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Results for “Mycobiome”

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PubMed2026

Cross-kingdom dynamics of the subgingival bacteriome and mycobiome: A pilot study on the effects of a novel HA-H₂O₂-Glycine formulation to treat periodontitis.

OBJECTIVES: Traditional periodontal therapy primarily focuses on bacterial biofilm control; however, recent evidence also suggests a critical role for the oral mycobiome. This study evaluated the clinical and ecological impact of a novel mouthwash formulation containing hyaluronic acid (HA), hydrogen peroxide (H2O2), and glycine on periodontal patients METHODS: This prospective, randomized split-mouth trial included 13 adult participants with periodontitis treated with HA-H2O2-glycine formula (BMG0703A) used twice a day for seven days. Subgingival plaque samples were collected from periodontal pocket and healthy control sites at baseline (T0) and one-week post-treatment (T1). Microbial and fungal communities were characterized using Next-Generation Sequencing (NGS) of the 16S rRNA and ITS2 regions. Linear Mixed Models (LMM) and Spearman correlation were used to assess taxonomic shifts and cross-kingdom relationships. RESULTS: Sequencing revealed a promising ecological shift: the bacteriome shifted from anaerobic dominance (Olsenella, Peptostreptococcus) toward a health-associated aerobic profile, with Rothia near-doubling (11.91% to 22.68%). The mycobiome underwent a "normalization" effect: Candida abundance decreased significantly (22.8% to 9.1%), while fungal Shannon diversity in pockets returned to healthy-site levels. Inter-kingdom analysis identified antagonistic relationships between expanding commensal bacteria and opportunistic fungi, suggesting that the intervention may help re-establish a protective bacterial niche. CONCLUSIONS: The HA-H2O2-glycine formulation seems to facilitate a rapid, cross-kingdom modulation of the subgingival niche. By reducing anaerobic pathogens and normalizing the mycobiome it appear to induce short-term changes, suggesting potential as adjunctive strategy in periodontal management. CLINICAL SIGNIFICANCE: The present work underlines the possible cross-Kingdom effects of a novel compound.

Humans↗

PubMed2025

Gut fungi are associated with human genetic variation and disease risk.

Human genetic determinants of the gut mycobiome remain uninvestigated despite decades of research highlighting tripartite relationships between gut bacteria, genetic background, and disease. Here, we present the first genome-wide association study on the number and types of human genetic loci influencing gut fungi relative abundance. We detect 148 fungi-associated variants (FAVs) across 7 chromosomes that statistically associate with 9 fungal taxa. Of these FAVs, several occur in the protein-coding genes PTPRC, ANAPC10, NAV2, and CDH13. Additional FAVs link to tissue-specific gene expression as fungi-associated expression quantitative trait loci. Notably, the relative abundance of gut yeast Kazachstania associates with genetic variation in CDH13 encoding T-cadherin, a protein linked to cardiovascular disease. Kazachstania forms a causal relationship with cardiovascular disease risk in a mendelian two-sample randomization analysis. These findings establish previously unrecognized connections between human genetics, gut fungi, and chronic disease, broadening the paradigm of human-microbe interactions in the gut to the mycobiome.

Humans↗

PubMed2026

Ergothioneine as an emerging food-derived bioactive compound protecting against age-related diseases: issues needing more research.

Ergothioneine (ET) is a chemically stable, tasteless, odorless, highly water-soluble diet-derived compound that is avidly absorbed and retained by the human body using a selective transporter, organic cation transporter novel 1 (often called the ET transporter). A substantial and growing body of evidence supports a role for ET in maintaining human health and protecting against age-related diseases, especially neurodegenerative diseases, and multiple studies indicate that low blood/plasma/serum ET concentrations increase risk of developing age-related diseases. Despite the growing interest in ET, much fundamental work remains to be done to investigate its metabolism, actions (if any) on the genome, lipidome, metabolome, and proteome, intracellular and intercellular transport (especially in the brain), precise mechanisms of cytoprotection, interactions with the microbiome, mycobiome, and human pathogens, and identifying the factors that control body ET levels. This narrative review explores these issues and suggests what research needs to be done to improve our understanding of ET biology.

M. tuberculosis↗

PubMed2026

Multi-Omic Insights Into Mediterranean Diet-Associated Microbiota.

