Search Results (450)

Background: Cutaneotrichosporon jirovecii is an under-characterized basidiomycetous yeast within the family Trichosporonaceae. Its taxonomic placement, ecological distribution, and functional potential remain incompletely understood because genome-scale resources for C. jirovecii and closely related lineages are limited. Methods: We characterized strain H0426_7, a C. jirovecii-related yeast recovered from a human fecal sample, using ITS-based type-strain comparison, ITS phylogenetic analysis, whole-genome sequencing, average nucleotide identity analysis, read-level assessment of public C. jirovecii-labeled datasets, and comparative functional annotation. Antifungal susceptibility was assessed using the Sensititre YeastOne plate. Results: The ITS sequence of H0426_7 closely matched type-strain material of C. jirovecii, including CBS 6864 and its equivalent deposits. The ITS-based tree placed H0426_7 adjacent to CBS 6864 with bootstrap support of 87%. The final draft genome comprised 38.66 Mb in 1974 contigs, with a GC content of 63.76% and BUSCO completeness of 80.0%. ANI analysis showed that H0426_7 was genomically distinct from the recognized Cutaneotrichosporon species included in the ANI analysis but highly similar to two unclassified feces-derived strains, P10-008 and PK4640, with ANI values exceeding 98.8%. Two public datasets labeled as C. jirovecii showed anomalously low ANI values with H0426_7; read-level taxonomic profiling indicated low target-fungal read proportions, suggesting that these datasets are unsuitable as definitive genome-level references. CAZyme annotation identified 285 family assignments in H0426_7, representing 278 non-redundant predicted proteins, including relatively high GH5 and GH31 counts, suggesting candidate carbohydrate-utilization features shared with the H0426_7/P10-008/PK4640 lineage. Conclusions: H0426_7 is best described as a C. jirovecii-related Cutaneotrichosporon isolate pending availability of a high-quality genome assembly from the C. jirovecii type strain. This study expands genome-scale resources for underrepresented basidiomycetous yeasts and provides a comparative framework for future taxonomic, ecological, and functional studies of feces-associated Cutaneotrichosporon lineages. Full article

Following the elucidation of the fungal bioluminescence pathway (FBP), it was quickly adopted as a reporter system in plants; however, no such application has been documented in fungi to date. In this study, we established for the first time a luminescent reporter in the commercially important mushroom Hypsizygus marmoreus by expressing the luciferase gene from the luminous fungus Neonothopanus nambi. Using an established Agrobacterium-mediated transformation method, we separately introduced the wild-type luciferase gene nnLuz and the previously reported optimized variant nnLuz-v4 that can enhance bioluminescence expression into H. marmoreus arthroconidia. Both genes were stably integrated into the genome and expressed under the control of the H. marmoreus Glycerol 3-phosphate dehydrogenase (GPD) gene promoter. Upon addition of exogenous luciferin, transformants carrying the wild-type nnLuz produced clear, readily detectable bioluminescence signals, whereas no luminescence was observed in untransformed controls. Unexpectedly, the wild-type luciferase consistently exhibited substantially higher luminescence intensity than the optimized nnLuz-v4 variant. This finding suggests that codon optimization may be unnecessary or even detrimental when the donor and host are phylogenetically close basidiomycetes. The successful deployment of the fungal luciferase gene in H. marmoreus provides a sensitive and non-invasive genetic tool that does not require external excitation. This system opens new avenues for promoter characterization, real-time gene expression monitoring during mushroom development, and molecular breeding efforts aimed at improving agronomically important traits. Full article

