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Fungal Genetics and Biology : FG & B Aug 2019Novel culture independent technologies have further elucidated the composition of the human mycobiome, though the role of fungi in human health and disease remains... (Review)
Review
Novel culture independent technologies have further elucidated the composition of the human mycobiome, though the role of fungi in human health and disease remains largely unknown. Recent studies have suggested conflicting roles for fungi in the gastrointestinal tract, underscoring the complexity of the interactions between the mycobiome, its bacterial counterpart, and the host. One key example is the observation that fungal taxa are overrepresented in patients with Clostridioides difficile infection (CDI), suggesting a role for fungi in this disease. Recent studies in murine models have demonstrated the ability of the commensal fungus Candida albicans to alter the course of CDI, supporting the notion that fungi play a role in this infection. This review summarizes current data on fungi and CDI, and shows that views of the dysbiotic state that is central to the pathogenesis of CDI are incomplete without consideration of the mycobiome.
Topics: Animals; Clostridioides difficile; Clostridium Infections; Disease Models, Animal; Dysbiosis; Fungi; Gastrointestinal Tract; Humans; Mice; Microbial Interactions; Mycobiome; Symbiosis
PubMed: 30978391
DOI: 10.1016/j.fgb.2019.04.007 -
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 -
Microbiome Apr 2022Extensive work has been accomplished to characterize the intestinal bacterial community, known as the microbiota, and its association with host health and disease....
BACKGROUND
Extensive work has been accomplished to characterize the intestinal bacterial community, known as the microbiota, and its association with host health and disease. However, very little is known about the spatiotemporal development and the origin of a minor intestinal fungal community, known as the mycobiota, in humans and animals, particularly in avian species.
RESULTS
In this study, we comprehensively characterized the biogeography and succession of the gastrointestinal (GI) mycobiota of broiler chickens and further revealed the fungal sources that are responsible for initial and long-term establishment of the mycobiota in the GI tract. Using Illumina sequencing of the internal transcribed spacer 2 (ITS2) region of fungal rRNA genes, we detected significant spatial and temporal differences in the mycobiota along the GI tract. In contrary to the microbiota, the mycobiota was more diverse in the upper than the lower GI tract with no apparent trend of succession up to 42 days of age. The intestinal mycobiota was dominated by the phyla Ascomycota and Basidiomycota with Gibberella, Aspergillus, and Candida being the most abundant genera. Although the chicken mycobiota was highly dynamic, Fusarium pseudonygamai was dominant throughout the GI tract regardless of age in this study. The core chicken mycobiome consisted of 26 fungal taxa accounting for greater than 85% of the fungal population in each GI location. However, we observed high variations of the intestinal mycobiota among different studies. We also showed that the total fungal population varied greatly from 1.0 × 10 to 1.1 × 10 /g digesta along the GI tract and only accounted for less than 0.06% of the bacteria in day-42 broilers. Finally, we revealed that the mycobiota from the hatchery environment was responsible for initial colonization in the GI tract of newly hatched chickens, but was quickly replaced by the fungi in the diet within 3 days.
CONCLUSIONS
Relative to the intestinal microbiota that consists of trillions of bacteria in hundreds of different species and becomes relatively stabilized as animals age, the chicken intestinal mycobiota is a minor microbial community that is temporally dynamic with limited diversity and no obvious pattern of successive changes. However, similar to the microbiota, the chicken mycobiota is spatially different along the GI tract, although it is more diverse in the upper than the lower GI tract. Dietary fungi are the major source of the intestinal mycobiota in growing chickens. Video abstract.
