Search Results (294)

Vairimorpha ceranae is a fungal pathogen that infects the honeybee midgut and poses a serious threat to colony health. However, the role of long noncoding RNAs (lncRNAs) of V. ceranae in its infection of the host remains poorly understood. Using lncRNA-seq data from the midguts of Apis mellifera workers at 7 and 10 days post-inoculation with V. ceranae (NcT1L and NcT2L groups), along with controls inoculated with spores (NcCKL group), we performed transcriptome-wide identification and structural characterization of lncRNAs. We identified lncRNAs in V. ceranae and analyzed the regulatory network of the differentially expressed lncRNAs (DElncRNAs). A total of 27 V. ceranae lncRNAs were identified in the midguts. The 19, 21, and 4 DElncRNAs were identified in the NcCKL vs. NcT1L, NcCKL vs. NcT2L, and NcT1L vs. NcT2L comparison groups. These DElncRNAs were predicted to regulate 26, 27, and 2 upstream/downstream genes. Furthermore, 15, 23, and 4 DElncRNAs were found to target 195, 211, and 94 miRNAs, which in turn targeted 204, 216, and 73 mRNAs into the respective comparisons. The ceRNA network prediction revealed that DElncRNAs, miRNAs and mRNAs form a complex regulatory network. This study presents the expression profile of lncRNAs during V. ceranae infection and highlights their potential regulatory functions in pathogenesis. Our findings provide new molecular insights into host–pathogen interactions at the RNA level and establish a foundation for developing targeted strategies to control nosemosis. Full article

Packing density regulates the microenvironment of tobacco (Nicotiana tabacum L.) fermentation and may thereby influence microbial activity and product quality. However, its effects on microbial community assembly and quality formation remain poorly understood. This study aimed to clarify how packing density affects flue-cured tobacco quality by shaping microbial communities, functional potential, and ecological interactions. Here, we investigated the effects of three packing densities (60%, 70%, and 80%) on chemical components, aroma compounds, microbial community structure, functional potential, co-occurrence networks, and assembly mechanisms of flue-cured tobacco (cv. Piaohe No. 2) after 10 days of fermentation. Moderate density (70%) achieved the most balanced chemical profile, with appropriate nicotine retention, potassium/chlorine ratio, and sugar/nicotine balance. T70 also exhibited the highest levels of total esters, total ketones, and β-ionone, key contributors to fruity, floral, and woody aromas. Microbial analysis revealed that T70 supported the highest diversity and was characterized by the enrichment of aroma-related bacterial taxa, including Bacillus and lactic acid bacteria, as well as the fungal genus Pichia. In contrast, T60 favored aerobic nicotine degraders, whereas T80 selected for obligate anaerobes associated with off-odor production. Functional predictions and network analysis showed that T70 upregulated fatty acid and carotenoid biosynthesis pathways and exhibited the highest modularity, indicating a compartmentalized, functionally complementary community. Neutral model fitting revealed increasing stochasticity with density, with T70 displaying a mixed assembly regime. Collectively, our findings show that packing density influences tobacco quality by regulating microbial community composition, functional potential, network interactions, and assembly processes. These results provide a scientific basis for optimizing packing density in tobacco processing. Full article

Background/Objectives: Mushroom-derived phenolic compounds are gaining attention as bioactive molecules with potential roles in gut microbiota modulation, intestinal health, and metabolic regulation. Although mushroom polysaccharides are well established as fermentable substrates, the contribution of fungal phenolics to microbiota–host interactions remains less defined. This review aimed to critically analyse the evidence supporting mushroom-derived phenolic compounds as emerging prebiotic-like modulators of gut microbiota, intestinal function, and host metabolism. Methods: A narrative critical review was conducted using scientific literature retrieved from PubMed, Scopus, Web of Science, and Google Scholar. Studies addressing phenolic profiling in edible and medicinal mushrooms, gastrointestinal digestion, colonic fermentation, microbial biotransformation, gut microbiota modulation, intestinal barrier function, inflammation, and metabolic outcomes were considered. Particular attention was given to chromatographic and mass spectrometry-based studies, in vitro digestion/fermentation models, mechanistic studies, animal experiments, clinical trials, systematic reviews, and meta-analyses. Results: Current evidence shows that mushrooms contain diverse phenolic compounds, mainly phenolic acids such as gallic, protocatechuic, caffeic, p-coumaric, ferulic, vanillic, syringic, and cinnamic acids. Due to limited small intestine absorption, a substantial fraction of these compounds may reach the colon, where they undergo microbial biotransformation into smaller phenolic metabolites. These metabolites may influence microbial ecology, support beneficial taxa, modulate short-chain fatty acid production indirectly, attenuate oxidative stress and inflammatory signaling, and contribute to intestinal barrier integrity. However, most evidence derives from in vitro and preclinical studies, while human data remain limited and are mainly based on whole-mushroom interventions. Conclusions: Mushroom-derived phenolic compounds are promising prebiotic-like modulators within the microbiota–metabolite–host axis. Nevertheless, their specific contribution cannot yet be quantitatively distinguished from that of other mushroom constituents, particularly β-glucans, chitin, and other fungal polysaccharides, because most available evidence derives from whole-mushroom matrices, crude extracts, or polysaccharide-rich preparations rather than isolated phenolic fractions. Future studies should compare whole mushroom preparations, polysaccharide-rich fractions, and standardized phenolic-rich extracts, integrating metabolomics, microbiome profiling, and well-designed clinical trials to clarify the relative mechanistic and therapeutic relevance of mushroom phenolics. Future studies should use standardized phenolic-rich extracts, metabolomics, microbiome analysis, and well-designed clinical trials to clarify their mechanistic relevance, clinical significance, and translational potential. Full article