This study aimed to evaluate the gut microbiota and mycobiota composition, depending on the Mediterranean diet (MD) adherence, using metataxonomics. Combining metagenomics and metatranscriptomics, we also investigate the gene expression level in the bacterial community. Two groups of healthy subjects greatly differing in adherence were selected. Significant differences in microbiota composition were observed between individuals with high adherence (HAMD; mean 10.5 +/- 0.9 points) and low adherence (LAMD; 5.23 +/- 83 points). Notably, the olive oil, vegetable, and fruit consumption presented an important discriminant power between groups. Saccharomyces, Penicillium, and Candida were the most abundant genera. Mycobiota richness was higher in LAMD than in HAMD. Aspergillus was identified as a biomarker for LAMD, whereas Yarrowia, a potential probiotic, was a biomarker for HAMD. Metatranscriptomics indicated that Bacillota was the most metabolically active phylum in the gut microbiota. The low-abundant genus, Methanobrevibacter, showed high transcriptional activity, contributing to the crucial methanogenesis process. Gene expression analyses further highlighted functional differences. Overall, HAMD microbiota presented increased metabolic activity, protein synthesis, and cellular mobility. Overexpression of flagellin and urease genes may enhance immune response in HAMD. Further metatranscriptomic studies are necessary to deepen our understanding of intestinal microbiota transcriptional programs and their interactions with the diet and human health.

Humans↗

PubMed2026

Species-specific structuring of gut bacterial and fungal communities in honey bees Apis cerana and Apis mellifera.

Honey bee gut microbiome studies have primarily emphasized bacteria, leaving fungal communities comparatively overlooked despite their ecological and functional importance. Whole-genome shotgun metagenomics of Apis cerana and Apis mellifera revealed fungal assemblages dominated by Ascomycota, with Basidiomycota and Microsporidia in minor proportions, alongside gut bacterial communities composed mainly of Pseudomonadota, Bacillota, and Actinomycetota. The bacterial diversity was markedly higher in A. mellifera (Shannon = 5.90; Simpson = 0.98) than in A. cerana (Shannon = 4.01; Simpson = 0.94; p > 0.05), while fungal diversity remained comparable between species (p > 0.05). Beta-diversity analyses revealed strong host-specific clustering for both bacterial (PERMANOVA R2 = 0.7989, p > 0.05) and fungal communities (R2 = 0.7218, p > 0.05), indicating distinct microbial organization driven by host species. Bacterial-fungal co-occurrence patterns exhibited host-specific structuring, suggesting differential inter-kingdom community organization between A. cerana and A. mellifera. Linear Discriminant Analysis Effect Size (LEfSe) identified 93 discriminatory fungal taxa (45 enriched in A. cerana, 48 in A. mellifera), highlighting yeast-dominated signatures in A. mellifera and Basidiomycota-affiliated enrichments in A. cerana. KEGG and CAZy profiling revealed host- and kingdom-specific functional differences, with bacterial communities of A. mellifera showing distinct representation of carbohydrate metabolism and nutrient-cycling functions, while fungal communities exhibited a comparatively narrower functional repertoire. Together, these findings provide a high-resolution view of honey bee bacterial and fungal microbiomes, highlighting strong host-driven divergence in taxonomy, function, and cross-kingdom interactions.

Animals↗

PubMed2026

Dynamics of soil fungal communities restored with biochar from a quarry site.

Quarrying activities have intensified due to population expansion, leading to landscape degradation and ecological destruction. Quarry restoration is usually mandatory in Hong Kong, China. Although biochar is used for sustainable soil amendment, its effectiveness in restoring quarry soil with poor properties has rarely been investigated. A 24-month field study was conducted to evaluate the ecological feasibility of restoring a quarry site by using native species (that is, Castanopsis fissa and Cyclobalanopsis edithiae) and biochar amendment. The results revealed that after 24 months, the application of biochar increased the organic carbon, phosphorus and potassium of the vegetated soil by at least 120 %, 31 % and 12 %, respectively, due to higher cation exchange capacity and better plant growth. The relative abundance of Ascomycota and Basidiomycota increased by 24 % and 47 % with biochar application when C. fissa was planted, which was likely associated with the improved nutrient cycling and soil fertility. Even though adding biochar to bare soil was found to increase the complexity of fungal co-occurrence networks, biochar application only increased fungal diversity in vegetated quarry soil but usually reduced its fungal richness. Moreover, fungal co-occurrence networks in vegetated soil became less complex, suggesting that biochar potentially helped plants to assemble specific, beneficial fungal communities. This effect is most pronounced in the soil planted with C. edithiae, where the structure of fungal communities after 24 months was significantly different from that at other restoration times. This study identifies key fungal phyla enhanced by biochar in quarry soil and provides an effective strategy for facilitating the restoration and management of degraded lands, especially quarry sites.

Charcoal↗

PubMed2026

Isoquinoline alkaloids enhance growth performance through multifaceted modulation of the bacterial-fungal microbiome, CAZyme profiles, gut health, and neuroendocrine function in broilers.