Cordyceps militaris is a well-known edible and medicinal entomopathogenic fungus that can be cultivated using silkworm larvae as hosts. However, no reports have been found regarding the gut microbiota of silkworms (Bombyx mori) following C. militaris injection. Based on three biological replicates, illumina 16S rRNA gene sequencing was used to investigate the changes over time in the gut bacteria and fungi of silkworms injected with C. militaris. The results indicated that following inoculation with C. militaris, the abundance of Bacillales and Basidiomycetes increased, while that of Pseudomonadales and Ascomycetes decreased. The abundance of Mammaliicoccus increased by 78% and 26% in dying silkworms compared to their pre-inoculated counterparts and blank control group, respectively. The relative abundance of Rhodotorula in dying silkworms was 2.89-fold and 80.51-fold higher than that in the pre-inoculation group and blank control group, respectively. After inoculation with C. militaris, fungi showed the greatest community variations at day 2, while bacteria displayed the most distinct differences at day 4. Under C. militaris infection, the abundance of all four pathways of Genetic Information Processing in silkworm larvae’s gut microbiota significantly increased. Taken together, the results demonstrate that inoculation with C. militaris induced significant alterations in the composition, structure, assembly, and predictive functional profiles of gut bacteria and fungi in silkworms. This study provides a theoretical basis for exploring the production of C. militaris using silkworm larvae as insect hosts. Full article

Stipitate stereoid fungi are saprotrophic basidiomycetes characterized by a leathery basidiome, a central-to-lateral stipe and infundibuliform pilei. Although numerous species of stipitate stereoid fungi have been recorded worldwide, understanding of their phylogenetic relationships remains extremely limited, and research on this group of fungi in China is insufficient. In this study, specimens of the three stipitate stereoid genera, namely Podoscypha s. l., Cymatoderma s. l. and Stereopsis s. l., from southern China were investigated. Phylogenetic analyses of the internal transcribed spacer (ITS) regions and the large subunit of the nuclear ribosomal RNA gene (LSU) using maximum likelihood (ML) and Bayesian inference (BI) methods revealed that all three genera are polyphyletic. Consequently, Podoscypha s. s. and Cymatoderma s. s. were delimited, and Cladoderris—previously synonymized with Cymatoderma—was resurrected. Cladoderris is characterized by an imbricate basidiome, tomentose pilei and basidiospores typically shorter than 4 μm in length. Three new species, Podoscypha casiae, Stereopsis buccinata and Cladoderris perennis, were described and illustrated. The morphological distinctions and affinities between the new species and closely related taxa were discussed, the thresholds for the intraspecific and interspecific demarcation within the three genera in this study were provided, and identification keys for the species of each genus were presented. Full article

An isolate of Peniophora lycii was obtained from grapevine, and its interactions with several grapevine-associated fungi and the plant host were examined. The fungus was not able to infect intact leaves, but necrotized the margins of foliar disks and caused necrosis and white rot in woody tissues. In dual cultures, P. lycii and Aureobasidium pullulans showed mutual antagonism. Mycoparsitism of P. lycii was observed on epiphytic Botrytis cinerea, Alternaria sp., and endophytic Botryosphaeria dothidea interaction partners. In contrast, P. lycii showed trophic growth towards endophytic Phaeomoniella chlamydospora without any signs of harmful interactions. Dual inoculations of foliar disks with epiphytic fungi revealed no effects of fungal interactions on necrosis development by pathogens and verified mycoparasitic interactions in planta. Co-infection assays of cuttings with endophytic pathogen fungi showed cumulative effects of fungal interactions on wood symptom expression, with the exclusive contribution of P. lycii to white rot development. In addition to providing the first isolation of P. lycii from grapevine and the description of its mycoparasitic behavior, the present study suggests that the fungus may act as an opportunistic grapevine pathogen, probably as a secondary colonizer in trunk diseases. The observed dual host preference may allow trunk disease pathogens to initially feed on fungi, followed by damage to the grapevine. This may be in connection with the exceptionally long latency of these syndromes. Full article

