Fungal Communities Research Articles

Distribution patterns of fungal community diversity in the dominant tree species Dacrydium pectinatum and Vatica mangachapoi in tropical rainforests.

Understanding the assembly of microbial communities across different compartments is a prerequisite for harnessing them to enhance plant growth. Our findings reveal significant differences in fungal community structures between the root and leaf compartments. Compared to the roots, the leaf compartments exhibited higher α-diversity. While soil pH mainly influenced fungal communities in the roots, the primary drivers for the leaves were rainfall and temperature. The dispersal-limited processes of fungal communities in the roots were greater than those in the leaves, primarily influenced by mycorrhizal fungi. These findings demonstrate compartment-specific plant-microbe interactions and environmental responses, offering actionable insights for conserving tropical tree species through habitat optimization (e.g., soil pH management) and dispersal corridor preservation. This compartment-aware perspective enhances our ability to leverage microbial functions to improve the resilience of endangered trees in the face of climate change.

Enriched Flavonoid Compounds Confer Enhanced Resistance to Fusarium-Induced Root Rot in Oil Tea Plants.

Root rot in Camellia oleifera complicates the development of targeted control measures owing to its complex aetiology. Although breeding resistant varieties of C. oleifera presents a promising solution, research into cultivation strategies and potential resistance mechanisms against root rot remains limited. In this study, we investigated six cultivars of C. oleifera that exhibit varying levels of resistance to root rot. We conducted transcriptome analysis, measurements of soil physicochemical properties and an analysis of the fungal microbiome to explore the relationship between Fusarium-induced root rot and flavonoid compounds in the rhizosphere. The resistant cultivar CL18 demonstrated superior performance concerning root rot incidence, root health status and the expression levels of genes associated with flavonoid biosynthesis in this study. Significant differences were observed in the composition and diversity of rhizosphere fungal communities among the various cultivars of C. oleifera. The abundance of Fusarium in the rhizosphere soil of CL18 was low, and a negative correlation was identified between the flavonoid content in the soil and the abundance of Fusarium. Our study uncovers the role of flavonoids in the resistance of C. oleifera to root rot, thereby offering new strategies for disease management and the breeding of resistant cultivars.

Genomic exploration of climate-driven evolution and evolutionary convergence in forest pathogens.

Climate significantly influences the distribution, composition, and diversity of fungal communities, impacting the growth, spread, and virulence of fungal forest pathogens. This study employs advanced landscape genomics methods to explore the genomic adaptations of three major fungal pathogens: those responsible for Dutch elm disease, dothistroma needle blight, and Swiss needle cast. Our findings reveal that precipitation and humidity are primary drivers of adaptation in these species. We use these insights to forecast potential adaptations under future climate scenarios (genomic offset) and identify specific genes and pathways associated with climate responses in each pathogen. Notably, we detect a convergence in moisture adaptation across these distantly related species, particularly in genes related to the cytoskeleton and transporters. This study enhances our understanding of fungal pathogen evolution in response to climate change, offering crucial insights for forest disease management.

Distinct Assembly Patterns of Soil Bacterial and Fungal Communities along Altitudinal Gradients in the Loess Plateau's Highest Mountain

A critical issue in microbial ecology is quantifying the relative contributions of deterministic and stochastic processes to microbial community assembly, and predicting ecosystem function by understanding the ecological processes of community composition is an integral part. However, the mechanisms driving microbial community assembly along altitudinal gradients in mountain ecosystems remain largely unexplored. Here, we used high-throughput sequencing to examine the structural characteristics and diversity maintenance mechanisms of soil bacterial and fungal communities along an altitudinal gradient (2632–3661 m) in Mahan Mountain, the highest peak of the Loess Plateau. Proteobacteria, Acidobacteriota and Actinobacteriota dominated the bacterial communities, while Ascomycota, Basidiomycota and Mortierellomycota were the predominant fungal groups. Although elevation did not significantly affect bacterial and fungal alpha diversity, notable shifts in community structure were observed along the altitudinal gradients. Bacterial communities were predominantly shaped by deterministic processes, leading to pronounced structural and compositional differentiation across altitudes. In contrast, fungal community assembly was primarily determined by a combination of deterministic and stochastic processes, leading to small pronounced structural divergence. The interplay of topography, climate, and soil conditions influenced the altitudinal distribution and community structure of soil bacteria in this mountain ecosystem.

