/10.1007/s12275-024-00118-z

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Abstract: Due to the ever-increasing demand for meat, it has become necessary to identify cheap and sustainable sources of protein for animal feed. Feathers are the major byproduct of poultry industry, which are rich in hard-to-degrade keratin protein. Previously we found that intact feathers can be digested into free amino acids, short peptides, and nano-/micro-keratin particles by the strain Bacillus licheniformis WHU in water, and the resulting feather hydrolysates exhibit prebiotic effects on mice. To explore the potential utilization of feather hydrolysate in the feed industry, we investigated its effects on the gut microbiota of broilers and fish. Our results suggest that feather hydrolysates significantly decrease and increase the diversity of gut microbial communities in broilers and fish, respectively. The composition of the gut microbiota was markedly altered in both of the animals. The abundance of bacteria with potentially pathogenic phenotypes in the gut microbial community of the fish significantly decreased. Staphylococcus spp., Pseudomonas spp., Neisseria spp., Achromobacter spp. were significantly inhibited by the feather hydrolysates. In addition, feather hydrolysates significantly improved proteolytic activity in the guts of broilers and fish. In fish, the expression levels of ZO-1 and TGF-α significantly improved after administration of feather hydrolysates. The results presented here suggest that feather hydrolysates generated by B. licheniformis WHU could be an alternative protein source in aquaculture and could exert beneficial effects on fish.

Mycobacterium tuberculosis PE_PGRS45 (Rv2615c) Promotes Recombinant Mycobacteria Intracellular Survival via Regulation of Innate Immunity, and Inhibition of Cell Apoptosis: Tao Xu , Chutong Wang , Minying Li , Jing Wei , Zixuan He , Zhongqing Qian , Xiaojing Wang , Hongtao Wang; J. Microbiol. 2024;62(1):49-62. Published online February 9, 2024; DOI: https://doi.org/10.1007/s12275-023-00101-0

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Abstract

Tuberculosis (TB), a bacterial infectious disease caused by Mycobacterium tuberculosis (M. tuberculosis), is a significant global public health problem. Mycobacterium tuberculosis expresses a unique family of PE_PGRS proteins that have been implicated in pathogenesis. Despite numerous studies, the functions of most PE_PGRS proteins in the pathogenesis of mycobacterium infections remain unclear. PE_PGRS45 (Rv2615c) is only found in pathogenic mycobacteria. In this study, we successfully constructed a recombinant Mycobacterium smegmatis (M. smegmatis) strain which heterologously expresses the PE_PGRS45 protein. We found that overexpression of this cell wall-associated protein enhanced bacterial viability under stress in vitro and cell survival in macrophages. MS_PE_PGRS45 decreased the secretion of pro-inflammatory cytokines such as IL-1β, IL-6, IL-12p40, and TNF-α. We also found that MS_PE_PGRS45 increased the expression of the anti-inflammatory cytokine IL-10 and altered macrophage-mediated immune responses. Furthermore, PE_PGRS45 enhanced the survival rate of M. smegmatis in macrophages by inhibiting cell apoptosis. Collectively, our findings show that PE_PGRS45 is a virulent factor actively involved in the interaction with the host macrophage.

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Evolution of the PE_PGRS Proteins of Mycobacteria: Are All Equal or Are Some More Equal than Others?
Bei Chen, Belmin Bajramović, Bastienne Vriesendorp, Herman Pieter Spaink
Biology.2025; 14(3): 247. CrossRef
Recent advances in research on Mycobacterium tuberculosis virulence factors and their role in pathogenesis
Ming-Rui Sun, Jia-Yin Xing, Xiao-Tian Li, Ren Fang, Yang Zhang, Zhao-Li Li, Ning-Ning Song
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Mycorrhizal Fungal Diversity Associated with Six Understudied Ectomycorrhizal Trees in the Republic of Korea: Ki Hyeong Park , Seung-Yoon Oh , Yoonhee Cho , Chang Wan Seo , Ji Seon Kim , Shinnam Yoo , Jisun Lim , Chang Sun Kim , Young Woon Lim; J. Microbiol. 2023;61(8):729-739. Published online September 4, 2023; DOI: https://doi.org/10.1007/s12275-023-00073-1

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Abstract: Mycorrhizal fungi are key components of forest ecosystems and play essential roles in host health. The host specificity of mycorrhizal fungi is variable and the mycorrhizal fungi composition for the dominant tree species is largely known but remains unknown for the less common tree species. In this study, we collected soil samples from the roots of six understudied ectomycorrhizal tree species from a preserved natural park in the Republic of Korea over four seasons to investigate the host specificity of mycorrhizal fungi in multiple tree species, considering the abiotic factors. We evaluated the mycorrhizal fungal composition in each tree species using a metabarcoding approach. Our results revealed that each host tree species harbored unique mycorrhizal communities, despite close localization. Most mycorrhizal taxa belonged to ectomycorrhizal fungi, but a small proportion of ericoid mycorrhizal fungi and arbuscular mycorrhizal fungi were also detected. While common mycorrhizal fungi were shared between the plant species at the genus or higher taxonomic level, we found high host specificity at the species/OTU (operational taxonomic unit) level. Moreover, the effects of the seasons and soil properties on the mycorrhizal communities differed by tree species. Our results indicate that mycorrhizal fungi feature host-specificity at lower taxonomic levels.

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