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Applied and Environmental Microbiology Nov 2022Grasses harbor diverse fungi, including some that produce mycotoxins or other secondary metabolites. Recently, Florida cattle farmers reported cattle illness, while the...
Grasses harbor diverse fungi, including some that produce mycotoxins or other secondary metabolites. Recently, Florida cattle farmers reported cattle illness, while the cattle were grazing on warm-season grass pastures, that was not attributable to common causes, such as nutritional imbalances or nitrate toxicity. To understand correlations between grass mycobiome and mycotoxin production, we investigated the mycobiomes associated with five prominent, perennial forage and weed grasses [Paspalum notatum Flügge, Cynodon dactylon (L.) Pers., Paspalum nicorae Parodi, Sporobolus indicus (L.) R. Br., and Andropogon virginicus (L.)] collected from six Florida pastures actively grazed by livestock. Black fungal stromata of and were observed on and leaves and were investigated. High-throughput amplicon sequencing was applied to delineate leaf mycobiomes. Mycotoxins from leaves were inspected using liquid chromatography-mass spectrometry (LC-MS/MS). Grass species, cultivars, and geographic localities interactively affected fungal community assemblies of asymptomatic leaves. Among the grass species, the greatest fungal richness was detected in the weed . The black fungal structures of leaves were dominated by the genus , while those of were codominated by the genus and a hypermycoparasitic fungus of the genus . When comparing mycotoxins detected in leaves with and without , emodin, an anthraquinone, was the only compound which was significantly different ( < 0.05). Understanding the leaf mycobiome and the mycotoxins it may produce in warm-season grasses has important implications for how these associations lead to secondary metabolite production and their subsequent impact on animal health. The leaf mycobiome of forage grasses can have a major impact on their mycotoxin contents of forage and subsequently affect livestock health. Despite the importance of the cattle industry in warm-climate regions, such as Florida, studies have been primarily limited to temperate forage systems. Our study provides a holistic view of leaf fungi considering epibiotic, endophytic, and hypermycoparasitic associations with five perennial, warm-season forage and weed grasses. We highlight that plant identity and geographic location interactively affect leaf fungal community composition. Yeasts appeared to be an overlooked fungal group in healthy forage mycobiomes. Furthermore, we detected high emodin quantities in the leaves of a widely planted forage species () whenever epibiotic fungi occurred. Our study demonstrated the importance of identifying fungal communities, ecological roles, and secondary metabolites in perennial, warm-season grasses and their potential for interfering with livestock health.
Topics: Cattle; Animals; Poaceae; Seasons; Mycobiome; Mycotoxins; Chromatography, Liquid; Emodin; Tandem Mass Spectrometry; Livestock; Geography; Plant Leaves; Fungal Structures
PubMed: 36226941
DOI: 10.1128/aem.00942-22 -
The Science of the Total Environment Dec 2023Air and dust harbor a dynamic fungal biome that interacts with residential environment inhabitants usually with negative implications for human health. Fungal air and...
Air and dust harbor a dynamic fungal biome that interacts with residential environment inhabitants usually with negative implications for human health. Fungal air and dust synthesis were investigated in houses across the Athens Metropolitan area. Active and passive culture dependent methods were employed to sample airborne and dustborne fungi for two sampling periods, one in winter and the other in summer. A core mycobiome was revealed both in air and dust constituted of the dominant Penicillium, Cladosporium, Aspergillus, Alternaria and yeasts and accompanied by several common and rare components. Penicillium and Aspergillus diversity included 22 cosmopolitan species, except the rarely found Penicillium citreonigrum, P. corylophilum, P. pagulum and Talaromyces albobiverticillius which are reported for the first time from Greece. Fungal concentrations were significantly higher during summer for both air and dust. Excessive levels of inhalable aerosol constituted mainly by certain Penicillium species were associated with indoor emission sources as these species are household molds related to food commodities rot. The ambient air fungal profile is a determinant factor of indoor fungal aerosol which subsequently shapes dustborne mycobiota. Indoor fungi can be useful bioindicators for indoor environment quality and at the same time provide insight to indoor fungal ecology.
