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Journal of Proteomics Feb 2022Fungi support a wide range of ecosystem processes such as decomposition of organic matter and plant-soil relationships. Yet, our understanding of the factors driving the...
Fungi support a wide range of ecosystem processes such as decomposition of organic matter and plant-soil relationships. Yet, our understanding of the factors driving the metaproteome of fungal communities is still scarce. Here, we conducted a field survey including data on fungal biomass (by phospholipid fatty acids, PLFA), community composition (by metabarcoding of the 18S rRNA gene from extracted DNA) and functional profile (by metaproteomics) to investigate soil fungi and their relation to edaphic and environmental variables across three ecosystems (forests, grasslands, and shrublands) distributed across the globe. We found that protein richness of soil fungi was significantly higher in forests than in shrublands. Among a wide suite of edaphic and environmental variables, we found that soil carbon content and plant cover shaped evenness and diversity of fungal soil proteins while protein richness correlated to mean annual temperature and pH. Functions shifted from metabolism in forests to information processing and storage in shrublands. The differences between the biomes highlight the utility of metaproteomics to investigate functional microbiomes in soil. SIGNIFICANCE: Understanding the structure and the function of fungal communities and the driving factors is crucial to determine the contribution to ecosystem services of fungi and what effect future climate has. While there is considerable knowledge on the ecosystem processes provided by fungi such as decomposition of organic matter and plant-soil relationships, our understanding of the driving factors of the fungal metaproteome is scarce. Here we present the first estimates of fungal topsoil protein diversity in a wide range of soils across global biomes. We report taxonomic differences for genes delivered by amplicon sequencing of the 18S rRNA gene and differences of the functional microbiome based on metaproteomics. Both methods gave a complementary view on the fungal topsoil communities, unveiling both taxonomic and functional changes with changing environments. Such a comprehensive multi-omic analysis of fungal topsoil communities has never been performed before, to our knowledge.
Topics: Ecosystem; Forests; Fungi; Mycobiome; Soil; Soil Microbiology
PubMed: 34818587
DOI: 10.1016/j.jprot.2021.104428 -
Microbiology Spectrum Jun 2017The term "microbiome" refers to microorganisms (microbiota) and their genomes (metagenome) coexisting with their hosts. Some researchers coined the term "second genome"... (Review)
Review
The term "microbiome" refers to microorganisms (microbiota) and their genomes (metagenome) coexisting with their hosts. Some researchers coined the term "second genome" to underscore the importance of the microbiota and its collective metagenome on their host's health and/or disease. It is now undeniable that the commensal fungal microorganisms, alongside the other components of the microbiota, play a central role in association with the human host. In recognition, projects were launched nationally and internationally to unify efforts to characterize the microbiome and elucidate the functional role of the microbiota and the mechanism(s) by which these organisms and their metabolites (metabolome) may affect health and disease states. In this article, we will highlight the role of the fungal community as an indispensable component of the microbiome.
Topics: Bacterial Physiological Phenomena; Cell Transplantation; Disease; Dysbiosis; Fungi; Health Status; Host-Pathogen Interactions; Humans; Metabolome; Metagenome; Microbial Interactions; Microbiota; Mycobiome; Neoplasms; Symbiosis
PubMed: 28597821
DOI: 10.1128/microbiolspec.FUNK-0045-2016 -
Advanced Science (Weinheim,... Jul 2023The oral bacteriome, gut bacteriome, and gut mycobiome are associated with coronavirus disease 2019 (COVID-19). However, the oral fungal microbiota in COVID-19 remains...
The oral bacteriome, gut bacteriome, and gut mycobiome are associated with coronavirus disease 2019 (COVID-19). However, the oral fungal microbiota in COVID-19 remains unclear. This article aims to characterize the oral mycobiome in COVID-19 and recovered patients. Tongue coating specimens of 71 COVID-19 patients, 36 suspected cases (SCs), 22 recovered COVID-19 patients, 36 SCs who recovered, and 132 controls from Henan are collected and analyzed using internal transcribed spacer sequencing. The richness of oral fungi is increased in COVID-19 versus controls, and beta diversity analysis reveals separate fungal communities for COVID-19 and control. The ratio of Ascomycota and Basidiomycota is higher in COVID-19, and the opportunistic pathogens, including the genera Candida, Saccharomyces, and Simplicillium, are increased in COVID-19. The classifier based on two fungal biomarkers is constructed and can distinguish COVID-19 patients from controls in the training, testing, and independent cohorts. Importantly, the classifier successfully diagnoses SCs with positive specific severe acute respiratory syndrome coronavirus 2 immunoglobulin G antibodies as COVID-19 patients. The correlation between distinct fungi and bacteria in COVID-19 and control groups is depicted. These data suggest that the oral mycobiome may play a role in COVID-19.
Topics: Humans; COVID-19; Microbiota; Mycobiome; Bacteria
PubMed: 37119437
DOI: 10.1002/advs.202205058 -
Cancer Cell Nov 2023Increasing evidence suggests that tumors harbor diverse microbiomes, adding complexity to the tumor microenvironment. In this issue of Cancer Cell, Liu et al. highlight...
