Journal of Fungi

11 pages, 466 KiB

Open AccessArticle

Epidemiology and Inpatient Outcomes of Invasive Aspergillosis in Patients with Liver Failure and Cirrhosis

by Aditya Sharma, Bashar Mohamad and Ayman O. Soubani

J. Fungi 2025, 11(5), 334; https://doi.org/10.3390/jof11050334 - 23 Apr 2025

Objective: The aim of this study was to estimate the incidence and inpatient outcomes of liver failure and cirrhosis (LFC) admissions with invasive aspergillosis (IA) in the United States. Methods: This retrospective cohort study utilized the 2016–2020 National Inpatient Sample (NIS) database to [...] Read more.

Objective: The aim of this study was to estimate the incidence and inpatient outcomes of liver failure and cirrhosis (LFC) admissions with invasive aspergillosis (IA) in the United States. Methods: This retrospective cohort study utilized the 2016–2020 National Inpatient Sample (NIS) database to analyze outcomes of IA in LFC admissions. Baseline variables, including demographics, comorbidities, and complications, were identified using International Classification of Diseases, Tenth Revision, Clinical Modification (ICD-10-CM) codes, and liver transplant admissions were excluded. Outcomes were compared between LFC admissions with and without IA. Results: During the study period, 9515 (0.36%) LFC admissions were associated with IA. This cohort experienced significantly higher rates of complications, including acute kidney injury (AKI) (73.36% vs. 42.96%; p < 0.001) and acute respiratory failure (ARF) (65.74% vs. 24.85%; p < 0.001). IA admissions required invasive mechanical ventilation (IMV) more frequently (58.17% vs. 18.78%; p < 0.001). All-cause inpatient mortality was significantly higher in the aspergillosis group (43.40% vs. 15.75%; p < 0.001). IA admissions had longer lengths of stay (LOS), with 38.89% exceeding 21 days compared to 6.20% (p < 0.001), and a mean LOS more than three times longer (22.9 vs. 7.5 days; p < 0.001). The IA group incurred over four times higher hospital charges (USD 459,414.9 vs. USD 104,389.4; p < 0.001) and hospitalization costs (USD 108,030.6 vs. USD 24,272.1; p < 0.001) compared to the LFC without aspergillosis group. Interpretation: LFC admissions with IA experienced poorer outcomes, longer hospital stays, and significantly higher healthcare costs, underscoring the need for targeted interventions in this high-risk, nonclassical population. Full article

(This article belongs to the Special Issue Fungal Infections in Intensive Care Medicine)

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29 pages, 2306 KiB

Open AccessReview

Gut Mycobiome: Latest Findings and Current Knowledge Regarding Its Significance in Human Health and Disease

by Bogdan Severus Gaspar, Oana Alexandra Roşu, Robert-Mihai Enache, Monica Manciulea (Profir), Luciana Alexandra Pavelescu and Sanda Maria Creţoiu

J. Fungi 2025, 11(5), 333; https://doi.org/10.3390/jof11050333 - 22 Apr 2025

Abstract

The gut mycobiome, the fungal component of the gut microbiota, plays a crucial role in health and disease. Although fungi represent a small fraction of the gut ecosystem, they influence immune responses, gut homeostasis, and disease progression. The mycobiome’s composition varies with age, [...] Read more.

The gut mycobiome, the fungal component of the gut microbiota, plays a crucial role in health and disease. Although fungi represent a small fraction of the gut ecosystem, they influence immune responses, gut homeostasis, and disease progression. The mycobiome’s composition varies with age, diet, and host factors, and its imbalance has been linked to conditions such as inflammatory bowel disease (IBD) and metabolic disorders. Advances in sequencing have expanded our understanding of gut fungi, but challenges remain due to methodological limitations and high variability between individuals. Emerging therapeutic strategies, including antifungals, probiotics, fecal microbiota transplantation, and dietary interventions, show promise but require further study. This review highlights recent discoveries on the gut mycobiome, its interactions with bacteria, its role in disease, and potential clinical applications. A deeper understanding of fungal contributions to gut health will help develop targeted microbiome-based therapies. Full article

(This article belongs to the Special Issue Gut Mycobiome, 2nd Edition)

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15 pages, 6223 KiB

Open AccessArticle

Antifungal Volatile Organic Compounds from Talaromyces purpureogenus CEF642^N: Insights from One Strain Many Compounds (OSMAC) Strategy for Controlling Verticillium dahliae in Cotton

by Peng Li, Yalin Zhang, Hongjie Feng, Jinglong Zhou, Lihong Zhao, Heqin Zhu, Feng Wei and Zili Feng

J. Fungi 2025, 11(5), 332; https://doi.org/10.3390/jof11050332 - 22 Apr 2025

Abstract

Verticillium wilt is a devastating soil-borne disease that significantly impacts cotton production, necessitating the development the effective biofumigants for its control. In this study, the inhibitory effect of total volatile organic compounds (VOCs) produced by Talaromyces purpureogenus CEF642^N against Verticillium dahliae were [...] Read more.