The bacterial-fungal microbiome and its carbohydrate-active enzyme (CAZyme) capacity play critical roles in regulating gut health and growth performance in broiler chickens. This study evaluated the effects of dietary isoquinoline alkaloids (IQ) on growth performance, gut microbiome composition, CAZyme profiles, and the microbiome-gut-neuroendocrine axis in broilers. A total of 400 Ross 308 (1-day-old) chicks were randomly assigned to either a Basal diet (CON) or IQ supplemented diet (IQ). Dietary IQ supplementation significantly increased final body weight and cumulative body weight gain (P < 0.0001) and improved feed conversion ratio (P < 0.05). Intestinal permeability was reduced (lower FITC-dextran; P < 0.05), accompanied by increased serotonin and serotonin-to-corticosterone ratio and decreased corticosterone (P < 0.05). Expression of inflammatory genes (TNF-α, NF-κB, IL-4, and TLR-1) was downregulated (P < 0.05). Microbiome analysis showed increased α-diversity (P < 0.05) and clear β-diversity separation (PERMANOVA, P < 0.001), with enrichment of beneficial bacteria (Akkermansia muciniphila, Lactobacillus salivarius, Turicibacter sanguinis, Bacillus subtilis) and suppression of fungal taxa (Aspergillus, Penicillium). CAZyme-related pathways involved in lignin and carbohydrate degradation were increased (P < 0.05). Microbial diversity was negatively correlated with inflammation and gut permeability, whereas network analysis identified 164 significant associations (|ρ| ≥ 0.50), revealing strong negative correlations between beneficial bacteria and inflammatory markers (ρ = -0.65 to -0.78) and positive associations for fungal taxa (ρ = 0.62-0.81). Serotonin was positively associated with microbial diversity (ρ = 0.63-0.70). In conclusion, IQ supplementation promotes a bacteria-dominant and metabolically active microbiome, reduces inflammation and intestinal permeability, and improves neuroendocrine balance, collectively enhancing gut health and growth performance in broiler chickens.

Bacteriome↗

PubMed2025

Intratumoral fungus Neurospora crassa is associated with worsened prognosis in ovarian cancer via modulation of extracellular matrix.

Landmark studies on intratumoral fungi (ITF) have raised concerns due to irreproducible results and data-analysis errors. We aimed to determine whether ITF exist in ovarian cancer (OvCa) and, if so, whether they play a role in disease biology. Formalin-fixed, paraffin-embedded OvCa samples and multiple controls underwent operational decontamination, qPCR, internal transcribed spacer sequencing, and post-hoc data decontamination. We also leveraged updated fungal reads from The Cancer Genome Atlas generated by the TCMbio group, which addressed human-read contamination and artificial inflation, to validate findings and assess prognostic associations. A murine syngeneic model established using mouse ovarian cancer cell line (OVHM) with intratumoral Neurospora crassa injection was established. Transcriptomic and metabolomic analyses were performed to explore mechanisms. Tumor-containing blocks harbored significantly higher fungal loads than environmental controls but had loads comparable to paraffin controls. Applying a two-pass decontamination filter reduced raw sequence features from 9289 amplicon sequence variants (ASVs) to 659 ASVs. We focused on high-abundance features present in human tissues but absent from xenografts and paraffin controls and identified one candidate, N. crassa, associated with unfavorable prognosis in OvCa. Integrating human and murine data, we found Neurospora correlated with eosinophils, whereas N. crassa itself was not immune-related. Neurospora crassa promoted OvCa progression with downregulation of integrin-linked kinase and decreased extracellular matrix-receptor interaction. Most ITF signals are likely contaminants. We identified N. crassa as associated with unfavorable prognosis in OvCa, potentially via modulation of the extracellular matrix.

Neurospora crassa↗

PubMed2025

The role of stochasticity in fungal community assembly: explaining apparent stochasticity with field experiments.

Stochasticity is a main process in community assembly. However, experimental studies rarely target stochasticity in natural communities, and hence experimental validation of stochasticity estimates in observational studies is lacking. Here, we combine experimental and observational data to unravel the role of stochasticity in the assembly of wood-inhabiting fungi. We carried out a replicated field experiment where the natural colonization of a focal fungal species was simulated through inoculation, and the local fungal communities were monitored through DNA metabarcoding before and after the inoculations. The amount of stochasticity in fungal colonization was less pronounced than expected from the amount of unpredictability in observational data, suggesting that stochasticity may play a smaller role in fungal occurrence than previously anticipated, or that it may be a stronger influence in the dispersal and establishment phases than in colonization per se. Stochasticity was more prominent in the initial phase of community succession, with the earliest successional stage involving a higher level of stochasticity than the later stage after 2 years. We conclude that experimentally measuring the role of stochasticity in community assembly is feasible for species-rich communities under natural conditions and highlight the importance of experimentally testing the accuracy of stochasticity estimates based on observational data.

Stochastic Processes↗