Ochetobibus elongatus (Kner) is a migratory fish found in the Yangtze River basin and areas south of it, and listed as a critically endangered (CR) fish on the China Red List of Vertebrates. To achieve group recovery and artificial breeding, this study investigated the dietary characteristics of O. elongatus based on high-throughput sequencing of its intestinal contents, and its digestive system morphology, and its histology. Results showed that the digestive system of O. elongatus lacked a stomach and mainly consisted of the oropharynx, pharyngeal teeth, esophagus, intestine, and anus. The gut index was 0.88, with clear segmentation of the foregut, midgut, and hindgut, and the visceral mass index was 7.35%. Histological analysis of the digestive system revealed the presence of keratinized dental plates or pharyngeal teeth in the pharynx, as well as a high density of taste bud cells in the soft palate of the oral cavity. The surface layer of the intestinal villi contained numerous mucous cells, with the average number of mucous cells per villus gradually increasing from the esophagus to the hindgut, and the foregut having the longest and most abundant mucosal folds. The esophagus exhibited well-developed circular and longitudinal muscle layers, while in the hindgut, both the circular and longitudinal muscle layers were slightly thicker than those in the midgut. High-throughput sequencing of the intestinal contents of O. elongatus revealed the following phyla based on 18S V4 meta-barcoding: Chlorophyta, Diatoms, Arthropoda, Basidiomycetes, and Ascomycetes, with the genus Hypophthalmichthys and algae being the main classifications. In contrast, based on COI meta-barcoding, the study newly identified the phyla Cnidaria and Mollusca, with the genera Chlorophyta, Scenedesmus, Pectinodesmus, and zooplankton such as Pseudodiaptomus. Metagenomic sequencing revealed that the gut microbiota at the phylum level was predominantly composed of Pseudomonadota, Ascomycota, Basidiomycota, Chytridiomycota, and Bacillota, with key genera including Cetobacter, Pseudomonas, Acinetobacter, Aeromonas, and Clostridium. This study indicates that O. elongatus is an omnivore with carnivorous tendencies. Basic biological research on O. elongatus is of great significance for the restoration of the population, artificial breeding, and the development of its artificially formulated feed. It also provides important data for the formulation of biodiversity conservation measures. Full article

Natural antioxidants are essential for protecting the body against oxidative stress and exhibit a wide range of biological activities. In this context, forty extracts derived from ten submerged cultivated mushroom species were analyzed for their mycochemical composition, antioxidant capacity, and cytotoxic effects against MCF7 breast cancer cells. Qualitative and quantitative screening revealed that, among the detected classes of bioactive compounds, the extracts were predominantly enriched in flavonoids, terpenoids, and phenolic constituents. Considerable variation was observed in the levels of total phenolics, flavonoids, and ascorbic acid among different species and solvent extracts. The highest total phenolic contents were detected in ethanol and ethyl acetate extracts of G. frondosa (110.0 ± 6.4, 227.6 ± 14.2, and 160.5 ± 5.3 mg GAE/g), while the water extract of F. velutipes also exhibited elevated phenolic levels (119.2 ± 6.5 mg GAE/g). Flavonoid concentrations ranged from 102.5 ± 10.5 to 359.9 ± 2.5 mg QE/g in biomass and culture liquid extracts obtained with organic solvents. Ascorbic acid content was generally highest in ethyl acetate culture liquid extracts, suggesting solvent-dependent enrichment of antioxidant metabolites. Free radical scavenging activity increased in a concentration-dependent manner, reaching inhibition values more than 90% at 20 mg/mL in all tested mushrooms. Cytotoxicity assays demonstrated that extract type, solvent, and incubation time strongly influenced the inhibition of MCF7 cell viability. Ethyl acetate extracts from H. erinaceus, P. ostreatus, T. versicolor, and T. pubescens exhibited the strongest cytotoxic effects, reducing cell viability by up to 70% at higher concentrations. The results demonstrate that mushroom extracts, particularly ethyl acetate extracts, possess significant antioxidant and cytotoxic activities. These findings highlight their potential as promising natural sources of medicinal bioactive compounds for antioxidant and anticancer applications. Full article