Topics: Animals; Chickens; Fungi; Gastrointestinal Tract; Intestines; Mycobiome
PubMed: 35365230
DOI: 10.1186/s40168-022-01252-9 -
The New Phytologist Nov 2020That arbuscular mycorrhizal (AM) fungi covary with plant communities is clear, and many papers report nonrandom associations between symbiotic partners. However, these... (Review)
Review
That arbuscular mycorrhizal (AM) fungi covary with plant communities is clear, and many papers report nonrandom associations between symbiotic partners. However, these studies do not test the causal relationship, or 'codependency', whereby the composition of one guild affects the composition of the other. Here we outline underlying requirements for codependency, compare important drivers for both plant and AM fungal communities, and assess how host preference - a pre-requisite for codependency - changes across spatiotemporal scales and taxonomic resolution for both plants and AM fungi. We find few examples in the literature designed to test for codependency and those that do have been conducted within plots or mesocosms. Also, while plants and AM fungi respond similarly to coarse environmental filters, most variation remains unexplained, with host identity explaining less than 30% of the variation in AM fungal communities. These results combined question the likelihood of predictable co-occurrence, and therefore evolution of codependency, between plant and AM fungal taxa across locations. We argue that codependency is most likely to occur in homogeneous environments where specific plant - AM fungal pairings have functional consequences for the symbiosis. We end by outlining critical aspects to consider moving forward.
Topics: Codependency, Psychological; Mycobiome; Mycorrhizae; Plant Roots; Plants; Soil Microbiology; Symbiosis
PubMed: 32452032
DOI: 10.1111/nph.16676 -
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 -
Journal of Translational Medicine Feb 2024The relationship between the gut mycobiome and end-stage renal disease (ESRD) remains largely unexplored.
BACKGROUND
The relationship between the gut mycobiome and end-stage renal disease (ESRD) remains largely unexplored.
METHODS
In this study, we compared the gut fungal populations of 223 ESRD patients and 69 healthy controls (HCs) based on shotgun metagenomic sequencing data, and analyzed their associations with host serum and fecal metabolites.
RESULTS
Our findings revealed that ESRD patients had a higher diversity in the gut mycobiome compared to HCs. Dysbiosis of the gut mycobiome in ESRD patients was characterized by a decrease of Saccharomyces cerevisiae and an increase in various opportunistic pathogens, such as Aspergillus fumigatus, Cladophialophora immunda, Exophiala spinifera, Hortaea werneckii, Trichophyton rubrum, and others. Through multi-omics analysis, we observed a substantial contribution of the gut mycobiome to host serum and fecal metabolomes. The opportunistic pathogens enriched in ESRD patients were frequently and positively correlated with the levels of creatinine, homocysteine, and phenylacetylglycine in the serum. The populations of Saccharomyces, including the HC-enriched Saccharomyces cerevisiae, were frequently and negatively correlated with the levels of various toxic metabolites in the feces.
CONCLUSIONS
Our results provided a comprehensive understanding of the associations between the gut mycobiome and the development of ESRD, which had important implications for guiding future therapeutic studies in this field.
Topics: Humans; Mycobiome; Saccharomyces cerevisiae; Gastrointestinal Microbiome; Feces; Metabolome; Kidney Failure, Chronic
PubMed: 38403655
DOI: 10.1186/s12967-024-05004-1 -
Journal of Translational Medicine Feb 2023Gut mycobiota plays a crucial role in benign liver diseases; however, its correlation with hepatocellular carcinoma (HCC) remains elusive. This study aimed to elucidate...
OBJECTIVE
Gut mycobiota plays a crucial role in benign liver diseases; however, its correlation with hepatocellular carcinoma (HCC) remains elusive. This study aimed to elucidate fungal differences in patients with HCC-associated cirrhosis compared to cirrhotic patients without HCC and healthy controls.
METHODS
The 72 fecal samples from 34 HCC patients, 20 cirrhotic patients, and 18 healthy controls were collected and analyzed using ITS2 rDNA sequencing.