Verticillium wilt is a devastating soil-borne disease that significantly impacts cotton production, necessitating the development the effective biofumigants for its control. In this study, the inhibitory effect of total volatile organic compounds (VOCs) produced by Talaromyces purpureogenus CEF642^N against Verticillium dahliae were evaluated using the one strain many compounds (OSMAC) strategy and analyzed through volatile metabolome. CEF642^N was found to produce two primary VOCs, 3-octanol and 2-octenal, (E)-, both of which demonstrated significant antifungal activity. Transcriptome analysis of mycelium grown on various solid media revealed notable differences in the expression of genes associated with arachidonic acid metabolism, lipoxygenase (LOX), and lytic enzymes. These findings provide a foundation for future research aimed at identifying key genes involved in the eight-carbon volatile biosynthetic pathway. Full article

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19 pages, 14137 KiB

Open AccessArticle

Morphology and Phylogeny Reveal New Species and Records of Diplodia, Dothiorella, and Phaeobotryon Associated with Tree Cankers in Xizang, China

by Jia Zhou, Aining Li and Ning Jiang

J. Fungi 2025, 11(5), 331; https://doi.org/10.3390/jof11050331 - 22 Apr 2025

Abstract

The fungal family Botryosphaeriaceae, which includes genera such as Diplodia, Dothiorella, and Phaeobotryon, comprises species commonly associated with woody plants such as endophytes, pathogens, and saprophytes. The Xizang Autonomous Region of China, known for its rich forest resources, harbors significant [...] Read more.

The fungal family Botryosphaeriaceae, which includes genera such as Diplodia, Dothiorella, and Phaeobotryon, comprises species commonly associated with woody plants such as endophytes, pathogens, and saprophytes. The Xizang Autonomous Region of China, known for its rich forest resources, harbors significant fungal diversity. However, limited research has been conducted on plant-disease-associated fungi in this region. In this study, we employed morphological characteristics and molecular phylogenetic analyses of the internal transcribed spacer region of rDNA (ITS), the ribosomal large subunit (LSU), the translation elongation factor 1-alpha (tef1) gene, and the partial beta-tubulin (tub2) gene to identify fungal species. As a result, two new species, Diplodia salicicola sp. nov. and Phaeobotryon xizangense sp. nov., are proposed and described herein. Additionally, Di. corticola, Di. mutila, Do. acericola, Do. magnoliae, Do. vidmadera, Do. yunnana comb. nov., and Do. zanthoxyli are reported for the first time in Xizang. Our findings contribute to advancing the knowledge of fungal biodiversity in Xizang’s high-altitude ecosystems. Full article

(This article belongs to the Special Issue Advanced Research of Ascomycota)

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14 pages, 8617 KiB

Open AccessArticle

Zinc Metalloprotease SlMEP1: An Essential Factor Required for Fungal Virulence in Stemphylium lycopersici

by Dezhen Zhang, Wenjuan Chi, Tingting Li, Cuicui Wang, Jing Zhang, Haoqin Pan, Ning Qiao, Jintang Li and Xiaoan Sun

J. Fungi 2025, 11(5), 330; https://doi.org/10.3390/jof11050330 - 22 Apr 2025

Abstract

Stemphylium lycopersici is the causal pathogen of the devastating tomato gray leaf spot with a wide range of alternative plant hosts. To mitigate its potential endemic in facility-cultivated tomatoes, novel disease control strategies should be attempted to minimize the use of chemical fungicides. [...] Read more.

Stemphylium lycopersici is the causal pathogen of the devastating tomato gray leaf spot with a wide range of alternative plant hosts. To mitigate its potential endemic in facility-cultivated tomatoes, novel disease control strategies should be attempted to minimize the use of chemical fungicides. In this study, we identified a metalloprotease from S. lycopersici genome and designated it as SlMEP1, as it appears to be a typical zinc metalloproteinase containing a WLM (WSS1-like metalloprotease) domain and a characteristic HEXXH motif, which we determined by analyzing its transcriptional profile and enzymatic functions. The transcription level of SlMEP1 increased greatly during the fungal invasion of tomato leaves. The deletion of the SlMEP1 gene from S. lycopersici hindered its mycelial growth and reduced its pathogenicity. An assessment of the functional dissection indicated that SlMEP1 induced cell collapse and inhibited the expression of the host chitinases, which consequently made tomato cells more susceptible to S. lycopersici and other pathogenic fungi. Full article

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15 pages, 1433 KiB

Open AccessArticle

A Silent Threat in Post-Tuberculosis Patients: Chronic Pulmonary Aspergillosis Survey in Multiple Regions of Indonesia (I-CHROME Study)

by Anna Rozaliyani, Findra Setianingrum, Fathiyah Isbaniah, Heidy Agustin, Raden Rara Diah Handayani, Rosamarlina Syahrir, Siti Pratiekauri, Robiatul Adawiyah, Hesti Setiastuti, Mohammad Nizam Erhamza, Retno Ariza S. Soemarwoto, Irvan Medison, Deddy Herman, Avissena Dutha Pratama, Jatu Apridasari, Jani Jane, Soedarsono Soedarsono, Tutik Kusmiati, Mufidatun Hasanah, Diah Adhyaksanti, Winda Sofvina, Ammar A. Hasyim, Chris Kosmidis and David W. Denning Show full author list Hide full author list

J. Fungi 2025, 11(5), 329; https://doi.org/10.3390/jof11050329 - 22 Apr 2025

Abstract

Background: A significant complication among post-tuberculosis patients is chronic pulmonary aspergillosis (CPA), with prevalence and outcomes varying by region. This study aimed to explore the epidemiology, clinical characteristics, and microbiological profiles of 219 post-tuberculosis patients with persistent respiratory symptoms and lung cavities in [...] Read more.