Topics: Humans; Dust; Mycobiome; Air Pollution, Indoor; Fungi; Allergens; Aspergillus; Alternaria; Air Microbiology; Aerosols
PubMed: 37591388
DOI: 10.1016/j.scitotenv.2023.166228 -
The mycobiome in murine intestine is more perturbed by food arsenic exposure than in excreted feces.The Science of the Total Environment Jan 2021Arsenic is a global pollutant that can accumulate in rice and has been confirmed to disturb the gut microbiome. By contrast, the influence on the gut mycobiome is seldom...
Arsenic is a global pollutant that can accumulate in rice and has been confirmed to disturb the gut microbiome. By contrast, the influence on the gut mycobiome is seldom concerned because fungi comprise a numerically small proportion of the whole gut microcommunity. To expand the detection of the mycobiome in different gut sections of mammals and investigate the influence of food arsenic on the gut mycobiome in the digestive tract, we treated mice with feeds containing different compositions of arsenic species (7.3% sodium arsenate, 72.7% sodium arsenite, 1.0% sodium monomethylarsonate, and 19.0% sodium dimethylarsinate) in rice at a total arsenic dose of 30 mg/kg. After 60 days of exposure, the feces of four different sites, the ileum, cecum, colon, and excreted feces, were collected and analyzed by internal transcribed spacer gene sequencing. Among the samples, the major fungal phyla were Ascomycota, Basidiomycota, and Zygomycota; the top 10 fungal genera were Aspergillus, Verticillium, Penicillium, Cladosporium, Alternaria, Fusarium, Ophiocordyceps, Trametes, Mucor, and Nigrospora. In control mice, along the murine digestive tract, the mycobial richness and composition were significantly changed; Aspergillus and Penicillium possessed the higher ability to be stabilized in the murine gut, and larger proportions of positive correlations were observed among the major fungi. After arsenic exposure, the fungal composition was more disturbed in the intestinal tract than in feces. Along the digestive tract, arsenic can trigger larger mycobial variations, and the sensitivities of major fungi to arsenic were changed. Thus, the murine intestinal spatial mycobiota are more perturbed than excreted fecal mycobiota after food arsenic exposure. Feces are insufficient to be selected as a representative of the gut mycobiota in arsenic exposure studies.
Topics: Animals; Arsenic; Feces; Fungi; Intestines; Mice; Mycobiome; Trametes
PubMed: 32891997
DOI: 10.1016/j.scitotenv.2020.141871 -
American Journal of Veterinary Research Nov 2021To investigate the mycobiome of the oral cavity in healthy dogs and dogs with various stages of periodontal disease.
OBJECTIVE
To investigate the mycobiome of the oral cavity in healthy dogs and dogs with various stages of periodontal disease.
ANIMALS
51 dogs without periodontal disease (n = 12) or with mild (10), moderate (19), or severe (10) periodontal disease.
PROCEDURES
The whole maxillary arcade of each dog was sampled with a sterile swab, and swabs were submitted for next-generation DNA sequencing targeting the internal transcribed spacer 2 region with a commercial sequencing platform.
RESULTS
Fungi were detected in all samples, with a total of 320 fungal species from 135 families detected in the data set. No single fungal species was found in all samples. The 3 most frequently found fungal species were Cladosporium sp (46/51 samples), Malassezia restricta (44/51 samples), and Malassezia arunalokei (36/51 samples). Certain fungi, specifically those of the family Didymellaceae, the family Irpicaceae, and the order Pleosporales, were significantly associated with different stages of periodontitis. Mycobial analysis indicated that Cladosporium sp could be considered part of the core oral cavity mycobiome.