Plant pathogens pose a severe threat to global agricultural production, and their pathogenicity is closely linked to the biosynthesis of secondary metabolites. Basidiomycete within the family Ustilaginaceae represent significant plant pathogens, among which Ustilago maydis, as a model species, has been extensively studied for its secondary metabolites. However, the biosynthetic potential of other species within this family remains poorly understood. In this study, we conducted whole-genome bioinformatic analyses of 16 Ustilaginaceae species, including U. maydis, to systematically identify the distribution of biosynthetic gene clusters (BGCs), core gene domain compositions, and interspecies similarities. A total of 181 predicted BGCs were identified, averaging approximately 11 per species. BGCs for mannosylerythritol lipids (MELs), siderophores, and itaconic acid, as well as the melanin-associated genes pks1 and pks2, were widely distributed across most species. Conversely, an additional melanin biosynthetic gene cluster was found exclusively in U. maydis strain 521, indicating species-specific occurrence. Furthermore, this study identified a novel class of polyketide synthase (PKS) gene clusters with uncharacterized functions across 15 species, exhibiting high sequence and structural conservation between species. These findings reveal the rich metabolic diversity and species-specific biosynthetic potential of Ustilaginaceae, and by using U. maydis as a reference model, we highlight several BGCs (e.g., for MELs, siderophores, itaconic acid, and melanin) that are known to contribute to virulence or pathogenicity in plant hosts. This provides new insights into their pathogenic mechanisms. Full article

Background/Objectives: Filamentous basidiomycetes are environmental fungi that rarely cause human infection but are increasingly recognized as opportunistic pathogens, particularly in immunocompromised hosts. However, their clinical epidemiology and antifungal management data remain limited. Methods: We conducted a retrospective study of patients with filamentous basidiomycetes isolated from clinical specimens at King Chulalongkorn Memorial Hospital, Thailand, between 2019 and 2025. Species identification was performed using internal transcribed spacer (ITS) or D1/D2 ribosomal DNA sequencing. Demographic characteristics, clinical features, antifungal management, and outcomes were analyzed. Results: Fourteen patients were identified with a mean age of 61.2 ± 18.3 (29–90), and 71.4% were female. In these patients, pulmonary infection was most common (64.3%), followed by ocular (14.3%), cutaneous (14.3%), and central-line-associated infection (7.1%). Bronchoalveolar lavage was the most frequent specimen (64.3%). ITS/D1D2 sequencing revealed broad species diversity, including Schizophyllum commune (n = 3), Candolleomyces spp. (n = 3), Coprinopsis cinerea, Fomitopsis spp., Geliporus exilisporus, Odontoefibula orientalis, Irpex laceratus, Volvariella volvacea, Deconica coprophila, and Agaricales spp. Antifungal therapy was largely empirical, with voriconazole used most frequently (46.6%). Overall, 85.7% of patients improved, whereas 14.3% did not respond clinically. Conclusions: Emerging filamentous basidiomycetes demonstrate substantial species diversity and pose ongoing diagnostic and antifungal management challenges. The absence of standardized susceptibility testing and clinical breakpoints may contribute to therapeutic uncertainty and challenges in antifungal selection. Integrating molecular diagnostics into routine clinical workflows may enhance antifungal stewardship in rare mold infections. Full article

Mating-type identification is fundamental to studies of genetic diversity and genetic breeding in fungi, especially for tetrapolar basidiomycetes, whose mating types are determined by two multiallelic loci, A and B. Traditional mating-type identification of monokaryons relies on manual inference based on hybridization experiments; however, this process is highly complex, time-consuming, and error-prone when applied to large-scale studies. In this study, we isolated 30 monokaryons from protoplasts derived from 15 dikaryons of Flammulina velutipes and developed a software tool, Mating-Type Imputation (MTI), to automatically, rapidly, and accurately infer monokaryon mating types in tetrapolar fungi using a combinatorial pruning traversal algorithm. Using a compatibility matrix derived from 435 hybridization experiments involving these 30 monokaryons, MTI required only a few minutes to accurately infer the mating types of all monokaryons-a task that typically takes several days for manual inference by experienced investigators. Furthermore, MTI enabled us to investigate how false-positive and false-negative interactions influence mating-type inference results. Using a simulated compatibility matrix, we found that MTI could accurately detect potential false negatives in compatibility and successfully infer the true mating-type combinations even in the presence of limited false negatives; conversely, the tool was easily misled by any false positives, resulting in incorrect mating-type combinations. This indicates that false-positive records in hybridization experiments must be strictly eliminated during mating-type inference. In summary, MTI provides an efficient tool for inferring the mating types of tetrapolar fungi, offering technical support for mating-type studies of edible and medicinal fungi, and holds significant theoretical value and broad application potential in the fields of fungal genetic diversity and breeding research. Full article