Background: A significant complication among post-tuberculosis patients is chronic pulmonary aspergillosis (CPA), with prevalence and outcomes varying by region. This study aimed to explore the epidemiology, clinical characteristics, and microbiological profiles of 219 post-tuberculosis patients with persistent respiratory symptoms and lung cavities in Indonesia. Methods: The patients were divided into CPA (n = 144) and non-CPA (n = 75) groups. This cross-sectional study diagnosed CPA in post-tuberculosis patients using ERS/ESCMID criteria, integrating clinical, radiological, and fungal assessments. Serological tests for Aspergillus-specific IgG were conducted using immunochromatographic (ICT) and ELISA on serum samples. Sputum specimens were used in parallel for fungal culture, and radiological evaluations (e.g., chest X-rays or CT scans) were performed to identify typical CPA features such as cavitation and fibrosis. Results: Persistent cough was significantly more common in CPA patients (83.3%, p = 0.015), highlighting its role as a clinical indicator for CPA. Radiological infiltrates were found in 165 patients (75.3%); critical diagnostic markers of CPA were cavitation and pericavitary fibrosis. Aspergillus-specific IgG testing demonstrated high diagnostic utility, with positivity rates of 69.4% for ICT and 63.2% for ELISA among CPA patients. Among those with infiltrates, a positive Aspergillus culture was not more common (p > 0.05), whereas Aspergillus IgG was more often raised (p = 0.037), as was a positive ICT (p = 0.021). Regional analysis revealed a higher CPA burden in Region 1 (75%) compared to Region 2 (56%, p = 0.003), with Aspergillus fumigatus and Aspergillus niger predominating in Region 1. Conclusions: These findings highlight the importance of comprehensive approaches and region-specific CPA management strategies in Indonesia. Full article

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37 pages, 3278 KiB

Open AccessReview

Alleviating Plant Density and Salinity Stress in Moringa oleifera Using Arbuscular Mycorrhizal Fungi: A Review

by Tshepiso Khoza, Absalom Masenya, Nokuthula Khanyile and Standford Thosago

J. Fungi 2025, 11(4), 328; https://doi.org/10.3390/jof11040328 - 21 Apr 2025

Abstract

Moringa oleifera (LAM) is a multipurpose tree species with extensive pharmacological and ethnomedicinal properties. Production of important medicinal plants is facing decline under changing climatic conditions, which brings along exacerbated abiotic stresses like salinity and intraspecific competition, particularly high planting densities. Increasing plant [...] Read more.

Moringa oleifera (LAM) is a multipurpose tree species with extensive pharmacological and ethnomedicinal properties. Production of important medicinal plants is facing decline under changing climatic conditions, which brings along exacerbated abiotic stresses like salinity and intraspecific competition, particularly high planting densities. Increasing plant density is seen as a strategy to increase production; however, the intraspecific competition and a lack of arable land limit productivity. Salinity has been estimated to harm approximately six percent of the Earth’s landmass. This leads to a loss of over 20% of agricultural output annually. These stressors can significantly curtail moringa’s growth and yield potential. Literature designates that Arbuscular Mycorrhizal Fungi (AMF), ubiquitous soil microorganisms forming symbiotic associations with plant roots, offer a promising avenue for mitigating these stresses. This narrative review aims to investigate the utilization of AMF to alleviate the detrimental effects of salinity and high planting density on Moringa oleifera. The different adaptive strategies M. oleifera undergoes to mitigate both stressors are explored. The review found that AMF inoculation enhances plant tolerance to these stressors by improving nutrient acquisition, water relations, and activating stress response mechanisms. By facilitating improved nutrient and water absorption, AMF enhance root architecture, modulate ROS scavenging mechanisms, and promote optimal biomass allocation, ensuring better survival in high-density plantings. Furthermore, AMF-mediated stress alleviation is linked to enhanced physiological efficiency, including increased chlorophyll content, root–shoot biomass balance, and ion homeostasis. This review is important because it could provide insights into a sustainable, natural solution for improving the resilience of Moringa oleifera under adverse environmental conditions, with potential applications in global agriculture and food security. Future research should prioritize identifying and characterizing moringa-specific AMF species and evaluate the long-term efficacy, feasibility, and economic viability of AMF application in real-world moringa cultivation systems to fully harness the potential of AMF in moringa cultivation. Full article

(This article belongs to the Special Issue Arbuscular Mycorrhiza Under Stress)

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11 pages, 619 KiB

Open AccessSystematic Review

Pneumocystis Infection in Pregnant Women: A Scoping Review

by Irene Calderón-Baturone, Rocío Salsoso, Elena Charpentier, Yaxsier de Armas, Pilar Guadix, Rubén Morilla, Enrique J. Calderón and Vicente Friaza

J. Fungi 2025, 11(4), 327; https://doi.org/10.3390/jof11040327 - 20 Apr 2025

Abstract

Pneumocystis jirovecii is an opportunistic fungus that causes severe pneumonia in immunosuppressed individuals. While Pneumocystis colonization, a subclinical form of infection, has been studied in different populations, its implications during pregnancy remain poorly understood. Given the immune modulation of pregnancy, maternal colonization or [...] Read more.