RESULTS
Our results revealed the presence of intestinal fungal dysbiosis with significant enrichment of opportunistic pathogenic fungi such as Malassezia, Malassezia sp., Candida, and C. albicans in HCC patients compared with healthy controls and cirrhosis patients. Alpha-diversity analysis demonstrated that patients with HCC and cirrhosis showed decreased fungal diversity compared to healthy controls. Beta diversity analysis indicated that the three groups exhibited significant segregated clustering. Besides, C. albicans was found to be significantly more abundant in the HCC patients with TNM stage III-IV than those with stage I-II, in contrast to the commensal organism S. cerevisiae. We also confirmed that the HCC patients were successfully classified with an area under the curve value of 0.906 based on the fecal fungal signature. Finally, our animal experiments confirm that aberrant colonization of the intestine by C. albicans and M. furfur can promote the development of HCC.
CONCLUSIONS
This study indicates that dysbiosis of the gut mycobiome might be involved in HCC development.
TRIAL REGISTRATION
ChiCTR, ChiCTR2100054537. Registered 19 December 2021, http://www.chictr.org.cn/edit.aspx?pid=144550&htm=4.
Topics: Animals; Mycobiome; Carcinoma, Hepatocellular; Saccharomyces cerevisiae; Dysbiosis; Liver Neoplasms; Candida albicans; Liver Cirrhosis
PubMed: 36793057
DOI: 10.1186/s12967-023-03940-y -
Mucosal Immunology Apr 2022Fungi are important yet understudied contributors to the microbial communities of the gastrointestinal tract. Starting at birth, the intestinal mycobiome undergoes a... (Review)
Review
Fungi are important yet understudied contributors to the microbial communities of the gastrointestinal tract. Starting at birth, the intestinal mycobiome undergoes a period of dynamic maturation under the influence of microbial, host, and extrinsic influences, with profound functional implications for immune development in early life, and regulation of immune homeostasis throughout life. Candida albicans serves as a model organism for understanding the cross-talk between fungal colonization dynamics and immunity, and exemplifies unique mechanisms of fungal-immune interactions, including fungal dimorphism, though our understanding of other intestinal fungi is growing. Given the prominent role of the gut mycobiome in promoting immune homeostasis, emerging evidence points to fungal dysbiosis as an influential contributor to immune dysregulation in a variety of inflammatory and infectious diseases. Here we review current knowledge on the factors that govern host-fungi interactions in the intestinal tract and immunological outcomes in both mucosal and systemic compartments.
Topics: Candida albicans; Dysbiosis; Fungi; Gastrointestinal Tract; Humans; Immunity, Mucosal; Infant, Newborn; Microbiota; Mycobiome
PubMed: 35474360
DOI: 10.1038/s41385-022-00515-w -
Scientific Reports Apr 2023The mycobiome is an integral component of every living organism. Among other fungi associated with plants, endophytes are an interesting and favorable group of...
The mycobiome is an integral component of every living organism. Among other fungi associated with plants, endophytes are an interesting and favorable group of microorganisms, but information regarding them is still largely unknown. Wheat is the most economically significant and essential crop for global food security, which is exposed to a range of abiotic and biotic stresses. Profiling plants' mycobiomes can help in sustainable, chemical-reducing wheat production. The main objective of this work is to understand the structure of endogenous fungal communities in winter and spring wheat cultivars growing under different growth conditions. Further, the study attempted to investigate the effect of host genotype, host organs and plant growth conditions on the composition and distribution of fungi in wheat plant tissues. Comprehensive, high throughput analyzes of the diversity and community structure of the wheat mycobiome were performed, complemented by the simultaneous isolation of endophytic fungi, resulting in candidate strains for future research. The findings of the study revealed that the type of plant organs and growth conditions influence the wheat mycobiome. It was also assessed that fungi representing the genera Cladosporium, Penicillium, and Sarocladium form the core mycobiome of Polish spring and winter wheat cultivars. The coexistence of both symbiotic and pathogenic species in the internal tissues of wheat was also observed. Those commonly considered beneficial for plants can be used in further research as a valuable source of potential biological control factors and/or biostimulators of wheat plant growth.
Topics: Mycobiome; Triticum; Seasons; Fungi; Endophytes
PubMed: 37055465
DOI: 10.1038/s41598-023-33195-y