Global food waste management necessitates circular bioeconomy solutions to transform organic residues into high-value nutrients to address nutritional demands. This study investigated the valorization of two abundant waste streams, stale bread and sunflower oil through solid state fermentation using food-grade filamentous fungi. Three strains, Neurospora intermedia, Aspergillus oryzae and Rhizopus oryzae were evaluated for the bioconversion of stale bread. Oil supplementation levels of 10, 20 and 30% (g/100 g dry matter) using both fresh and spent sunflower oil were tested to assess changes in proximate composition, characterizing fungal growth dynamics and mycelial development. Furthermore, modifications in fatty acid profiles and hydrolytic enzyme activities were analyzed to determine species responses to oil source and concentration. The results demonstrated that N. intermedia achieved peak protein levels of 36% (g/100 g) alongside efficient starch catabolism, while 10% fresh oil supplementation induced a significant protein increase (26%) in A. oryzae. Regarding lipid accumulation, 10% spent oil supported higher fat content in R. oryzae (19%) compared to fresh oil (17%). PUFA/SFA ratio reached its maximum in A. oryzae with the highest of 5.91 ± 0.56 under 10% fresh oil. Enzymatic analysis identified A. oryzae as the most efficient lipase producer, reaching a maximum activity of approximately 0.10 U/g at 10% spent oil supplementation. Conversely, R. oryzae lipase activity peaked at 20% supplementation (0.08 U/g), reflecting its high capacity for lipid accumulation. These findings establish a potent bioprocess for upcycling mixed food wastes into enhanced functional ingredients for sustainable food and feed systems. Full article

Fusarium oxysporum-associated disease symptoms in rice (Oryza sativa L.) seedlings represent an experimentally tractable model for evaluating microbiome-mediated disease suppression under controlled conditions. Biological control of Fusarium-associated disease development in rice provides a promising ecological alternative to chemical fungicides. However, the mechanisms underlying the spatial reconfiguration of the host plant multicompartment microbiome in response to complex inoculants remain insufficiently understood. In this study, we investigated the ability of the monoculture Bacillus amyloliquefaciens Bn1 (B. amyloliquefaciens Bn) and phototrophic–heterotrophic consortia composed of Nostoc sp. J-1 and B. amyloliquefaciens Bn1 to suppress Fusarium oxysporum infection, with parallel profiling of bacterial and fungal communities in rhizosphere soil, the root endosphere, and the phyllosphere using 16S rRNA and ITS amplicon sequencing. Phenotypic screening showed that microbial inoculant application significantly reduced the disease index by up to 55% while maintaining plant dry weight. The protective phenotype was not primarily associated with shifts in alpha diversity, but rather with compartment-specific reorganization of microbial communities. These findings suggest that biological control efficacy was associated less with the overall taxonomic scale of microbiome disturbance than with the formation of a functionally balanced, compartment-specific holobiont architecture but by the formation of a functionally balanced, compartment-specific holobiont architecture, providing a conceptual basis for the targeted design of next-generation phototrophic–heterotrophic biopreparations. Full article