Legacy of Repeated Cultivation Drives Cyclical Microbial Community Development in a Tropical Oxisol Soil

Agricultural practices and the crop being actively cultivated are some of the most important contributors to soil microbial community assembly processes in agroecosystems. However, it is not well-understood how the cultivation of diverse crop species can directionally shift complex soil microbial communities, especially under continuous monoculture systems. Here, we conducted a field experiment to assess how three crop species (Lactuca sativa, Brassica juncea, and Zea mays) may shift soil microbial (bacteria/archaea and fungi) communities when planted in a monoculture and repeatedly grown for three cycles in a tropical Oxisol soil. We found that while plant species made limited contributions to microbial community differentiation, repeated cultivation was a strong driver of community development over time. The bacterial/archaeal communities exhibited a cyclical community development pattern, initially with strong differentiation that attenuated to a steady state at the end of the three cycles. In contrast, fungal communities generally developed more linearly and may have only started to stabilize after three cropping cycles. These developments may speak to the stronger legacy effects on fungal communities. Together, these results highlight the differences between how bacteria/archaea and fungal communities develop, especially in tropical, underdeveloped, intensively degraded, or marginal soils.

Pneumocystis jirovecii is a potential pivotal ecological driver contributing to shifts in microbial equilibrium during the early-life lower airway microbiome assembly

Early life gut microbiota is being increasingly recognized as a major contributor to short and/or long-term human health and diseases. However, little is known about these early-life events in the human microbiome of the lower respiratory tract. This study aims to investigate fungal and bacterial colonization in the lower airways over the first year of life by analyzing lung tissue from autopsied infants. The fungal and bacterial communities of lung tissue samples from 53 autopsied infants were characterized by Next-Generation Sequencing (NGS), based on universal PCR amplification of the ITS region and the 16S rRNA gene, respectively. Our study highlights a high degree of inter-individual variability in both fungal and bacterial communities inhabiting the infant lung. The lower respiratory tract microbiota is mainly composed of transient microorganisms that likely travel from the upper respiratory tract and do not establish permanent residence. However, it could also contain some genera identified as long-term inhabitants of the lung, which could potentially play a role in lung physiology or disease. At 3–4 months of age, important dynamic changes to the microbial community were observed, which might correspond to a transitional time period in the maturation of the lung microbiome. This timeframe represents a susceptibility period for the colonization of pathogens such as Pneumocystis. The asymptomatic colonization of Pneumocystis was associated with changes in the fungal and bacterial communities. These findings suggest that the period of 2–4 months of age is a “critical window” early in life. Pneumocystis jirovecii could be a potential pivotal ecological driver contributing to shifts in microbial equilibrium during the early-life lower airway microbiome assembly, and to the future health of children.

Characterizing the Soil Microbial Community Associated with the Fungal Pathogen Coccidioides immitis

Coccidioidomycosis is a fungal disease affecting humans and other mammals caused by environmental pathogens of the genus Coccidioides. Human exposure to the pathogen occurs via inhalation of spores aerosolized from soil. Thus, understanding the ecological factors that shape the distribution of Coccidioides in soils is important for minimizing the risk of human exposure, though this task remains challenging due to the pathogen’s highly variable spatial distribution. Here, we examined the associations between the soil microbial community and Coccidioides immitis’ presence within the Carrizo Plain National Monument, a minimally disturbed grassland ecosystem, and the site of a longitudinal study examining the effects of rodents and their burrows on C. immitis’ presence in soils. Using internal transcribed spacer 2 (ITS2) and 16S amplicon sequencing to characterize the soil fungal and bacterial communities, we found over 30 fungal species, including several other members of the Onygenales order, that co-occurred with C. immitis more frequently than would be expected by chance. Coccidioides-positive samples were significantly higher in fungal and bacterial diversity than negative samples, an association partly driven by higher Coccidioides presence within rodent burrows compared to surface soils. Soil source (i.e., rodent burrow versus surface soil) explained the largest amount of variation in bacterial and fungal community diversity and composition, with soils collected from rodent burrows having higher fungal and bacterial diversity than those collected from adjacent surface soils. While prior evidence is mixed regarding the relationship between the presence of Coccidioides and microbial diversity, we find that favorable microhabitats, such as rodent burrows, lead to a positive association between soil microbial diversity and Coccidioides presence, particularly in otherwise resource-limited natural environments.