CONCLUSIONS AND CLINICAL RELEVANCE
Results highlighted that fungi are present in the oral cavity of dogs and are characterized by substantial species diversity, with different fungal communities associated with various stages of periodontal disease. The next-generation DNA sequencing used in the present study revealed substantially more species of fungi than previous culture-based studies.
Topics: Animals; Dog Diseases; Dogs; Mycobiome; Periodontal Diseases
PubMed: 34727047
DOI: 10.2460/ajvr.20.11.0200 -
Microbial Ecology Oct 2023Bats are widespread mammals that play key roles in ecosystems as pollinators and insectivores. However, there is a paucity of information about bat-associated microbes,...
Bats are widespread mammals that play key roles in ecosystems as pollinators and insectivores. However, there is a paucity of information about bat-associated microbes, in particular their fungal communities, despite the important role microbes play in host health and overall host function. The emerging fungal disease, white-nose syndrome, presents a potential challenge to the bat microbiome and understanding healthy bat-associated taxa will provide valuable information about potential microbiome-pathogen interactions. To address this knowledge gap, we collected 174 bat fur/skin swabs from 14 species of bats captured in five locations in New Mexico and Arizona and used high-throughput sequencing of the fungal internal transcribed (ITS) region to characterize bat-associated fungal communities. Our results revealed a highly heterogeneous bat mycobiome that was structured by geography and bat species. Furthermore, our data suggest that bat-associated fungal communities are affected by bat foraging, indicating the bat skin microbiota is dynamic on short time scales. Finally, despite the strong effects of site and species, we found widespread and abundant taxa from several taxonomic groups including the genera Alternaria and Metschnikowia that have the potential to be inhibitory towards fungal and bacterial pathogens.
Topics: Animals; Mycobiome; Chiroptera; Fungi; Microbiota; Geography
PubMed: 37126126
DOI: 10.1007/s00248-023-02230-w -
The European Respiratory Journal Mar 2021The chronic obstructive pulmonary disease (COPD) bacteriome associates with disease severity, exacerbations and mortality. While COPD patients are susceptible to fungal...
INTRODUCTION
The chronic obstructive pulmonary disease (COPD) bacteriome associates with disease severity, exacerbations and mortality. While COPD patients are susceptible to fungal sensitisation, the role of the fungal mycobiome remains uncertain.
METHODS
We report the largest multicentre evaluation of the COPD airway mycobiome to date, including participants from Asia (Singapore and Malaysia) and the UK (Scotland) when stable (n=337) and during exacerbations (n=66) as well as nondiseased (healthy) controls (n=47). Longitudinal mycobiome analysis was performed during and following COPD exacerbations (n=34), and examined in terms of exacerbation frequency, 2-year mortality and occurrence of serum specific IgE (sIgE) against selected fungi.
RESULTS
A distinct mycobiome profile is observed in COPD compared with controls as evidenced by increased α-diversity (Shannon index; p<0.001). Significant airway mycobiome differences, including greater interfungal interaction (by co-occurrence), characterise very frequent COPD exacerbators (three or more exacerbations per year) (permutational multivariate ANOVA; adjusted p<0.001). Longitudinal analyses during exacerbations and following treatment with antibiotics and corticosteroids did not reveal any significant change in airway mycobiome profile. Unsupervised clustering resulted in two clinically distinct COPD groups: one with increased symptoms (COPD Assessment Test score) and dominance, and another with very frequent exacerbations and higher mortality characterised by , and with a concomitant increase in serum sIgE levels against the same fungi. During acute exacerbations of COPD, lower fungal diversity associates with higher 2-year mortality.
CONCLUSION
The airway mycobiome in COPD is characterised by specific fungal genera associated with exacerbations and increased mortality.
Topics: Asia; Disease Progression; Humans; Malaysia; Mycobiome; Pulmonary Disease, Chronic Obstructive; Scotland; Singapore
PubMed: 32972986
DOI: 10.1183/13993003.02050-2020 -
Applied Microbiology and Biotechnology Sep 2022Smokeless tobacco (SLT) alters the oral microbiome of smokeless tobacco users. Dysbiosis of oral bacteriome has been determined; however, the mycobiome of SLT users has...