Pneumocystis jirovecii is an opportunistic fungus that causes severe pneumonia in immunosuppressed individuals. While Pneumocystis colonization, a subclinical form of infection, has been studied in different populations, its implications during pregnancy remain poorly understood. Given the immune modulation of pregnancy, maternal colonization or infection may contribute to vertical transmission and neonatal respiratory complications. This scoping review aims to map the existing evidence on Pneumocystis colonization/infection during pregnancy, identifying knowledge gaps, prevalence, risk factors, and potential neonatal outcomes. A systematic literature search was conducted in three databases following PRISMA-ScR guidelines. A total of 26 studies were included, covering Pneumocystis pneumonia cases (n = 19) and Pneumocystis colonization (n = 7). The review found that most Pneumocystis pneumonia cases in pregnant women were associated with HIV before antiretroviral therapy. More recent cases were related to hematologic malignancies. Pneumocystis colonization rates varied widely (5.4–46.5%). Evidence of vertical transmission was observed, but neonatal impact remains underexplored. This review highlights the need for HIV screening in pregnant women and the need to include Pneumocystis in the diagnosis of pregnant women with pneumonia. Increased awareness and research on Pneumocystis in pregnancy are necessary to improve maternal and neonatal outcomes. Future studies should focus on vertical transmission and neonatal respiratory health. Full article

(This article belongs to the Special Issue Fungal Infections: New Challenges and Opportunities, 3rd Edition)

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21 pages, 7800 KiB

Open AccessArticle

Revolutionizing Eco-Friendly Leather Production: A Freeze-Thaw and Liquid Fermentation Approach with Fungal Mycelium

by Linxin Song, Yuxin Liu, Shijun Xiao, Xiaohui Yuan and Xuerong Han

J. Fungi 2025, 11(4), 326; https://doi.org/10.3390/jof11040326 - 19 Apr 2025

Abstract

The environmental impact and resource demands of traditional leather manufacturing have driven the search for sustainable alternatives. Fungal mycelium leather, recognised for its eco-friendly and renewable characteristics, has emerged as a promising option. This study established a cyclic freeze-thaw dehydration protocol for preparing [...] Read more.

The environmental impact and resource demands of traditional leather manufacturing have driven the search for sustainable alternatives. Fungal mycelium leather, recognised for its eco-friendly and renewable characteristics, has emerged as a promising option. This study established a cyclic freeze-thaw dehydration protocol for preparing mycelial leather using Ganoderma mycelium produced through liquid fermentation. By precisely controlling the fermentation parameters (pH 5.5, 150 rpm agitation, 28 °C), the liquid fermentation process ensures uniform mycelial growth, which is critical for subsequent structural enhancement during freeze-thaw cycles. After three freeze-thaw cycles were performed at −15 °C, uniformly distributed ice crystals facilitated effective water removal, achieving a minimum moisture content of 47.6%. The optimized freeze-thaw process produced membranes with a tensile strength of 6.22 MPa and elongation at break of 18.92%, demonstrating high mechanical performance. The freeze-thaw process was demonstrated to enhance structural integrity and mechanical properties while offering reduced energy consumption compared to conventional dehydration methods. This research provides a theoretical foundation and technical guidance for optimising fungal mycelium leather production and contributes to the development of sustainable bio-based materials for industrial applications. Full article

(This article belongs to the Special Issue Fungi in Sustainable Applications and the Circular Economy: A Themed Issue Dedicated to Academician Yu Li)

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13 pages, 12905 KiB

Open AccessArticle

Metabolic Influence of S. boulardii and S. cerevisiae in Cross-Kingdom Models of S. mutans and C. albicans

by Ting Li, Xingyi Lu, Yan Wu, Tongtong Wu and Jin Xiao

J. Fungi 2025, 11(4), 325; https://doi.org/10.3390/jof11040325 - 19 Apr 2025

Abstract

Recent studies highlight the potential of Saccharomyces species as probiotics due to their ability to modulate microbial interactions and reduce cariogenic activity, yet the underlying metabolic mechanisms remain unclear. This study investigates the cross-kingdom metabolic effects of Saccharomyces boulardii and Saccharomyces cerevisiae on [...] Read more.

Recent studies highlight the potential of Saccharomyces species as probiotics due to their ability to modulate microbial interactions and reduce cariogenic activity, yet the underlying metabolic mechanisms remain unclear. This study investigates the cross-kingdom metabolic effects of Saccharomyces boulardii and Saccharomyces cerevisiae on the metabolic processes of Streptococcus mutans and Candida albicans using a metabolomics-based approach. Untargeted LC-MS/MS analysis was conducted to assess metabolites in a planktonic model, followed by metabolomic profiling and pathway analysis to identify key metabolic alterations. The results revealed that S. boulardii and S. cerevisiae demonstrated metabolic regulatory effects on S. mutans and C. albicans. Specifically, S. boulardii down-regulated 262 metabolites and up-regulated 168, while S. cerevisiae down-regulated 265 metabolites and up-regulated 168. Both yeast species down-regulated carbohydrate and amino acid metabolism in S. mutans and C. albicans, resulting in reduced biomolecule synthesis and a less acidic environment. S. boulardii and S. cerevisiae also up-regulated certain metabolic processes, including purine metabolism, suggesting a compensatory mechanism for nucleotide synthesis. Notably, dual regulatory effects were observed, where specific metabolites were simultaneously up-regulated and down-regulated, indicating complex metabolic crosstalk. These findings suggest that both S. boulardii and S. cerevisiae modulate microbial metabolism through a shared mechanism, offering potentials for dental caries prevention. Full article