Inoculation of Arbuscular Mycorrhizal Fungi Alters Fungal Communities in Organic Tomato Cultivation

Inoculation of Arbuscular Mycorrhizal Fungi Alters Fungal Communities in Organic Tomato Cultivation

Beyond seasonal and host factors: ecosystem dynamics drive palm-associated root fungal communities at a local scale

Abstract Background and Aims The increase of extreme weather events due to climate change may alter ecosystem dynamics. In the tropics, little is known about how ecosystems and species will respond to droughts or floods. Identifying the most important biotic and abiotic factors in ecosystems at the local level is key to developing better forest management practices and understanding the effects of climate change on the fungal community. Methods We conducted a random sampling of adult individuals from several palm species across three adjacent ecosystems with different hydrological conditions, during rainy and dry seasons. Using next-generation sequencing, we identified fungal communities and determined the influence of soil physicochemical properties, as well as host and seasonal variables, on the relative abundance of the root- and rhizosphere-associated fungal communities. Results The composition of the fungal communities was similar between the seasonally flooded forest and the terra-firme forest, while the palm swamp diverged due to differences in soil physicochemical properties. Seasonal analyses revealed significant differences in the relative abundance of several taxa, mainly associated with the seasonally flooded forest. However, no influence of palm species on fungal abundance was detected at any taxonomic level. Conclusion This study highlights the importance of studying ecosystems at the local scale and considering ecosystem dynamics into the study of fungal communities and other microorganisms. Such an approach is crucial for improving predictions under climate change scenarios and understanding the consequences of altering these dynamics in vulnerable, often understudied ecosystems.

A Helping Hand: Fungi, as Well as Bacteria, Support Ecophysiological Descriptors to Depict the Posidonia oceanica Conservation Status

The crucial role of plant–microbe interactions in seagrass growth and overall fitness is widely recognized and known to influence plant response to stress. Human-induced changes in coastal ecosystems necessitate efficient descriptors for seagrass monitoring. Recently, for Posidonia oceanica meadows, an integrative approach combining ecophysiological descriptors with bacterial communities has been successfully applied. Conversely, the mycobiota remains largely unexplored and fungal communities cannot be included yet as a putative descriptor. This study aims to evaluate the ecological status of two P. oceanica meadows in the Akrotiri Bay (Cyprus), located under different geomorphological features (depth and seabed type) and degrees of human pressure (port proximity vs. Marine Protected Area). A set of descriptors including morphometry, biochemical markers and bacterial communities collected in 2023 are compared with those collected, at the same sites, in 2017. Furthermore, the investigation of the leaf-associated microbial community included the underrepresented fungal communities, in addition to the bacterial ones, to evaluate their usefulness in evaluating the plant conservation status. Results indicated a good P. oceanica conservation status at both sites, showing an amelioration in the Limassol port meadow from 2017. In 2023, the biometrical/biochemical descriptors were found comparable across sites as the bacterial communities, differing from 2017 results. Noteworthy, fungal communities exhibited significant differences between sites, with a clear reduction, in the Limassol port meadow, of the dominant Posidoniomyces atricolor which is known as a specific colonizer of P. oceanica roots. These results confirm the strong relationship between P. atricolor and P. oceanica host, and suggest its sensitivity to environmental changes, able to keep track of ecological shifts.

Host Developmental Stage and Vegetation Type Govern Root EcM Fungal Assembly in Temperate Forests

Ectomycorrhizal (EcM) fungi are critical mediators of forest succession, yet the relative contributions of stochastic (neutral) and deterministic (niche-based) processes in shaping their communities are still poorly understood. We investigated the assembly processes in root EcM fungal communities across juvenile and adult coniferous (Abies nephrolepis, Picea jezoensis, and Pinus koraiensis) and broadleaf (Acer mono, Betula platyphylla, and Quercus mongolica) tree species in northeastern China. Employing neutral theory modeling, alpha and beta diversity metrics, and a random forest analysis, we identified patterns of EcM fungal community assembly and the specific taxa associated with developmental stages of various hosts. Neutral processes contributed to the variation in fungal communities, with adult trees showing a higher explanation power (more than 33% of variation) compared to juvenile trees (less than 7% of variation), reflecting a successional shift in assembly mechanisms. Dispersal dynamics was pronounced in juveniles but diminished with host age. Additionally, alpha diversity increased with host age and was slightly moderated by host identity, while beta diversity reflected stronger effects of host age (PERMANOVA R2 = 0.057) than host identity (R2 = 0.033). Host age and identity further structured communities, with distinct taxa varying between juvenile vs. adult, and coniferous vs. broadleaf hosts. Our results demonstrate that host maturity drives a transition from deterministic to stochastic assembly, modulated by tree species identity, improving our understanding of plant–fungal dynamics during forest succession.