Smokeless tobacco (SLT) alters the oral microbiome of smokeless tobacco users. Dysbiosis of oral bacteriome has been determined; however, the mycobiome of SLT users has not been characterized. The oral mycobiome was assayed by amplification and sequencing of the fungal internal transcribed spacer (ITS1) region from oral swab samples of non-SLT users, SLT users (with or without oral lesions), and SLT with alcohol users. We observed that the richness and diversity of oral mycobiome were significantly decreased in SLT with oral lesions users than in non-users. The β-diversity analysis showed significant dissimilarity of oral mycobiome between non-users and SLT with oral lesions users. Linear discriminant analysis effect size and random forest analysis of oral mycobiome affirm that the genus Pichia was typical for SLT with oral lesions users. Prevalence of the fungal genus Pichia correlates positively with Starmerella, Mortierella, Fusarium, Calonectria, and Madurella, but is negatively correlated with Pyrenochaeta, Botryosporium, and Alternaria. Further, the determination of oral mycobiome functionality showed a high abundance of pathotroph-saprotroph-symbiotroph and animal pathogen-endophyte-epiphyte-undefined saprotroph at trophic and guild levels, respectively, indicating possibly major changes in normal growth repression of types of fungi. The oral mycobiome in SLT users was identified and comprehensively analyzed for the first time. SLT intake is associated with oral mycobiome dysbiosis and such alterations of the oral mycobiome may contribute to oral carcinogenesis in SLT users. This study will provide a basis for further large-scale investigations on the potential role of the mycobiome in SLT-induced oral cancer. KEY POINTS: • SLT induces dysbiosis of the oral microbiome that can contribute to oral cancer. • Oral mycobiome diversity is noticeably reduced in SLT users having oral lesions. • Occurrence of Pichia can be used as a biomarker for SLT users having oral lesions.
Topics: Dysbiosis; Humans; Mouth Neoplasms; Mycobiome; Pilot Projects; Tobacco Use; Tobacco, Smokeless
PubMed: 35913514
DOI: 10.1007/s00253-022-12096-6 -
Science (New York, N.Y.) Jul 2022Mycobiota modulate immunity and behavior.
Mycobiota modulate immunity and behavior.
Topics: Animals; Candida; Clostridioides difficile; Clostridium Infections; Fecal Microbiota Transplantation; Gastrointestinal Microbiome; Host-Pathogen Interactions; Humans; Immunity; Mice; Microbial Interactions; Mycobiome
PubMed: 35857570
DOI: 10.1126/science.abq6056 -
Nutrients Apr 2023While the human gut is home to a complex and diverse community of microbes, including bacteria and fungi, research on the gut microbiome has largely focused on bacteria,... (Randomized Controlled Trial)
Randomized Controlled Trial
While the human gut is home to a complex and diverse community of microbes, including bacteria and fungi, research on the gut microbiome has largely focused on bacteria, with relatively little attention given to the gut mycobiome. This study aims to investigate how diets with different dietary macronutrient distributions impact the gut mycobiome. We investigated gut mycobiome response to high-carbohydrate, low-fat (HC) and low-carbohydrate high-fat (LC) diet interventions based on a series of 72-day feeding-based n-of-1 clinical trials. A total of 30 participants were enrolled and underwent three sets of HC and LC dietary interventions in a randomized sequence. Each set lasted for 24 days with a 6-day washout period between dietary interventions. We collected and analyzed the fungal composition of 317 stool samples before and after each intervention period. To account for intra-individual variation across the three sets, we averaged the mycobiome data from the repeated sets for analysis. Of the 30 participants, 28 (aged 22-34 years) completed the entire intervention. Our results revealed a significant increase in gut fungal alpha diversity ( < 0.05) and significant changes in fungal composition (beta diversity, < 0.05) after the HC dietary intervention. Specifically, we observed the enrichment of five fungal genera (, , , , sp.; FDR < 0.052) and depletion of one fungal genus (; FDR = 0.03) after the HC intervention. After the LC dietary intervention, one fungal genus was enriched ( sp.; FDR = 0.003), and five fungal genera were depleted ( spp., , , and ; FDR < 0.1). This study provides novel evidence on how the gut mycobiome structure and composition change in response to the HC and LC dietary interventions and reveals diet-specific changes in the fungal genera.