Basidiomycetes can colonize sweet chestnut (Castanea sativa Mill) xylem, causing white or brown rot and losses in wood quality. The aim of this study was to assess the degradative potential of five Basidiomycota strains (Armillaria mellea (Vahl) P. Kumm. (Am), Fistulina hepatica (Shaeff.) With. (Fh), and Laetiporus sulphureus (Bull.) Murrill (Ls), and two strains of Ganoderma resinaceum Boud.) on three chestnut woods differing in chemistry. The woods differed in nitrogen content (0.3%–1.0%), carbon/nitrogen (C/N) ratio (43–150), and phenolic-related traits. In a 39-day laboratory assay, the five fungal strains were inoculated on three chestnut woods and compared for colonization time, extracellular enzymatic activity, and C mineralization. Fungal colonization strongly depended on fungus × wood interaction: L. sulphureus colonized all woods within 6 days, whereas the two G. resinaceum strains required 9–33 days depending on wood type; A. mellea and F. hepatica colonized only selected woods (up to 39 days). Enzymatic screening indicated laccase activity mainly in G. resinaceum (and to a lesser extent A. mellea), while L. sulphureus expressed cellulolytic activity but no laccase. Over 39 days, total C mineralization peaked under G. resinaceum on the two Sicilian woods (up to 270–300 mg CO₂–C g⁻¹ dry wood), whereas the Tuscan wood (highest C/N and phenolic content) markedly inhibited most strains; only L. sulphureus increased mineralization in this wood (85 mg CO₂–C g⁻¹ dry wood). These findings indicate that wood chemistry, especially C/N ratio and phenolic traits, strongly modulates strain-specific decay patterns. Overall, these results highlight the need for an integrated biological–biochemical approach to evaluate fungal decay potential and to inform both the selection of more durable chestnut woods for wood products and the identification of efficient strains to accelerate lignocellulosic biomass composting. Full article

Sparassis latifolia is an edible and medicinal mushroom with significant economic value, now commercially cultivated on a large scale in China. However, current cultivars face challenges, including an extended mycelial growth period and unstable fruiting body yields. Advances in molecular breeding and functional genomics for this species are hindered by the absence of a reliable genetic transformation system. In this study, we first determined that S. latifolia is highly sensitive to carboxin and hygromycin, two selective agents commonly used in fungal genetics. We subsequently constructed a novel binary vector, pCbxHyg, harboring a carboxin resistance cassette driven by its native Pleurotus eryngii promoter and a hygromycin resistance cassette under the control of the P. eryngii Glycerol 3-phosphate dehydrogenase (GPD) gene promoter. Initial transformation attempts using Agrobacterium-mediated transformation of liquid-cultured mycelial pellets were unsuccessful. During microscopic examination, we discovered that S. latifolia mycelia produce abundant asexual chlamydospores. Using these chlamydospores as recipient material, we efficiently and reproducibly obtained transformants with the pCbxHyg vector under both carboxin and hygromycin selection. This method highlights the advantage of using asexual spores of Basidiomycetes as recipients for genetic transformation. PCR analysis confirmed the stable integration of the exogenous resistance genes into the fungal genome. The functionality of the system was further validated by transforming chlamydospores with a vector carrying a β-glucuronidase (GUS) reporter gene, whose expression was confirmed via histochemical staining of the resulting transformant mycelia. This work establishes the first successful Agrobacterium-mediated genetic transformation system for S. latifolia, providing a foundational platform for future gene function studies and molecular breeding efforts. Full article