Multi-kingdom gut microbiota dysbiosis is associated with the development of pulmonary arterial hypertension.

Multi-kingdom gut microbiota dysbiosis is associated with the development of pulmonary arterial hypertension.

Long-term effects of grazing exclosure and plateau pika disturbance on soil biochemistry in alpine meadows.

Grazing exclusion is an effective measure of restoring patchily degraded alpine meadows, but a controversy still surrounds it as whether it will have a continuously positive ecological impact on degraded alpine meadows as the duration of exclosure prolongs. Under grazing exclosure, plateau pika disturbance can also alter soil characteristics. To address the uncertaint effects of long-term exclosure and plateau pika disturbance on soil biochemistry in alpine meadows, this study compared soil properties in a 10-year enclosed meadow encompassing both pika-active (FP) and pika-free (FN) zones to those of a regularly grazed area (CK). The results indicated that the light fraction organic carbon content and microbial biomass carbon content in FN were significantly higher than those in CK, but the dissolved organic carbon content and leucine aminopeptidase activity were significantly lower than those in CK. The SOC fractions and soil enzyme activities in FP were significantly lower than those in CK and FN (P < 0.05). Long-term exclosure and plateau pika disturbance significantly altered the composition of the soil bacterial and fungal communities, and the soil bacterial diversity in FN was significantly lower than that in CK and FP. Changes in bacterial diversity were significantly correlated with SOC fractions. Therefore, long-term exclosure on SOC fractions, enzyme activities, and microbial diversity in degraded alpine meadows brings out minimal positive effects, and plateau pika disturbance is not conducive to maintaining ecosystem balance in the alpine meadow.

Fungi in Mangrove: Ecological Importance, Climate Change Impacts, and the Role in Environmental Remediation

Mangroves are coastal ecosystems of great ecological importance, located in transition areas between marine and terrestrial environments, predominantly found in tropical and subtropical regions. In Brazil, these biomes are present along the entire coastline, playing essential environmental roles such as sediment stabilization, coastal erosion control, and the filtration of nutrients and pollutants. The unique structure of the roots of some mangrove tree species facilitates sediment deposition and organic matter retention, creating favorable conditions for the development of rich and specialized biodiversity, including fungi, bacteria, and other life forms. Furthermore, mangroves serve as important nurseries for many species of fish, crustaceans, and birds, being fundamental to maintaining trophic networks and the local economy, which relies on fishing resources. However, these ecosystems have been significantly impacted by anthropogenic pressures and global climate change. In recent years, the increase in average global temperatures, rising sea levels, changes in precipitation patterns, and ocean acidification have contributed to the degradation of mangroves. Additionally, human activities such as domestic sewage discharge, pollution from organic and inorganic compounds, and alterations in hydrological regimes have accelerated this degradation process. These factors directly affect the biodiversity present in mangrove sediments, including the fungal community, which plays a crucial role in the decomposition of organic matter and nutrient cycling. Fungi, which include various taxonomic groups such as Ascomycota, Basidiomycota, and Zygomycota, are sensitive to changes in environmental conditions, making the study of their diversity and distribution relevant for understanding the impacts of climate change and pollution. In particular, fungal bioremediation has gained significant attention as an effective strategy for mitigating pollution in these sensitive ecosystems. Fungi possess unique abilities to degrade or detoxify environmental pollutants, including heavy metals and organic contaminants, through processes such as biosorption, bioaccumulation, and enzymatic degradation. This bioremediation potential can help restore the ecological balance of mangrove ecosystems and protect their biodiversity from the adverse effects of pollution. Recent studies suggest that changes in temperature, salinity, and the chemical composition of sediments can drastically modify microbial and fungal communities in these environments, influencing the resilience of the ecosystem. The objective of this narrative synthesis is to point out the diversity of fungi present in mangrove sediments, emphasizing how the impacts of climate change and anthropogenic pollution influence the composition and functionality of these communities. By exploring these interactions, including the role of fungal bioremediation in ecosystem restoration, it is expected that this study would provide a solid scientific basis for the conservation of mangroves and the development of strategies to mitigate the environmental impacts on these valuable ecosystems.

