Search Results (268)

Caries is the most prevalent chronic disease affecting oral health in preschool children. In this 12-month prospective cohort study of 3–4-year-olds, we investigated the community-level bacterial–fungal interkingdom interactome and its role in cariogenic microenvironments, using 16S rRNA gene (bacterial) sequencing and ITS2 gene (fungal) sequencing of unstimulated saliva. Longitudinal analysis identified 19 key bacterial and fungal species that were associated with both caries progression and clinical features. Salivary bacteria Desulfovibrio, Bacteroides heparinolyticus, Alloprevotella, Anaerobiospirillum, and fungus Candida tropicalis not only showed altered abundances during caries development but also correlated with severity of caries, establishing diagnostic microbial signatures for caries prediction. The salivary mycobiome exhibited highly active and complex intra-network interactions in the caries-active state, suggesting that fungal networks may drive the broader community-wide microbiota interaction network in the caries state. Metabolic profiling further revealed distinct pathway shifts before and after caries onset. The findings demonstrate that caries progression follows ecological succession governed by cross-domain interactions. This study highlighted the fungal network’s important role in driving dysbiosis, advancing the current understanding of early childhood caries beyond bacterial-centric models, and also highlighted fungi not only as modulators but as active contributors to cariogenesis, which could guide future antimicrobial strategies. Full article

Background: Lung cancer is the leading cause of cancer-related mortality globally, with lung adenocarcinoma (LUAD) as the most common subtype. Dysbiotic intratumoral mycobiomes drive LUAD pathogenesis, and Aspergillus sydowii (A. sydowii) acts as a key oncogenic fungal species. Ginseng polysaccharides (GPs), bioactive phytochemicals with immunomodulatory and oncostatic properties, counteract fungal infections and restore immunosurveillance in LUAD. Methods: Subcutaneous and orthotopic LUAD murine models were established by implanting Lewis lung carcinoma (LLC) cells. Subcutaneous tumors were infected intratumorally and orthotopic models via nasal inoculation. GPs (200 mg/kg/day) were orally administered to evaluate tumor growth. Metagenomic and targeted bile acid metabolomic profiling of fecal and tumor tissues was performed, with Spearman correlations analyzed using R packages. Results: GPs significantly inhibited A. sydowii-induced tumor growth in both models. In subcutaneous tumors; GPs reduced volume (p < 0.05) and weight vs. infected controls. In orthotopic models, GPs decreased pathological nodules and lung weight, with micro-CT/H&E confirming attenuated hyperplasia. Metagenomics showed GPs restored gut homeostasis by enriching Lactobacillus/Muribaculum intestinale and suppressing pro-inflammatory Alistipes. Targeted metabolomics revealed reduced β-Hyodeoxycholic Acid (3β-HDCA), Chenodeoxycholic acid 24-acyl-b-D-glucuronide (CDCA-24G) and 3β-hydroxychol-5-en-24-oic acid (5-isoLCA) after GP treatment. Network analysis confirmed significant microbe–bile acid interactions. Conclusions: GPs exert antitumor effects against A. sydowii-induced LUAD by modulating gut microbiota and bile acid metabolism. This identifies GPs as a promising therapy for mycobiome-influenced cancers, with dual targeting of fungal infection and metabolic reprogramming. Full article

Background and Objective: The oral microbiome plays an important role in oral health and disease, including periodontitis, which affects about 40% of the adult population in the United States. Bacterial pathogens have been well studied and documented in their relationship with periodontitis; however, the role of fungi in periodontitis is still unclear. The purpose of this study is to determine the relationship of specific fungal species with periodontal pathogenic bacteria in healthy, mild periodontitis, and severe periodontitis patients. Methods: In this study, human participants were recruited, and saliva samples were collected. Twelve participants representing periodontal health (n = 2), mild periodontitis (n = 3), and severe periodontitis (n = 7) were included. Salivary samples were sequenced for analysis of their mycobiome (ITS sequencing) and microbiome (16s RNA sequencing). Results: A total of 375 species of bacteria and 39 species of fungi were identified among all samples. Clustering was observed for bacteria in healthy and mild periodontitis, but more variability was observed in the severe periodontal disease group. Variability was observed for fungi among all samples and groups. Red complex bacteria were negatively correlated with Candida species for the disease groups, although the correlation was not statistically significant. A significant correlation was observed between red-complex bacteria in the severe periodontal disease group. Additionally, a significant correlation was observed among Candida species in all groups. Conclusions: This pilot study simultaneously processed saliva samples for microbiome and mycobiome sequencing and found a trend towards negative correlation between Candida species and red complex bacteria. Full article

