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Digestive Diseases and Sciences Jan 2022Although intestinal fungi are known to interact with the immune system, the relationship between intestinal fungi and childhood celiac disease (CeD), an immune-mediated...
BACKGROUND
Although intestinal fungi are known to interact with the immune system, the relationship between intestinal fungi and childhood celiac disease (CeD), an immune-mediated condition, has rarely been reported.
AIMS
The aim of this study was to describe gut fungal profiles in a cohort of children with new-onset CeD.
METHODS
Mucosal and fecal samples were collected from children with CeD and controls and subjected to metagenomics analysis of fungal microbiota communities. DNA libraries were sequenced using Illumina HiSeq platform 2 × 150 bp. Bioinformatic analysis was performed to quantify the relative abundance of fungi. Shannon alpha diversity metrics and beta diversity principal coordinate (PCo) analyses were calculated, and DESeq tests were performed between celiac and non-celiac groups.
RESULTS
Overall more abundant taxa in samples of children with CeD included Tricholomataceae, Saccharomycetaceae, Saccharomycetes Saccharomyces cerevisiae, and Candida, whereas less abundant taxa included Pichiaceae, Pichia kudriavzevii, Pneumocystis, and Pneumocystis jirovecii. Alpha diversity between CeD and control individuals did not differ significantly, and beta diversity PCo analysis showed overlap of samples from CeD and controls for both fecal or mucosal samples; however, there was a clear separation between mucosal and fecal overall samples CONCLUSIONS: We report fungal dysbiosis in children with CeD, suggesting a possible role in the pathogenesis of CeD. Further larger, controlled, prospective and longitudinal studies are needed to verify the results of this study and clarify the functional role of fungi in CeD.
Topics: Celiac Disease; Child; Dysbiosis; Feces; Female; Fungi; Humans; Intestinal Mucosa; Male; Metagenomics; Microbiological Phenomena; Mycobiome; Saudi Arabia
PubMed: 33723701
DOI: 10.1007/s10620-021-06823-8 -
Frontiers in Cellular and Infection... 2023infection (CDI) is common in patients with inflammatory bowel disease (IBD) and has been reported as a risk factor for poor outcome. However, gut microbiome and...
BACKGROUND
infection (CDI) is common in patients with inflammatory bowel disease (IBD) and has been reported as a risk factor for poor outcome. However, gut microbiome and mycobiome of IBD patients with CDI have been barely investigated. This study aimed to assess the gut microbiome and mycobiome in IBD patients with CDI.
METHODS
We collected fecal samples from patients with active IBD and concomitant CDI (IBD-CDI group, n=25), patients with active IBD and no CDI (IBD-only group, n=51), and healthy subjects (HC, n=40). Patients' characteristics including demographic data, disease severity, and medication history were collected. Metagenomic sequencing, taxonomic and functional analysis were carried out in the samples.
RESULTS
We found that the bacterial alpha diversity of the IBD-CDI group was decreased. The bacterial and fungal beta diversity variations between IBD patients and HC were significant, regardless of CDI status. But the IBD-CDI group did not significantly cluster separately from the IBD-only group. Several bacterial taxa, including , , and were overrepresented in the IBD-CDI group. Furthermore, IBD patients with CDI were distinguished by several fungal taxa, including overrepresentation of . We also identified functional differences in IBD patients with CDI include enrichment of peptidoglycan biosynthesis. The network analysis indicated specific interactions between microbial markers in IBD-CDI patients.
CONCLUSION
IBD patients with CDI had pronounced microbial dysbiosis. Gut micro-ecological changes in IBD patients with CDI might provide insight into the pathological process and potential strategies for diagnosis and treatment in this subset of patients.
Topics: Humans; Gastrointestinal Microbiome; Mycobiome; Clostridioides difficile; Inflammatory Bowel Diseases; Bacteria; Clostridium Infections
PubMed: 36814443
DOI: 10.3389/fcimb.2023.1129043 -
FEMS Microbiology Ecology Mar 2022Rock-dwelling fungi play critical ecological roles in drylands, including soil formation and nutrient cycling; however, we know very little about the identity, function... (Meta-Analysis)
Meta-Analysis
Rock-dwelling fungi play critical ecological roles in drylands, including soil formation and nutrient cycling; however, we know very little about the identity, function and environmental preferences of these important organisms, and the mere existence of a consistent rock mycobiome across diverse arid regions of the planet remains undetermined. To address this knowledge gap, we conducted a meta-analysis of rock fungi and spatially associated soil communities, surveyed across 28 unique sites spanning four major biogeographic regions (North America, Arctic, Maritime and Continental Antarctica) including contrasting climates, from cold and hot deserts to semiarid drylands. We show that rocks support a consistent and unique mycobiome that was different from that found in surrounding soils. Lichenized fungi from class Lecanoromycetes were consistently indicative of rocks across contrasting regions, together with ascomycetous representatives of black fungi in Arthoniomycetes, Dothideomycetes and Eurotiomycetes. In addition, compared with soil, rocks had a lower proportion of saprobes and plant symbiotic fungi. The main drivers structuring rock fungi distribution were spatial distance and, to a larger extent, climatic factors regulating moisture and temperature (i.e. mean annual temperature and mean annual precipitation), suggesting that these paramount and unique communities might be particularly sensitive to increases in temperature and desertification.