Multi-omics analyses reveal fecal microbial community and metabolic alterations in finishing cattle fed probiotics-fermented distiller's grains diets.

Probiotics-fermented distiller's grains (FDG) are potential feed sources for livestock. Here, we investigated the effects of partially replacing concentrates with FDG on fecal bacterial and fungal community structure and metabolic profiles in finishing cattle. The results reveal that feeding FDG-based diets alters intestinal metabolite profiles and up-regulates bile secretion pathways through the regulation of relative abundance of certain fecal genera. These findings provide some new insights into clarifying the role and potential mechanisms of FDG diets and also offer a scientific basis for the development of FDG into functional feed resources.

Marine Mycobiomes Colonize Mediterranean Sponge Hosts in a Random Fashion

Marine sponges are widespread, sessile, filter-feeding animals, known for living in association with complex prokaryotic communities structured by host species. Though marine fungi are ubiquitous across marine environments, little is known about sponge-associated fungal communities (mycobiome). Indeed, aside from a few studies based on the isolation of fungal strains for biotechnological purposes, little information is available to understand the diversity and structure of sponge mycobiome. Here, a metabarcoding approach based on the ITS1 marker was applied to examine the structure and composition of fungal communities associated with four Mediterranean sponges. The species: Petrosia ficiformis, Chondrosia reniformis, Crambe crambe, and Chondrilla nucula were analyzed along with the surrounding seawater, revealing Aspergillus (1–56%), Cladosporium (1–75%), Malassezia (1–38.5%), and Pennicillium (1.5–36%) as the most represented fungal genera. Our data showed high intra-specific variability and no clear core mycobiome within each of the sponge species host, suggesting stochastic and perhaps transient community membership. This study sheds light on one of the most abundant yet least understood components of the marine ecosystem. Unraveling the dynamics of fungal interactions within sponge holobionts is essential to advance our understanding of their ecological roles and functions. By addressing the enigmatic nature of sponge-associated fungi, this research opens new avenues for exploring their contributions to marine ecosystems and resolving the many unanswered questions in this field.

Effects of the fungicide penconazole on the leaf litter associated aquatic mycobiome in artificial stream channel and flask experiments.

Effects of the fungicide penconazole on the leaf litter associated aquatic mycobiome in artificial stream channel and flask experiments.

Relationships between rumen methanogens and fungal communities and their response to changes in alfalfa forms and starch in sheep diets

Alfalfa forms and rumen degradable starch (RDS) levels in diets can profoundly affect growth performance and rumen fermentation patterns, this influence may result in variations in rumen microbiota. However, the effects of RDS levels on methanogenic and fungal communities in alfalfa hay (AH) or alfalfa silage (AS) diets, and the interaction between methanogens and fungi with growth performance and rumen fermentation patterns, remain unknown. In this study, a 2 × 2 factorial design resulted in four diets: two alfalfa forms (AH and AS) and two RDS levels (LR: 14.85% DM RDS; and HR: 20.21% DM RDS). We used 32 female Suffolk sheep for the experiment. On day 75 (including a 15-day transition period and a 60-day trial period), rumen content was collected after slaughter to examine the ruminal methanogens and fungi. The AHHR diet reduced the methanogen Chao 1 index compared to the AS diets (P &amp;lt; 0.05), and the Shannon index was lower than in the ASLR diet (P &amp;lt; 0.05). The fungi Chao 1 index was higher in the AH diets than in the ASHR diet (P &amp;lt; 0.05), and the fungi Shannon index was higher in the LR diets than in the HR diets (P &amp;lt; 0.05). The relative abundance of Aspergillus in the AHLR diet was significantly higher than in the AS diets (P &amp;lt; 0.01), and the relative abundance of Occultifur and Meyerozyma were decreased in the AH diets than in the AS diets (P &amp;lt; 0.05). The LEfSe analysis showed that Methanobrevibacter_sp_YE315 and Methanobrevibacter_sp_AbM4 were enriched in the ASLR diet, while Methanobrevibacter_millerae was enriched in the ASHR diet. For the fungal biomarkers, the AHLR diet included Aspergillus, Metschnikowia, and unclassified_f:Stachybotryaceae; the AHHR diet included stachybotrys, Stemphylium, and Cystobasidium; the ASLR diet included unclassified_k:Fungi, Trichothecium, and Psathyrella; and the ASHR diet included Alfaria. The correlation analysis results showed the relative abundance of Methanobrevibacter, Methanoculleus, Penicillium, Cladosporium, and Exophiala and the concentrations of isobutyrate and isovalerate, which may provide deeper insights into the previously observed differences.