Patients with cystic fibrosis (CF) are frequently exposed to antibiotic treatments, which can alter the fungal communities (mycobiome) across their mucosal sites. This pilot study investigated the impact of antibiotic exposure on the mycobiome by analyzing fungal community dynamics in the upper respiratory- (nasal lavage) and gastrointestinal- (stool samples) tracts of 12 patients with CF following (a) long-term antibiotic treatment over a three-year period and (b) short-term antibiotic therapy during acute pulmonary exacerbations. Mycobiome profiles of the samples obtained from 38 healthy individuals were also analyzed and used for comparison purposes. The ITS1 region of the fungal rRNA gene cluster was sequenced to characterize and quantify the fungal community composition in both cohorts. Compared to healthy controls, samples from the patients with CF who had undergone long-term antibiotic treatment revealed a significantly increased fungal biomass in both sino-nasal and stool samples. Moreover, diversity metrics revealed significant differences in nasal lavage samples, whereas the stool samples showed no significant variation. Candida spp. was significantly enriched in both nasal and stool samples from CF patients. Further analyses demonstrated a strong positive correlation between the relative abundance of Candida spp. and the cumulative antibiotic intake over the three-year period in sino-nasal samples, but not in stool samples. Acute antibiotic treatment during a pulmonary exacerbation episode also led to a marked increase in the abundance of Candida spp. in sino-nasal samples. These findings highlight the increased sensitivity of the sino-nasal mycobiome to both chronic and acute antibiotic exposure in CF patients, as characterized by a site-specific fungal overgrowth, particularly of Candida spp. Full article

The genus Aspergillus, widely distributed across natural and urban environments, may cause allergies and opportunistic infections such as chronic or invasive pulmonary aspergillosis. Its high pathogenic potential for immunocompromised patients, together with the alarming increase of azole resistance reported in clinical and environmental isolates, claims urgent actions to assess and control the Aspergillus community in hospital environments. To contribute to that, here, we combine a large environmental survey covering numerous air and surface samples from different zones of three hospitals in Spain, with an integrated approach including general and selective culture- and eDNA-based analyses. Despite the high prevalence of Aspergillus observed, present in almost all indoor zones (mostly in air but also on surfaces) of the three hospitals, its relative abundance in the whole fungal community was limited and dependent on the used methods, with median values ranging from 1.4% (eDNA data) and 6.8% (cultivation at 28 °C) to 28.3% (cultivation at 37 °C). Remarkably, the most protected zones (intensive care units) showed the highest proportion of Aspergillus eDNA sequences. A total of 32 species belonging to 10 Aspergillus sections were molecularly identified, including well-known causal agents of invasive pulmonary infections such as A. fumigatus, A. flavus, A. terreus, A. niger, A. oryzae, A. sydowii, and A. tubingensis. This highlights the importance of such environmental assessments for monitoring and controlling the fungal burden in hospitals. Full article

Rosacea is a chronic inflammatory skin disorder with multifactorial pathogenesis involving immune dysregulation and microbial alterations. This study compared the mycobiomes of skin, blood, and stool samples in rosacea patients and healthy controls to assess fungal diversity, abundance, and possible translocation, as well as associations with bacterial microbiomes. Internal transcribed spacer (ITS) region sequencing was performed on samples from 14 rosacea patients and 8 controls. While distinct fungal community compositions were observed across sample types, no significant differences in fungal diversity or genus abundance were found between the patient and control groups in any compartment. Malassezia dominated the skin mycobiome, while stool samples showed higher abundances of Candida and Saccharomyces, which were inversely correlated. Patients with high skin and blood Malassezia also exhibited increased Cutibacterium abundance, suggesting a potential role in impaired skin barrier integrity. Stool samples with elevated Saccharomyces correlated with higher levels of anti-inflammatory bacteria Prevotella and Agathobacter, whereas Candida dominance showed the opposite. These findings suggest that fungal dysbiosis, in the interplay with bacterial communities, may influence rosacea pathogenesis through the gut–skin axis. This work underscores the significance of integrated microbiome research across multiple biological compartments in order to enhance our understanding and potential targeting of microbial factors in rosacea. Full article