(This article belongs to the Special Issue Alternative Therapeutic Approaches of Candida Infections, 4th Edition)

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15 pages, 4624 KiB

Open AccessArticle

Antifungal Efficacy of Luliconazole-Loaded Nanostructured Lipid-Carrier Gel in an Animal Model of Dermatophytosis

by Robab Ebrahimi Barogh, Seyyed Mobin Rahimnia, Mohsen Nosratabadi, Abolfazl Maleki, Fatemeh Khosravi Ebrahimi, Zahra Yahyazade, Iman Haghani, Pedram Ebrahimnejad, Majid Saeedi, Darius Armstrong-James, Mahdi Abastabar and Hamid Badali

J. Fungi 2025, 11(4), 324; https://doi.org/10.3390/jof11040324 - 19 Apr 2025

Abstract

Background: Trichophyton indotineae terbinafine-resistant infections are emerging in healthy individuals. Luliconazole, an imidazole antifungal that is effective against skin infections, faces challenges due to low water solubility and poor skin penetration. This study aimed to formulate a luliconazole-loaded nanostructured lipid-carrier (NLC) gel [...] Read more.

Background: Trichophyton indotineae terbinafine-resistant infections are emerging in healthy individuals. Luliconazole, an imidazole antifungal that is effective against skin infections, faces challenges due to low water solubility and poor skin penetration. This study aimed to formulate a luliconazole-loaded nanostructured lipid-carrier (NLC) gel in a Carbopol-based system to enhance drug absorption and efficacy in a guinea pig model of dermatophytosis. Methods: Luliconazole-loaded nanostructured lipid carriers (NLCs) were prepared using a solvent evaporation method and gel formulation. Skin absorption and retention were assessed via Franz diffusion cells. The antifungal efficacy was tested against T. indotineae in thirty guinea pigs with induced tinea corporis, divided into five treatment groups. Mycological, clinical, and histopathological evaluations were conducted, along with skin irritation studies for safety. Results: LCZ-NLC demonstrated significantly better skin penetration than simple luliconazole gel, with cumulative drug penetration of 71.8 ± 3.7 μg/cm² versus 50.9 ± 4.2 μg/cm² after 24 h. Both formulations achieved complete infection resolution after 21 and 28 days, with reduced inflammation and no local irritations. On day 21, the LCZ-NLC 1% gel significantly reduced lesion scores and mycological evidence of infection compared to the terbinafine-treated groups, untreated controls, and NLC-gel-treated group (p < 0.05). Histopathological analysis indicated a reduction in both epidermal thickening and fungal burden in the models that received treatment with the LCZ-NLC 1% gel. Conclusions: Luliconazole-loaded lipid carriers enhance drug absorption and efficacy, suggesting shorter treatment durations and improved patient outcomes for resistant fungal infections. However, further studies are warranted to correlate these findings with clinical outcomes. Full article

(This article belongs to the Special Issue Design and Mechanism of Action of Genomic-Based Antifungals)

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31 pages, 5940 KiB

Open AccessArticle

Genomic and Multi-Omics Analysis of Phlebopus portentosus: Effects of Cultivation on Secondary Metabolites

by Zujiang Kang, Xiaolong Yuan, Chuanguang Zhang, Yi Wang, Lu Li and Yuan Zheng

J. Fungi 2025, 11(4), 323; https://doi.org/10.3390/jof11040323 - 18 Apr 2025

Abstract

Phlebopus portentosus is an edible and medicinal ectomycorrhizal mushroom with delicious and high nutritional value. However, the mechanism of secondary metabolite biosynthesis in P. portentosus is still unclear. In this study, the genomics, metabolomics, and transcriptomics were integrated to reveal the biosynthesis mechanism [...] Read more.

Phlebopus portentosus is an edible and medicinal ectomycorrhizal mushroom with delicious and high nutritional value. However, the mechanism of secondary metabolite biosynthesis in P. portentosus is still unclear. In this study, the genomics, metabolomics, and transcriptomics were integrated to reveal the biosynthesis mechanism of secondary metabolites in P. portentosus under different cultivation conditions. The 31.4 Mb genome of P. portentosus YAF023 with 15 scaffolds was assembled by Illumina and Nanopore sequencing and annotated, and 206 cytochrome P450s, 201 carbohydrate-active enzymes, 186 transcription factors, 18 terpene synthases (TPSs), and 5 polyketide synthases (PKSs) were identified. Multi-omics analysis showed that PpPKS1 is probably involved in the biosynthesis of Ethyl orsellinate; PpPKS2 and PpPKS5 are probably involved in the synthesis of 6-Methylsalicylic acid and Cytochalasin Z5, respectively; PpTRI5 was involved in the tetracyclic sesquiterpene β-type trichodiene compounds; and PpSTCs was involved in the synthesis of β-copaene analogs or derivatives. Co-expression network analysis and binding site prediction of the promoter regions suggested that PpHOX4 and PpHSF1 regulated the gene expression of PpPKS1, and Ppzf-C2H2 32 and PpHSF5 regulated the gene expression of PpSTCs 8, and PpSTCs 3, respectively. This study will provide an important foundation for further development and utilization of secondary metabolites of P. portentosus. Full article