The Yellow River Delta is a representative coastal saline–alkaline ecosystem in China, where high salinity and complex soil properties create a distinct habitat that significantly shapes microbial community structure and function. In this study, we analyzed 34 saline–alkaline soil samples from four regions within the delta. We characterized soil physicochemical properties (salt content, electrical conductivity, and pH) and systematically assessed fungal diversity, potential ecological functions, and their relationships with environmental variables using both internal transcribed spacer high-throughput sequencing and culture-based isolation. Sequencing generated 1,137,196 sequences that clustered into 13,574 operational taxonomic units (OTUs), with Good’s coverage values ranging from 0.96 to 1.00, indicating sufficient sequencing depth. The soils were generally alkaline and exhibited pronounced spatial heterogeneity in salinity and electrical conductivity. Sequencing analyses revealed Ascomycota and Basidiomycota as the dominant fungal phyla. Alpha diversity tended to decline with increasing salt content and electrical conductivity; however, substantial within-group variability indicated strong microenvironmental influences. Beta diversity analyses revealed distinct clustering patterns in community structure among regions based on PCoA ordinations. Redundancy analysis revealed that soil pH had the only significant unique contribution to fungal community variation. However, all three measured edaphic factors together explained only 17% of the total community variation. Functional inference using the FUNGuild database identified diverse fungal trophic modes and several plant-associated taxa in several samples. Culture-based approaches yielded 347 isolates representing 52 genera. Among the isolates, the vast majority (>95%) belonged to Ascomycota, with Basidiomycota represented by only a few isolates, which is consistent with the dominance of Ascomycota observed in the high-throughput sequencing data. Comparisons between sequencing and cultivation results demonstrated complementary diversity profiles and highlighted a substantial reservoir of nonculturable fungi in these soils. Overall, this study clarifies spatial patterns and key environmental drivers of fungal diversity in the Yellow River Delta and establishes a foundational culture collection for future ecological restoration efforts. Full article

Soil organic matter (SOM) stabilization is closely linked to microbial community structure and function, yet reliable biological indicators remain insufficiently defined. This study aimed to identify microbial and biochemical markers of SOM accumulation under different land use systems (cropland, mown with phytomass removal, mown without phytomass removal, and fallow) in gray forest soils. Soil profiles were investigated in four land use types (cropland, mown with phytomass removal, mown without phytomass removal, and fallow) in the Laishevsky District (Russia). Physicochemical properties, SOM fractions, basal respiration, substrate-induced respiration, Biolog EcoPlates, quantitative PCR, and metagenomic data were used to assess microbial diversity and activity. Microbial communities differed substantially among land use systems and soil horizons, with bacterial communities in fallow soils dominated by oligotrophic taxa, such as RB41, Candidatus Udaeobacter, and KD4-96, whereas arable and managed grassland soils showed increased relative abundance of copiotrophic genera, particularly Pseudomonas and Polaromonas. Fungal communities were primarily represented by Mortierella, Penicillium, Trechispora, and Metarhizium, while both bacterial and fungal diversity decreased with soil depth, and metabolic profiling indicated preferential utilization of carbohydrates and carboxylic acids across all land use types. The highest organic matter and total organic carbon (TOC) were in soils under mowing without phytomass removal and fallow land, while arable soils showed the lowest values. Microbial diversity decreased with soil depth across all variants. Hay meadow soils exhibited elevated metabolic activity and higher metabolic quotient (qCO₂), indicating intensified carbon turnover or microbial stress, whereas arable soils were characterized by reduced substrate utilization and simplified community structure. Oligotrophic bacterial taxa were associated with more stable SOM conditions, while copiotrophic dominance reflected rapid carbon turnover. The results demonstrate that microbial community composition, functional activity, and specific taxa (e.g., oligotrophic bacteria, saprotrophic fungi, arbuscular mycorrhizal fungi) can serve as sensitive indicators of SOM stabilization processes. These findings support the development of microbiome-based diagnostic tools for assessing soil carbon dynamics and guiding sustainable land management strategies. Full article

Soil fungi are key drivers of terrestrial ecosystem functioning, contributing to organic matter decomposition, nutrient cycling, and plant–microorganism interactions. Despite their importance, the global distribution and structural biases of public sequence records for soil fungi remain incompletely characterized. In this study, we analyzed soil-associated fungal DNA sequences retrieved from the NCBI GenBank database using a custom R-based bioinformatics pipeline. Following filtering and metadata standardization, 544,554 filtered sequence records were obtained. The taxonomic composition of the dataset consisted primarily of Ascomycota (69.62%), followed by Basidiomycota, Glomeromycota, and Mucoromycota, with Trichoderma, Penicillium, and Aspergillus representing the most frequent genera. The geographic distribution revealed strong sampling bias, with China and the United States accounting for over one-third of all records. Ecological metadata indicated that rhizospheric and forest soils were the most common sources of the deposited sequences. At the same time, gene marker analyses confirmed the widespread use of the ITS region as the primary fungal barcode. Sequence diversity analyses revealed continental variation, with Europe and Asia showing higher medians, while the ordination highlighted clustering of sequence profiles, particularly among records from extreme environments. This study demonstrates the potential of public sequence databases for large-scale biodiversity assessments while highlighting the influence of sampling bias and the limitations of metadata. Full article