Topics: Humans; Mycobiome; Nutrients; Diet, Fat-Restricted; Gastrointestinal Microbiome; Carbohydrates
PubMed: 37432284
DOI: 10.3390/nu15092152 -
Microbiology Spectrum Feb 2023The gut microbiota plays an essential role in the regulation of the immune system and the etiology of human autoimmune diseases. However, a holistic understanding of the...
The gut microbiota plays an essential role in the regulation of the immune system and the etiology of human autoimmune diseases. However, a holistic understanding of the gut bacteriome, mycobiome, and virome in patients with osteoarthritis (OA) remains lacking. Here, we explored the gut microbiotas of 44 OA patients and 46 healthy volunteers via deep whole-metagenome shotgun sequencing of their fecal samples. The gut bacteriome and mycobiome were analyzed using a reference-based strategy. Gut viruses were identified from the metagenomic assembled contigs, and the gut virome was profiled based on 6,567 nonredundant viral operational taxonomic units (vOTUs). We revealed that the gut microbiome (including bacteriome, mycobiome, and virome) of OA patients is fundamentally altered, characterized by a panel of 279 differentially abundant bacterial species, 10 fungal species, and 627 vOTUs. The representative OA-enriched bacteria included Anaerostipes hadrus (GENOME147149), sp900313215 (GENOME08259), Eubacterium_E hallii (GENOME000299), and A (GENOME001004), while Bacteroides plebeius A (GENOME239725), Roseburia inulinivorans (GENOME 001770), sp900343095 (GENOME075103), Phascolarctobacterium faecium (GENOME233517), and several members of and were depleted in OA patients. Fungi such as Debaryomyces fabryi (GenBank accession no. GCA_003708665), Candida parapsilosis (GCA_000182765), and Apophysomyces trapeziformis (GCA_000696975) were enriched in the OA gut microbiota, and Malassezia restricta (GCA_003290485), Aspergillus fumigatus (GCA_003069565), Mucor circinelloides (GCA_010203745) were depleted. The OA-depleted viruses spanned (95 vOTUs), (70 vOTUs), and (5 vOTUs), while 30 vOTUs were enriched in OA patients. Functional analysis of the gut bacteriome and virome also uncovered their functional signatures in relation to OA. Moreover, we demonstrated that the OA-associated gut bacterial and viral signatures are tightly interconnected, suggesting that they may impact disease together. Finally, we showed that the multikingdom signatures are effective in discriminating the OA patients from healthy controls, suggesting the potential of gut microbiota for the prediction of OA and related diseases. Our results delineated the fecal bacteriome, mycobiome, and virome landscapes of the OA microbiota and provided biomarkers that will aid in future mechanistic and clinical intervention studies. The gut microbiome of OA patients was completely altered compared to that in healthy individuals, including 279 differentially abundant bacterial species, 10 fungal species and 627 viral operational taxonomic units (vOTUs). Functional analysis of the gut bacteriome and virome also revealed their functional signatures in relation to OA. We found that OA-associated gut bacterial and viral signatures were tightly interconnected, indicating that they may affect the disease together. The OA patients can be discriminated effectively from healthy controls using the multikingdom signatures, suggesting the potential of gut microbiota for the prediction of OA and related diseases.
Topics: Humans; Mycobiome; Virome; Microbiota; Gastrointestinal Microbiome; Viruses; Bacteria
PubMed: 36515546
DOI: 10.1128/spectrum.01711-22