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21 pages, 4951 KiB

Open AccessArticle

The Nearly Complete Genome of Grifola frondosa and Light-Induced Genes Screened Based on Transcriptomics Promote the Production of Triterpenoid Compounds

by Yang Yang and Xuebo Hu

J. Fungi 2025, 11(4), 322; https://doi.org/10.3390/jof11040322 - 18 Apr 2025

Abstract

Grifola frondosa, commonly known as turkey tail, is a valuable fungus with medicinal and culinary uses, rich in bioactive compounds like triterpenoid polysaccharides that contribute to health benefits. Here, we constructed a nearly complete genome of G. frondosa CH1 using Illumina, PacBio [...] Read more.

Grifola frondosa, commonly known as turkey tail, is a valuable fungus with medicinal and culinary uses, rich in bioactive compounds like triterpenoid polysaccharides that contribute to health benefits. Here, we constructed a nearly complete genome of G. frondosa CH1 using Illumina, PacBio HiFi, and Hi-C sequencing technologies, resulting in a 35.74 Mb genome with 12,526 protein-coding genes. The genome spans 12 chromosomes, all with intact telomeric structures and no gaps. The BUSCO completeness scores of 95.1% and 99.1% for the genome and genes, respectively, indicate high assembly quality and high completeness of gene prediction. Phylogenetic analysis showed a close relationship between G. frondosa CH1 and Trametes cinnabarina. Transcriptomic analysis under varying light conditions showed changes in the expression of genes, especially those related to terpenoid synthesis, with several CAZymes and CYP450 genes also exhibiting light-induced variations. Ten triterpenoid secondary metabolite gene clusters were identified, three of which were light-sensitive, indicating that light exposure regulates triterpenoid metabolism. This study provides valuable data supporting the high-quality genome of G. frondosa and offers new insights into the light-induced regulation of its metabolism. Full article

(This article belongs to the Section Fungal Genomics, Genetics and Molecular Biology)

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36 pages, 13548 KiB

Open AccessArticle

Morpho-Molecular Characterization of Hypocrealean Fungi Isolated from Rice in Northern Thailand

by Sahar Absalan, Alireza Armand, Ruvishika S. Jayawardena, Nakarin Suwannarach, Jutamart Monkai, Nootjarin Jungkhun Gomes de Farias, Saisamorn Lumyong and Kevin D. Hyde

J. Fungi 2025, 11(4), 321; https://doi.org/10.3390/jof11040321 - 18 Apr 2025

Abstract

Hypocreales is one of the largest orders within the class Sordariomycetes and is renowned for its diversity of lifestyles, encompassing plant, insect, and human pathogens, as well as endophytes, parasites, and saprobes. In this study, we focused on saprobic hypocrealean fungi isolated from [...] Read more.

Hypocreales is one of the largest orders within the class Sordariomycetes and is renowned for its diversity of lifestyles, encompassing plant, insect, and human pathogens, as well as endophytes, parasites, and saprobes. In this study, we focused on saprobic hypocrealean fungi isolated from rice in northern Thailand. Species identification was conducted using morphological characteristics and multilocus phylogenetic analyses, including the internal transcribed spacer region (ITS), 28S large subunit nuclear ribosomal DNA (LSU), translation elongation factor 1–alpha (tef1-α), RNA polymerase II second-largest subunit (rpb2), and calmodulin (cmdA). This research confirmed the presence of 14 species of hypocrealean taxa, viz. Fusarium (9), Ochronectria (1), Sarocladium (2), Trichothecium (1), and Waltergamsia (1). Among these were two new species (Fusarium chiangraiense and F. oryzigenum), four new host records (Fusarium kotabaruense, Ochronectria thailandica, Sarocladium bactrocephalum, and Waltergamsia fusidioides), and three new geographical records (Fusarium commune, F. guilinense, and F. hainanese). Full article

(This article belongs to the Collection Fungal Biodiversity and Ecology)

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11 pages, 998 KiB

Open AccessArticle

Epidemiology and Trends of Cutaneous Fungal Infections (2019–2022) in Israel: A Single Tertiary-Center Study

by Eran Galili, Auriella Taieb, Avner Shemer, Gil Leor, Anna Lyakhovitsky, Aviv Barzilai and Sharon Baum

J. Fungi 2025, 11(4), 320; https://doi.org/10.3390/jof11040320 - 18 Apr 2025

Abstract

Cutaneous fungal infections predominantly caused by dermatophytes are a global concern. These infections vary widely by region, age, and body site, with recent shifts in the pathogen distribution. This study examines the distribution and trends of superficial fungal infections in a large tertiary [...] Read more.