Microbiome studies report a decrease in diversity associated with active infections. Under the endozoan hypothesis, Coccidioides can inhabit a host without causing disease. In this study, we describe and compare the lung mycobiome of Coccidioides-positive and -negative samples obtained from wildlife. If Coccidioides is not causing infection, we predict there will be no differences in the mycobiome between positive and negative samples. Lung samples were obtained from mammals previously trapped in Tucson, Arizona, USA (n = 26), and Mesa, Arizona, USA (n = 14). Samples were screened for Coccidioides with CocciDx, and mycobiome was characterized through Illumina-based amplicon sequencing of the internal transcribed spacer 2 (ITS2). We compared alpha and beta diversity of the mycobiome to assess the effects of Coccidioides’ presence and host taxonomy. A greater number of reads were captured from Tucson samples (114,706.4 ± 57,945.8) than from Mesa (384.9 ± 953.5); however, Mesa (16.8 ± 8.8) and Tucson (12 ± 7.8) had a similar number of fungal genera per sample. CocciDx detected Coccidioides in more samples than the ITS2 amplicon sequencing. All samples from Mesa and five from Tucson tested positive for Coccidioides. Therefore, Mesa samples were excluded from statistical analysis. No difference in alpha and beta diversity was associated with Coccidioides presence, which is consistent with the endozoan hypothesis. Host taxonomy had a significant effect on beta diversity. This effect is likely driven by host behavioral and physiological differences. Full article

Hurricanes and flooding events substantially elevate indoor fungal spore levels, which have been associated with increased risks of developing childhood asthma and other adverse respiratory outcomes. Although environmental fungal compositions following major hurricanes have been well characterized, the fungal communities within the nasal cavity (i.e., the nasal mycobiome) of exposed individuals remain unexplored. We collected nasal swab samples from infants following Hurricane Maria in San Juan, Puerto Rico, during two periods (March to August 2018 and February to September 2019). We processed a total of 58 samples (26 from the first year and 32 from the second year post-Hurricane Maria) and performed internally transcribed spacer (ITS) rRNA gene sequencing to characterize and compare the infant nasal mycobiome between the two groups. Although alpha-diversity did not differ significantly, beta-diversity analyses revealed significantly different fungal compositions between the two groups (p <0.01). Infants exposed during the first year post-Hurricane Maria had significantly higher abundances of Alternaria, Eutypella, Schizophyllum, and Auricularia, compared to infants from the second year. Alternaria was also more prevalent in the first-year than in the second-year infants (42% vs. 9%, p = 0.01). Our study provides evidence linking early-life hurricane exposures to elevated risks of developing childhood asthma. Full article

The fungal component of microbiota, known as the mycobiome, inhabits different body niches such as the skin and the gastrointestinal, respiratory, and genitourinary tracts. Much information has been gained on the bacterial component of the human microbiota, but the mycobiome has remained somewhat elusive due to its sparsity, variability, susceptibility to environmental factors (e.g., early life colonization, diet, or pharmacological treatments), and the specific in vitro culture challenges. Functionally, the mycobiome is known to play a role in modulating innate and adaptive immune responses by interacting with microorganisms and immune cells. The latter elicits anti-fungal responses via the recognition of specific fungal cell-wall components (e.g., β-1,3-glucan, mannan, and chitin) by immune system receptors. These receptors then regulate the activation and differentiation of many innate and adaptive immune cells including mucocutaneous cell barriers, macrophages, neutrophils, dendritic cells, natural killer cells, innate-like lymphoid cells, and T and B lymphocytes. Mycobiome disruptions have been correlated with various diseases affecting mostly the brain, lungs, liver and pancreas. This work reviews our current knowledge on the mycobiome, focusing on its composition, research challenges, conditioning factors, interactions with the bacteriome and the immune system, and the known mycobiome alterations associated with disease. Full article