Digital phenotyping is increasingly recognized as an essential tool for the quantitative analysis of fungal morphology, particularly in controlled indoor cultivation systems where large numbers of fruiting bodies must be assessed consistently and non-destructively. While YOLOv8-based deep learning approaches have previously been applied in phenotypic analyses of edible mushrooms, the applicability of newer YOLO architectures to fungal phenotyping remains largely unexplored. In this study, we present a controlled-environment digital phenotyping framework for indoor mushroom cultivation and conduct a systematic benchmarking evaluation of YOLOv11 for phenotypic segmentation in comparison with YOLOv8. Using bottle-cultivated Pleurotus ostreatus and Flammulina velutipes as representative edible basidiomycetes, we performed a controlled comparison of YOLOv8-seg and YOLOv11-seg using identical datasets, preprocessing pipelines, and hyperparameter configurations. The results demonstrate that YOLOv11 achieves segmentation performance comparable to that of YOLOv8 across all evaluated metrics (ΔmAP_50–95 < 0.01) while substantially reducing computational complexity, including fewer trainable parameters, lower FLOPs, and decreased gradient load. Validation against caliper-based physical measurements revealed moderate, trait-dependent agreement, whereas inter-model consistency between YOLOv8 and YOLOv11 remained consistently high across diverse morphological and segmentation scenarios. These findings suggest that recent developments in object detection architectures can improve computational efficiency without compromising phenotypic measurement fidelity. More broadly, this study highlights the importance of periodically evaluating emerging detection architectures within biological phenotyping pipelines to ensure scalable, sustainable, and high-throughput fungal phenotyping under controlled-environment cultivation systems. Full article

Antimicrobial metabolite production in basidiomycetes varies by strain and growing conditions. This study compared the antimicrobial activity of extracts from nine fungal strains at both their vegetative and reproductive stages. Wild-growing fungal fruiting bodies were collected and identified through both morphological characterization and molecular sequencing. Extracts from fruiting bodies, mycelia, and culture liquids were tested using the agar well diffusion method and by determining the minimum inhibitory concentration (MIC). Analysis revealed that the highest antimicrobial activity was associated with culture liquid extracts. Antimicrobial properties were detected in the submerged mycelium extracts of only two strains: Stereum hirsutum 1 and Flammulina rossica 16. For fruiting bodies, activity was restricted to extracts of strains from the genus Fomitopsis. The strain S. hirsutum 1 was determined to be the most effective producer of antibacterial compounds. The highest activity was exhibited by the S. hirsutum 1 culture liquid extract, with an MIC of 320 µg/mL against clinical Gram-positive strains (Staphylococcus aureus, S. epidermidis, S. haemolyticus, vancomycin-resistant Enterococcus faecium) and Gram-negative Proteus vulgaris. The studied strains demonstrated higher production of antimicrobial metabolites during vegetative growth, with the active compounds being primarily extracellular. Submerged cultivation of basidiomycetes offers an efficient method for obtaining antimicrobial metabolites, permitting their subsequent isolation, physicochemical characterization, and biomedical evaluation. Full article

This study investigated the secondary fermentation of cocoa beans using mushrooms to further improve the quality of beans. Cocoa beans were fermented using 42 species of basidiomycetes and ascomycetes. Mycelial growth was observed in 29 strains. When 75% cocoa chocolate was prepared using the cocoa beans in which mycelial growth was observed, theobromine concentration was higher in 17 strains compared with the control. Furthermore, caffeine concentration was similar to or lower than the control in all strains. Chocolate produced using cocoa beans fermented with particularly Polyporus arcularius, Peziza vesiculosa, and Urnula craterium exhibited significantly higher theobromine concentrations. Compared to the control theobromine concentration of 7.53 mg/g, P. arcularius showed 9.25 mg/g, 9.13 mg/g for P. vesiculosa, and 9.05 mg/g for U. craterium. Furthermore, the reducing sugar concentration and total polyphenol concentration increased, and the antioxidant activity was similar to or higher than that of the control. These results suggest that secondary fermentation using mushrooms could be used to develop chocolate characterized by high theobromine, low caffeine, and rich polyphenol content. Full article