Cutaneous fungal infections predominantly caused by dermatophytes are a global concern. These infections vary widely by region, age, and body site, with recent shifts in the pathogen distribution. This study examines the distribution and trends of superficial fungal infections in a large tertiary care center in Israel from 2019 to 2022. A retrospective analysis of 2244 patients with suspected fungal infections was performed, utilizing PCR and fungal cultures for diagnosis. Confirmed fungal infections were present in 53.0% of cases. In adults, infections predominantly affected the nails and feet, while in children, the scalp and nails were the most involved sites. Trichophyton rubrum was the most common pathogen overall, but T. tonsurans was the leading cause of scalp, face, and neck infections, as well as tinea corporis in children. T. tonsurans incidence significantly increased in adults and became the most frequent agent of upper-body tinea corporis by 2022. These findings highlight a shift in pathogen distribution, with T. tonsurans emerging as the leading cause of upper-body skin infections, underscoring the need for targeted prevention strategies and further investigation of its transmission routes. Full article

(This article belongs to the Special Issue Advances in Onychomycosis Research)

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20 pages, 5432 KiB

Open AccessArticle

The Effect of the Application of Chemical Fertilizer and Arbuscular MyCorrhizal Fungi on Maize Yield and Soil Microbiota in Saline Agricultural Soil

by Ye Yuan, Zhengjun Feng, Shengxin Yan, Junjie Zhang, Huiping Song, Yan Zou and Dapeng Jin

J. Fungi 2025, 11(4), 319; https://doi.org/10.3390/jof11040319 - 17 Apr 2025

Abstract

The overuse of chemical fertilizers not only leads to resource wastage but also causes problems such as environmental pollution and soil degradation. In particular, crop growth in saline–sodic soils is severely restricted due to high salinity and alkalinity, further exacerbating challenges in agricultural [...] Read more.

The overuse of chemical fertilizers not only leads to resource wastage but also causes problems such as environmental pollution and soil degradation. In particular, crop growth in saline–sodic soils is severely restricted due to high salinity and alkalinity, further exacerbating challenges in agricultural production. The aim of this study was to investigate different fertilization strategies that combine chemical fertilizer reduction with arbuscular mycorrhizal fungi (AMF) for improving saline–sodic soils and to assess the effects of these protocols on crop yield, soil properties, and microbial communities. Field experiments across two sites (BeiWuLao and XuJiaZhen) demonstrated that integrating AMF with CF reduction (AHCF treatment) significantly enhanced maize yield by 23.5% at BeiWuLao (from 11,475 to 14,175 kg/ha) and 81.2% at XuJiaZhen (from 7245 to 13,125 kg/ha) compared to conventional fertilization (CK) (p < 0.01). Soil nutrient analysis revealed substantial improvements: available potassium (AK) increased by 77.7% (61.35 vs. 39.33 mg/kg), available phosphorus (AP) by 33.9% (20.50 vs. 15.50 mg/kg), ammonium nitrogen (AN) by 57.3% (64.17 vs. 40.83 mg/kg), and soil organic matter (SOM) by 96.4% (46.98 vs. 23.91 mg/kg) under AHCF treatment (p < 0.05). Although pH and electrical conductivity (ECe) remained unaffected, AMF inoculation shifted microbial composition, elevating salinity-tolerant taxa such as Actinobacteria (+24.7%) and Anabaena. Beta diversity analysis (PCoA) confirmed distinct microbial community structures between treatments, with ECe and AN identified as primary drivers of bacterial (RDA variance: 74.08%) and fungal (RDA variance: 54.63%) communities, respectively. Overall, the combination of chemical fertilizer reduction and AMF effectively improved soil fertility, microbial community structure, and crop yield. These findings have important implications for improving saline soils and promoting environmental sustainability. Full article

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15 pages, 21648 KiB

Open AccessArticle

Fungal Pathogens of Peach Palm Leaf Spot in Thailand and Their Fungicide Sensitivity

by Prisana Wonglom, Nakarin Suwannarach, Jaturong Kumla and Anurag Sunpapao

J. Fungi 2025, 11(4), 318; https://doi.org/10.3390/jof11040318 - 17 Apr 2025

Abstract

Peach palm (Bactris gasipaes Kunth) is a long-lived tropical palm valued for its edible, nutritious fruits. The cultivation area of peach palm, which was introduced to Thailand for fruit production, has been steadily expanding. Small brown spots that expanded into irregular lesions [...] Read more.

Peach palm (Bactris gasipaes Kunth) is a long-lived tropical palm valued for its edible, nutritious fruits. The cultivation area of peach palm, which was introduced to Thailand for fruit production, has been steadily expanding. Small brown spots that expanded into irregular lesions with dark margins were first observed on B. gasipaes seedlings in commercial nurseries in Phetchaburi Province, southern Thailand. To identify the causal pathogens, ten fungal isolates were obtained from symptomatic leaves and subjected to pathogenicity tests, confirming their ability to cause the disease. Morphological and molecular analyses identified five isolates as Colletotrichum fructicola (BGC02.2, BGC03) and C. theobromicola (BGC01, BGC02.1, BGC04) and five isolates as Fusarium pernambucanum (BGF01, BGF02, BGF03, BGF04.1, BGF04.2). Phylogenetic analysis was based on act, cal, gapdh, ITS, and tub2 regions for Colletotrichum spp. and cal, rpb2, and tef1-α for Fusarium spp. In vitro fungicide assays revealed that C. fructicola and C. theobromicola were the most sensitive to carbendazim, mancozeb, and prochloraz, while F. pernambucanum was effectively inhibited by mancozeb and prochloraz. This study represents the first report of C. fructicola, C. theobromicola, and F. pernambucanum causing leaf spot disease on B. gasipaes in Thailand, providing essential insights for disease management strategies in the region. Full article