Beach Sand Mycobiome is currently among the most important health challenges for viticulture in the world. Remarkably, the study of fungal communities in coastal beach sand and recreational waters remains underexplored despite their potential implications for human health. This research aimed to assess the prevalence of fungal species and the antifungal susceptibility profiles of fungi recovered from the beaches of the Persian Gulf and the Sea of Oman. Sand and seawater samples from 39 stations distributed within 13 beaches along the coastline were collected between May and July 2023. The grown isolates were identified at the species level based on morphological characteristics and DNA sequencing. Antifungal susceptibility testing was performed according to the Clinical Laboratory Standards Institute guidelines. Of 222 recovered isolates, 206 (92.8%) filamentous fungi and 16 (7.2%) yeast strains were identified. Sand-recovered fungi comprised 82.9%, while water-originated fungi accounted for 17.1%. The DNA sequencing technique categorized 191 isolates into 13 genera and 26 species. The most recovered genus was Aspergillus (68.9%), and Aspergillus terreus sensu stricto was the commonly identified species (26.14%). Voriconazole was the most effective antifungal drug against Aspergillus species. Research on fungal contamination levels at these locations could provide a foundation for establishing regulatory frameworks to diminish fungal risks, thereby enhancing public health protection. The ecological significance of fungal communities in sandy beaches to human infections remains to be explored, and earlier reports in the literature may motivate researchers to focus on detecting this mycobiome in natural environments where further investigation is warranted. Ultimately, our discovery serves as a reminder that much remains to be learned about pathogenic fungi and underscores the need for vigilance in areas where emerging pathogens have not yet been identified. Full article

Background: Phenylketonuria (PKU) is a metabolic disorder managed through a strict, lifelong low-phenylalanine diet, which may influence gut microbiome dynamics. While gut bacterial alterations in PKU are increasingly investigated, the fungal community (mycobiome) remains largely unexplored. This study compared gut mycobiome composition and dietary profiles of paediatric PKU patients and healthy controls, stratified by age (<10 and 10–18 years). Methods: Stool samples from 20 children (10 PKU, 10 controls) were analysed using ITS1/ITS2 amplicon sequencing. Nutritional status was assessed using Body Mass Index percentiles (Polish standards), and nutrient intake was evaluated from three-day dietary records compared to national reference values. Correlations between fungal taxa and dietary factors were explored. Results: Although alpha diversity did not differ significantly, beta diversity and LEfSe analyses revealed distinct fungal profiles between PKU patients and controls, indicating a trend toward group separation (PERMANOVA: F = 1.54646, p = 0.09; ANOVA: p = 0.0609). PKU patients showed increased Eurotiales (p = 0.029), Aspergillaceae (p = 0.029), and Penicillium (p = 0.11) and decreased Physalacriaceae (0% vs. 5.84% in controls) and Malassezia (p = 0.13). Spearman’s analysis showed significant correlations between Geotrichum and intake of protein (ρ = 0.55, p = 0.0127) and phenylalanine (ρ = 0.70, p = 0.0005). Conclusions: Dietary treatment in PKU is associated with age-dependent shifts in the gut mycobiome, notably increasing the abundance of taxa such as Eurotiales, Aspergillaceae, and Penicillium, involved in carbohydrate/lipid metabolism and mucosal inflammation. These findings highlight the potential of gut fungi as nutritional and clinical biomarkers in PKU. Full article

Petroleum-derived contaminants pose a significant threat to the soil microbiome. Therefore, it is essential to explore materials and techniques that can restore homeostasis in disturbed environments. The aim of the study was to assess the response of the soil microbiome to contamination with diesel oil (DO) and gasoline (G) and to determine the capacity of sorbents, vermiculite (V), dolomite (D), perlite (P) and agrobasalt (A), to enhance the activity of microorganisms under Zea mays cultivation conditions in pot experiments. The restoration and activity of the soil microbiome were evaluated based on the abundance and diversity of bacteria and fungi, using both classical microbiological methods and Next Generation Sequencing (NGS). Bioinformatic tools were employed to calculate the physicochemical properties of proteins. DO increased the abundance of cultured microorganisms, whereas G significantly reduced it. Both DO and G increased the number of ASVs of Proteobacteria and decreased the relative abundance of Gemmatimonadetes, Chloroflexi, Acidobacteria, Verrucomicrobia, Planctomycetes, and fungal OTUs. These contaminants stimulated the growth of bacteria from the genera Rhodanobacter, Sphingomonas, Burkholderia, Sphingobium, and Mycobacterium, as well as fungi belonging to the Penicillium genus. Conversely, they had a negative effect on Kaistobacter, Rhodoplanes, and Ralstonia, as well as the fungi Chaetomium, Pseudaleuria, and Mortierella. DO caused greater changes in microbial alpha diversity than G. The stability of microbial proteins was higher at 17 °C than at −1 °C. The most stable proteins were found in bacteria and fungi identified within the core soil microbiome. These organisms exhibited greater diversity and more compact RNA secondary structures. The application of sorbents to contaminated soil altered the composition of bacterial and fungal communities. All sorbents enhanced the growth of organotrophic bacteria (Org) and fungi (Fun) in DO-contaminated soils, and actinobacteria (Act) and fungi in G-contaminated soils. V and A had the most beneficial effects on cultured microorganisms. In DO-contaminated soils, all sorbents inhibited the growth of Rhodanobacter, Parvibaculum, Sphingomonas, and Burkholderia, while stimulating Salinibacterium and Penicillium. In G-contaminated but otherwise unamended soils, all sorbents negatively affected the growth of Burkholderia, Sphingomonas, Kaistobacter, Rhodoplanes, Pseudonocardia, and Ralstonia and increased the abundance of Gymnostellatospora. The results of this study provide a valuable foundation for developing effective strategies to remediate soils contaminated with petroleum-derived compounds. Full article