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

Fungal iterative non-reducing polyketide synthases (NR-PKS) contain a unique product template (PT) domain for aromatic cyclization. Among them, some NR-PKSs, such as the sorbicillin NR-PKS (SorB), have an apparently inactive PT. It is unknown what role such PT plays in NR-PKS programming. In this study, the PT domain of SorB was first dissected and engineered. Removal of the PT domain from SorB did not change the product profile, but the yield decreased. Meanwhile, a significantly lower transcriptional level of the ketoacyl synthase (KS) domain was observed in the knockout mutant (UvSorB∆PT). Phylogenetic tree analysis and multiple sequence alignments revealed this PT belongs to group I (C2–C7, monocyclic ring), and mutations were found at catalytic dyad sites when compared with functional fungal PTs. However, mutating these residues back to the conserved ones did not give rise to products corresponding to a functional PT, but rendered the NR-PKS unproductive. Likewise, removal of the C-methyltransferase (CMT) domain from SorB destroyed the polyketide production. Furthermore, in an attempt to alter the methylation pattern, mutations of the key substrate-binding sites of the CMT domain were made. Site-directed mutations of the C-MT led to cessation of the polyketide production. This reveals CMT is vulnerable to engineering in a collaborating NR-PKS (SorB). These results provide additional insights for catalytic reprogramming in fungal NR-PKS. Full article

Elephant grass–ramie mixed silage represents a promising strategy to valorize tropical forage resources for ruminant production, yet the dynamic changes in microbial community and fermentation quality during semi-commercial silo bag ensiling remain poorly understood. Elephant grass and ramie were co-ensiled at a 70:30 (w/w) ratio and stored at room temperature for 15, 30, and 45 days. Fermentation quality was evaluated by pH, lactic acid, acetic acid, and ammonia nitrogen, while bacterial and fungal communities were analyzed via 16S and ITS rRNA high-throughput sequencing in triplicate. The results revealed limited fermentation efficiency across all periods, characterized by relatively high pH (≥5.1), restricted lactic acid accumulation, and substantial butyric acid concentrations. Vertically, silage at day 30 exhibited a transient, relatively better acidification profile (lowest pH and highest lactic acid) compared to days 15 and 45, though still sub-optimal overall. Bacterial diversity increased significantly by day 45, concurrent with a marked reduction in the relative abundance of Firmicutes, whereas fungal diversity declined progressively throughout the ensiling period. Enterococcus was identified as the core functional bacterium closely correlated with key fermentation parameters, while most fungal taxa exerted negative effects on silage quality. These findings demonstrate that while a 30-day ensiling duration offers a relatively stable window under restricted acidification, the high fibrous nature and baseline composition of the mixed material present challenges for preservation. This study provides a transparent theoretical basis and underscores the critical need for technical interventions in semi-commercial elephant grass–ramie ensiling. Full article

Cervicovaginal dysbiosis is an established co-factor of high-risk human papillomavirus (HPV) persistence and cervical neoplastic development, yet most studies address the bacterial compartment in isolation, leaving fungal communities and bacterial–fungal cross-kingdom interactions underexplored, particularly in Central Asian populations. We performed shotgun metagenomic sequencing (mNGS) of cervicovaginal samples from 311 Kazakhstani women undergoing routine cervical screening. HPV status was determined using combined PCR and mNGS methods, and cervical screening was completed using liquid-based cytology (NILM, ASC-US, LSIL, ASC-H). Bacterial, viral, and fungal taxa were profiled from a single shotgun dataset with Kraken2 pipeline. Bacterial community state types (CSTs) were determined based on dominant bacterial species, functional gene content was annotated against KEGG using eggNOG, and covariate-adjusted associations were estimated using MaAsLin3. Mycobiome β-diversity differed significantly by HPV status (p = 0.003). In particular, Candida positivity was significantly associated with HPV presence and with high-risk α-9 HPV in cytologically normal (NILM) samples (OR = 3.6, [1.6–9.6], p ≤ 0.001). Covariate-adjusted analysis was consistent with this positive association (q < 0.05). Concurrently, among CSTs, Lactobacillus iners-dominated CST III and dysbiotic Gardnerella vaginalis-dominated CST IV showed a 3-fold higher Candida albicans prevalence (p < 0.01). Further analysis demonstrated that, functionally, both of these CSTs had depleted capacity for lactate metabolism (ko00620, p < 0.0001) and, in particular, for the genetic capacity for pyruvate-dependent H₂O₂ generation (half that of the L. crispatus-dominated CST I). These findings support L. iners as a metabolically permissive rather than protective Lactobacillus and suggest cross-kingdom functional signatures as candidate biomarkers for HPV acquisition and persistence in Central Asia, a region previously absent from the cervicovaginal microbiome literature. Full article