(This article belongs to the Special Issue Diversity of Microscopic Fungi)

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15 pages, 2888 KiB

Open AccessArticle

Functional Analysis of FoCrpA in Fusarium oxysporum Causing Rice Seedling Blight

by Chun Wang, Liang Wang, Xuanjie Zhao, Lei Hou, Qingran Liu, Rui Ren, Anqi Lv, Xinyang Liu, Tianliang Xiong, Peng Guo, Xiaofeng Xu, Zhe Ni, Chunlai Liu and Junhua Zhang

J. Fungi 2025, 11(4), 317; https://doi.org/10.3390/jof11040317 - 17 Apr 2025

Abstract

Fusarium oxysporum is one of the main pathogens causing rice seedling blight disease. Revealing its pathogenic mechanism is of great significance for formulating prevention and control strategies for rice seedling blight disease. Copper transporting P-type ATPases (Cu-ATPase) is a large class of proteins [...] Read more.

Fusarium oxysporum is one of the main pathogens causing rice seedling blight disease. Revealing its pathogenic mechanism is of great significance for formulating prevention and control strategies for rice seedling blight disease. Copper transporting P-type ATPases (Cu-ATPase) is a large class of proteins located on the plasma membrane that utilize the energy provided by ATP hydrolysis phosphorylation to transport substrates across the membrane. It plays a crucial role in signal transduction, the maintenance of cell membrane stability, and material transport. The main function of Cu-ATPase is to maintain the homeostasis of copper in cells, which is essential for the normal growth and development of organisms. This study utilized the ATMT-mediated gene knockout method to obtain the knockout mutant ∆FoCrpA and the complementation strain ∆FoCrpA-C, which are highly homologous to the P-type heavy metal transport ATPase family in F. oxysporum. The results showed that, compared with the wild-type strain, the knockout mutant ∆FoCrpA had a lighter colony color; a reduced tolerance to copper ion, osmotic, and oxidative stress; a weakened ability to penetrate glass paper; and decreased pathogenicity. However, there was no significant difference in pathogenicity and other biological phenotypes between the complementation strain ∆FoCrpA-C and the wild-type strain. In summary, the FoCrpA gene is involved in osmotic and oxidative stress, affecting the invasion and penetration ability and pathogenicity of F. oxysporum, laying a theoretical foundation for understanding the development and pathogenic mechanism of F. oxysporum. Full article

(This article belongs to the Special Issue Plant Pathogens and Mycotoxins)

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18 pages, 6839 KiB

Open AccessArticle

Microaggregates as Nutrient Reservoirs for Fungi Drive Natural Regeneration in Larch Plantation Forests

by Yiping Lin, Kefan Wang, Zilu Wang, Xin Fang, Haomin Wang, Nuo Li, Cong Shi and Fuchen Shi

J. Fungi 2025, 11(4), 316; https://doi.org/10.3390/jof11040316 - 16 Apr 2025

Abstract

The natural regeneration of Larix gmelinii plantations plays a pivotal role in rehabilitating ecosystem services in Northeast China’s degraded forests. However, mechanistic linkages between soil aggregate nutrient fluxes and fungal community assembly remain poorly constrained. Combining space-for-time substitution with particle-size fractionation and high-throughput [...] Read more.

The natural regeneration of Larix gmelinii plantations plays a pivotal role in rehabilitating ecosystem services in Northeast China’s degraded forests. However, mechanistic linkages between soil aggregate nutrient fluxes and fungal community assembly remain poorly constrained. Combining space-for-time substitution with particle-size fractionation and high-throughput sequencing, this study examined successional trajectories across regeneration in Langxiang National Nature Reserve to resolve nutrient–fungal interplay during long-term forest restructuring. The results demonstrated that microaggregates (<0.25 mm) functioned as nutrient protection reservoirs, exhibiting significantly higher total carbon (TC) and nitrogen (TN) contents and greater fungal diversity (p < 0.05). Both stand regeneration stage and aggregate size significantly influenced fungal community composition and structural organization (p < 0.05). Aggregate-mediated effects predominated in upper soil horizons, where fungal dominance progressively transitioned from Mortierellomycota to Ascomycota with increasing particle size. In contrast, lower soil layers exhibited regeneration-dependent dynamics: Basidiomycota abundance declined with L. gmelinii reduction, followed by partial recovery through mycorrhizal reestablishment in Pinus koraiensis broadleaf communities. Fungal co-occurrence networks displayed peak complexity during Juglans mandshurica germination (Node 50, Edge 345), with 64.6%positive correlations, indicating the critical period for functional synergy. Basidiomycota showed significant negative correlations with nutrients and major fungal phyla (R² = 0.89). This study confirms that natural vegetation regeneration reshapes belowground processes through litter inputs and mycorrhizal symbiosis, while microaggregate management enhances soil carbon sequestration. Near-natural plantation management should incorporate broadleaf species to preserve mycorrhizal diversity and amplify ecosystem services. These findings provide an essential soil ecological theoretical basis for sustainable plantation management in Northeast China. Full article

(This article belongs to the Section Environmental and Ecological Interactions of Fungi)

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