Fungi are ubiquitous organisms that are capable of transient or persistent colonization in humans. Their polymorphic nature and complex host–mycobiome interactions remain incompletely understood. Emerging evidence highlights the role of resident fungi in modulating immune responses and adapting to host changes, which can trigger a shift from commensalism to parasitism, particularly in immunocompromised individuals. This study evaluated the effects of two major β-glucans—zymosan and curdlan—on the expression of pattern recognition receptors (Dectin1, Dectin2, TLR2, TLR4) in human peripheral blood mononuclear cells (PBMCs). It also examined their impact on reactive oxygen species (ROS) production, cytokine/chemokine gene expression, and antioxidant enzyme expression. Both β-glucans significantly increased the mRNA levels of all tested receptors and enhanced ROS generation. Curdlan downregulated key antioxidant enzymes (SOD1, CAT, GPX1), while zymosan markedly upregulated SOD1. These findings demonstrate that the β-glucans zymosan and curdlan have a substantial influence on PBMC reactivity and oxidative stress responses. Further studies are needed to deepen our understanding of host–fungal interactions and their implications in health and disease. Full article

Amphibians face severe threats from chytridiomycosis, and their skin microbiota plays a crucial role in pathogen defense. However, studies on their mycobiomes are limited. We hypothesized that amphibian cutaneous mycobiomes vary with seasonal variations and host species. To test this hypothesis, we used internal transcribed spacer (ITS) amplicon sequencing to identify the cutaneous fungal communities of two frogs from the Qinling Mountains of China, namely Pelophylax nigromaculatus and Nanorana quadranus. We also compared our ITS amplicon data with those of 30 known anti-Bd fungal ITS sequences to identify Bd-inhibiting fungi in the samples. The results showed that seasonal variation exerted a significantly stronger influence than host species on the fungal community structure (alpha diversity, beta diversity, species composition, abundance, and biomarkers). In the fungal community composition, intergroup consistency was significantly higher at the phylum level than at the genus level; however, one unidentified genus was present in samples from both frogs from different seasons. Anti-Bd fungi were detected in the skin fungal communities of P. nigromaculatus and N. quadranus, although their types and abundances varied seasonally and interspecifically. Overall, this study highlights seasonal dynamics and host-specific variations in amphibian cutaneous fungal ecology and identifies potential Bd-inhibiting fungal taxa. Full article

This review outlines technological advances in pathogen identification and describes the development and evolution of next-generation sequencers that can be applied to the ocular microbiome. Traditional methods such as culture and PCR have limitations in detecting the full spectrum of resident microorganisms, prompting a transition toward metagenomic analysis. As microbiome research expands across body systems, the comprehensive identification of ocular bacteria, fungi, and viruses has become possible. The commensal ocular microbiome may influence disease development through changes in the immune system and ocular environment. Next-generation sequencing enables detailed microbial profiling, aiding in disease diagnosis and treatment selection. Alterations in the microbiome may also induce metabolic changes, offering insights into novel treatment methods. This review outlines the evolution of next-generation sequencing technology, summarizes current knowledge of microorganisms found on the ocular surface and in intraocular fluid, and discusses future challenges and prospects. However, the large volume of microbiome data obtained must be interpreted with caution due to possible analytical biases. Furthermore, determining whether the microbiome is truly pathogenic requires comprehensive interpretation beyond the clinical findings and results of traditional identification methods. Full article