Candida albicans is an opportunistic fungal pathogen of clinical relevance, and plant-derived antifungal agents have attracted interest because of rising resistance to conventional drugs. This study aimed to characterize the chemical composition of Mespilodaphne quixos (Lam.) Rohwer essential oil (EO) by GC/MS, evaluate its in vitro antifungal activity against C. albicans, model its concentration-dependent response using one-factor quadratic polynomial modeling, and investigate the interactions of its constituents with selected fungal targets using molecular docking. Freshly collected leaves were subjected to steam distillation, then the EO was characterized using GC/MS. Antifungal activity was determined using the Kirby–Bauer disk diffusion method. A one-factor quadratic polynomial model was fitted to describe the inhibition halo diameter as a function of EO concentration. Moreover, 22 identified compounds were docked against 14-α-demethylase, Δ(14)-sterol reductase, and exo-β-(1,3)-glucanase. The EO was mainly composed of (E)-cinnamaldehyde (47.2%), caryophyllene (10.8%), and α-humulene (5.37%). The EO reached an inhibitory capacity of 87.3% relative to ketoconazole. The quadratic model showed good predictive performance. Molecular docking revealed favorable affinities for several sesquiterpenes present in M. quixos essential oil: α-copaene showed the best interaction profile against 14-α-demethylase and Δ(14)-sterol reductase, whereas α-guaiene and spathulenol performed best against exo-β-(1,3)-glucanase. These findings provide preliminary in vitro and in silico evidence supporting the antifungal activity of M. quixos EO. Full article

Opportunistic bacterial and fungal infections from surface wounds remain a persistent threat to aquaculture, resulting in significant economic losses and reduced stock welfare. Topical wound sealants are widely employed in recreational aquaculture applications, yet no market regulation or efficacy data exist to support their usage. The broader biological/environmental impacts of these products also remain poorly characterized. This study provides the first quantitative assessment of the antibacterial, antifungal and cellular toxicity of a panel of commercially available topical ‘carp care’ formulations. Our data highlights highly variable to no functional growth inhibition or killing of microbial pathogens, significant inherent cyprinid cellular toxicity, and lack of submerged wet adhesion in all products tested. We show for the first time that commercial propolis solutions are ineffective against the four main pathogenic microorganisms affecting carp. Propolis formulations were also found to induce apoptosis and ROS generation in cyprinid cells in vitro, and permeabilise intact carp skin, questioning the foundation of propolis formulations in topical wound-care treatments for carp rearing/angling. We show improved efficacies can be attained through natural compound implementation, with increased antibacterial and antifungal effects, inherent regenerative benefits to cyprinid fibroblasts, and improved human and environmental safety profiles. This research demonstrates the widespread lack of efficacy in currently commercially available wound sealants for carp; of those tested here, many popular formulations are in fact inherently toxic to carp cells, and also have a permeabilizing effect on intact carp skin due to carrier solvent effects, providing a route for secondary infection; most show no activity against any common carp pathogens; and all uniformly lacked wet adhesion. This work provides a framework standard for the future development of topical wound-care formulations for carp and highlights the need for better dialogue between trade and academia when designing novel wound-care products. Full article

Although solid-state fermentation (SSF) has long been used in food production in various traditional contexts, it is now emerging as a particularly promising strategy for the development of functional food ingredients from plant materials and agro-industrial side streams. This review examines recent advances in the application of SSF to enhance the nutritional, functional, sensory, and technological properties of food matrices. Current evidence indicates that SSF can increase the bioactive potential of plant-based substrates by promoting the release and biotransformation of phenolic compounds, while also improving antioxidant capacity, protein digestibility, and techno-functional performance. In addition, the process may support the formation of food-relevant metabolites, including vitamins, peptides, organic acids, and other secondary compounds, while reducing selected antinutritional, allergenic, and undesirable constituents. These compositional changes are often accompanied by modifications in aroma, volatile profiles, visual attributes, and, more recently, gut microbiota-related effects. Attention is given to the use of fungal-based processes for the valorization of cereals, legumes, fruit by-products, and other underutilized substrates. The review also addresses the growing industrial interest in SSF, especially in relation to mycelium-based foods, alternative proteins, functional ingredients, and feed applications. Despite its clear potential, the broader implementation of SSF will require further research and development to support its effective translation into food applications. Full article