Changes in the community composition and function of the rhizosphere microbiome in tobacco plants with Fusarium root rot

IntroductionTobacco root rot caused by Fusarium spp. is a soil-borne vascular disease that severely affects tobacco production worldwide. To date, the community composition and functional shifts of the rhizosphere microbiome in tobacco plants infected with Fusarium root rot remain poorly understood.MethodsIn this study, we analyzed the differences in the compositions and functions of the bacterial and fungal communities in the rhizosphere and root endosphere of healthy tobacco plants and tobacco with Fusarium root rot using amplicon sequencing and metagenomic sequencing.Results and discussionOur results showed that Fusarium root rot disrupted the stability of bacteria–fungi interkingdom networks and reduced the network complexity. Compared to healthy tobacco plants, the Chao1 index of bacterial communities in the rhizosphere soil of diseased plants increased by 4.09% (P &amp;lt; 0.05), while the Shannon and Chao1 indices of fungal communities decreased by 13.87 and 8.17%, respectively (P &amp;lt; 0.05). In the root tissues of diseased plants, the Shannon index of bacterial and fungal communities decreased by 17.71–27.05% (P &amp;lt; 0.05). Additionally, we observed that the rhizosphere microbial community of diseased tobacco plants shifted toward a pathological combination, with a significant increase in the relative abundance of harmful microbes such as Alternaria, Fusarium, and Filobasidium (89.46–921.29%) and a notable decrease in the relative abundance of beneficial microbes such as Lysobacter, Streptomyces, Mortierella, and Penicillium (48.48–81.56%). Metagenomic analysis further revealed that the tobacco rhizosphere microbial communities of diseased plants played a significant role in basic biological metabolism, energy production and conversion, signal transduction, and N metabolism, but their functions involved in C metabolism were significantly weakened. Our findings provide new insights into the changes in and interactions within the rhizosphere and root endosphere microbiomes of tobacco plants under the stress of Fusarium soil-borne fungal pathogens, while laying the foundation for the exploration, development, and utilization of beneficial microbial resources in healthy tobacco plants in the future.

Exploring Fungi Within the Human Gut Microbiota: Obstacles, Innovations, Therapeutic Applications and Prospects Ahead

Review Exploring Fungi Within the Human Gut Microbiota: Obstacles, Innovations, Therapeutic Applications and Prospects Ahead Peng Xue 1,†, Chao Luo 2,†, Jiashu Li 3, Liang Yang 3,* and Yuanyuan Ma 1,* 1 Nantong Key Laboratory of Environmental Toxicology, Department of Occupational Medicine and Environmental Toxicology, School of Public Health, Nantong University, Nantong 226019, China 2 The People’s Hospital of Rugao, Affiliated Rugao Hospital of Xinglin College, Nantong University, Nantong 226500, China 3 School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China * Correspondence: yangl@sustech.edu.cn (L.Y.); myycsd@ntu.edu.cn (Y.M.) Received: 15 September 2024; Revised: 23 October 2024; Accepted: 23 October 2024; Published: 9 April 2025 Abstract: Fungi in the human gut microbiota participate in the maintenance of health and regulation of physiological processes. This review examines the complex role of gut fungi, highlighting challenges such as diverse fungal populations, cultivation difficulties, and knowledge gaps in their functional roles. Recent advancements in metagenomics and metabolomics have enabled innovative investigations into fungal communities, revealing their influence on host metabolism and immune responses. Future research should address the existing knowledge gaps and explore the therapeutic applications of gut fungi. Interdisciplinary collaborations and new methodologies are proposed to enhance the current understanding of fungi-host interactions, ultimately improving health outcomes and guide the development of novel treatment strategies. This review emphasizes the need to integrate fungal research into microbiome studies to provide a comprehensive understanding of gut health.