Topics: Desert Climate; Earth, Planet; Fungi; Mycobiome; Soil Microbiology
PubMed: 35298630
DOI: 10.1093/femsec/fiac030 -
Cells Apr 2022Bacteria, as well as eukaryotes, principally fungi, of the upper respiratory tract play key roles in the etiopathogenesis of respiratory diseases, whereas the potential... (Review)
Review
Bacteria, as well as eukaryotes, principally fungi, of the upper respiratory tract play key roles in the etiopathogenesis of respiratory diseases, whereas the potential role of archaea remains poorly understood. In this review, we discuss the contribution of all three domains of cellular life to human naso- and oropharyngeal microbiomes, i.e., bacterial microbiota, eukaryotes (mostly fungi), as well as the archaeome and their relation to respiratory and atopic disorders in infancy and adolescence. With this review, we aim to summarize state-of-the-art contributions to the field published in the last decade. In particular, we intend to build bridges between basic and clinical science.
Topics: Archaea; Asthma; Bacteria; Child; Eukaryota; Fungi; Humans; Microbiota; Mycobiome
PubMed: 35455967
DOI: 10.3390/cells11081287 -
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 -
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 -
Wiley Interdisciplinary Reviews.... Jan 2019Mammalian barrier surfaces are densely populated by symbiont fungi in much the same way the former are colonized by symbiont bacteria. The fungal microbiota, otherwise... (Review)
Review
Mammalian barrier surfaces are densely populated by symbiont fungi in much the same way the former are colonized by symbiont bacteria. The fungal microbiota, otherwise known as the mycobiota, is increasingly recognized as a critical player in the maintenance of health and homeostasis of the host. Here we discuss the impact of the mycobiota on host physiology and disease, the factors influencing mycobiota composition, and the current technologies used for identifying symbiont fungal species. Understanding the tripartite interactions among the host, mycobiota, and other members of the microbiota, will help to guide the development of novel prevention and therapeutic strategies for a variety of human diseases. This article is categorized under: Physiology > Mammalian Physiology in Health and Disease Laboratory Methods and Technologies > Genetic/Genomic Methods Models of Systems Properties and Processes > Organismal Models.
Topics: Animals; Bacteria; Fungi; Humans; Mycobiome
PubMed: 30255552
DOI: 10.1002/wsbm.1438 -
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 -
American Journal of Veterinary Research Sep 2023To report the density, and constituents, of the mycobiome on the skin surface of normal dogs.
OBJECTIVE
To report the density, and constituents, of the mycobiome on the skin surface of normal dogs.
ANIMALS
20 normal dogs were recruited for this study, with informed consent in all cases.
METHODS
Flocked swabs were used to sample the skin surface and to sample the skin surface after superficial scraping with a blunted scapula. Both samples were taken within a brass guide with an internal area of 3.5 cm-2. Next-generation DNA sequencing was used to identify and quantify components of the mycobiome.
RESULTS
The median density of the mycobiome was 1.1 X 105 cm-2 (IQR, 27,561, 409,572). Cladosporium spp and Vishniacozyma victoriae were found on all 20 dogs.
CLINICAL RELEVANCE
Knowledge of the density and the composition of the cutaneous mycobiome will increase our understanding of skin biology and may have relevance to future therapeutic trials.
Topics: Dogs; Animals; Mycobiome; Skin; Fungi
PubMed: 37536686
DOI: 10.2460/ajvr.23.04.0071 -
PloS One 2023Eukaryotic hosts harbor tremendously diverse microbiomes that affect host fitness and response to environmental challenges. Fungal endophytes are prominent members of...
Eukaryotic hosts harbor tremendously diverse microbiomes that affect host fitness and response to environmental challenges. Fungal endophytes are prominent members of plant microbiomes, but we lack information on the diversity in functional traits affecting their interactions with their host and environment. We used two culturing approaches to isolate fungal endophytes associated with the widespread, dominant prairie grass Andropogon gerardii and characterized their taxonomic diversity using rDNA barcode sequencing. A randomly chosen subset of fungi representing the diversity of each leaf was then evaluated for their use of different carbon compound resources and growth on those resources. Applying community phylogenetic analyses, we discovered that these fungal endophyte communities are comprised of phylogenetically distinct assemblages of slow- and fast-growing fungi that differ in their use and growth on differing carbon substrates. Our results demonstrate previously undescribed and cryptic functional diversity in carbon resource use and growth in fungal endophyte communities of A. gerardii.
Topics: Mycobiome; Poaceae; Phylogeny; Fungi; Fungi, Unclassified; Endophytes
PubMed: 37471328
DOI: 10.1371/journal.pone.0287990