Increasing evidence suggests that tumors harbor diverse microbiomes, adding complexity to the tumor microenvironment. In this issue of Cancer Cell, Liu et al. highlight the role of the intratumor mycobiome, specifically Aspergillus sydowii, in promoting lung adenocarcinoma progression. A. sydowii enhances the recruitment and activation of myeloid-derived suppressor cells via IL-1β signaling driven by the β-glucan-mediated Dectin-1/CARD9 pathway.
Topics: Humans; Mycobiome; Signal Transduction; beta-Glucans; Adenocarcinoma of Lung; Bacteria; Tumor Microenvironment
PubMed: 37774700
DOI: 10.1016/j.ccell.2023.09.002 -
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 -
Current Allergy and Asthma Reports Sep 2018The evolution of molecular-based methods over the last two decades has provided new approaches to identify and characterize fungal communities or "mycobiomes" at... (Review)
Review
PURPOSE OF REVIEW
The evolution of molecular-based methods over the last two decades has provided new approaches to identify and characterize fungal communities or "mycobiomes" at resolutions previously not possible using traditional hazard identification methods. The recent focus on fungal community assemblages within indoor environments has provided renewed insight into overlooked sources of fungal exposure. In occupational studies, internal transcribed spacer (ITS) region sequencing has recently been utilized in a variety of environments ranging from indoor office buildings to agricultural commodity and harvesting operations.
RECENT FINDINGS
Fungal communities identified in occupational environments have been primarily placed in the phylum Ascomycota and included classes typically identified using traditional fungal exposure methods such as the Eurotiomycetes, Dothideomycetes, Sordariomycetes, and Saccharomycetes. The phylum Basidiomycota has also been reported to be more prevalent than previously estimated and ITS region sequences have been primarily derived from the classes Agaricomycetes and Ustilaginomycetes. These studies have also resolved sequences placed in the Basidiomycota classes Tremellomycetes and Exobasidiomycetes that include environmental and endogenous yeast species. These collective datasets have shown that occupational fungal exposures include a much broader diversity of fungi than once thought. Although the clinical implications for occupational allergy are an emerging field of research, establishing the mycobiome in occupational environments will be critical for future studies to determine the complete spectrum of worker exposures to fungal bioaerosols and their impact on worker health.
Topics: Air Pollutants; DNA, Intergenic; Fungi; Humans; Mycobiome; Occupational Exposure; Workplace
PubMed: 30259186
DOI: 10.1007/s11882-018-0818-2 -
Applied and Environmental Microbiology May 2021Seagrasses are marine flowering plants that provide critical ecosystem services in coastal environments worldwide. Marine fungi are often overlooked in microbiome and...
Seagrasses are marine flowering plants that provide critical ecosystem services in coastal environments worldwide. Marine fungi are often overlooked in microbiome and seagrass studies, despite terrestrial fungi having critical functional roles as decomposers, pathogens, or endophytes in global ecosystems. Here, we characterize the distribution of fungi associated with the seagrass using leaves, roots, and rhizosphere sediment from 16 locations across its full biogeographic range. Using high-throughput sequencing of the ribosomal internal transcribed spacer (ITS) region and 18S rRNA gene, we first measured fungal community composition and diversity. We then tested hypotheses of neutral community assembly theory and the degree to which deviations suggested that amplicon sequence variants (ASVs) were plant selected or dispersal limited. Finally, we identified a core mycobiome and investigated the global distribution of differentially abundant ASVs. We found that the fungal community is significantly different between sites and that the leaf mycobiome follows a weak but significant pattern of distance decay in the Pacific Ocean. Generally, there was evidence for both deterministic and stochastic factors contributing to community assembly of the mycobiome, with most taxa assembling through stochastic processes. The core leaf and root mycobiomes were dominated by unclassified Sordariomycetes spp., unclassified Chytridiomycota lineages (including Lobulomycetaceae spp.), unclassified Capnodiales spp., and sp. It is clear from the many unclassified fungal ASVs and fungal functional guilds that knowledge of marine fungi is still rudimentary. Further studies characterizing seagrass-associated fungi are needed to understand the roles of these microorganisms generally and when associated with seagrasses. Fungi have important functional roles when associated with land plants, yet very little is known about the roles of fungi associated with marine plants, like seagrasses. In this study, we report the results of a global effort to characterize the fungi associated with the seagrass across its full biogeographic range. Although we defined a putative global core fungal community, it is apparent from the many fungal sequences and predicted functional guilds that had no matches to existing databases that general knowledge of seagrass-associated fungi and marine fungi is lacking. This work serves as an important foundational step toward future work investigating the functional ramifications of fungi in the marine ecosystem.
Topics: Fungi; Geography; Geologic Sediments; High-Throughput Nucleotide Sequencing; Models, Theoretical; Mycobiome; Plant Leaves; Plant Roots; Zosteraceae
PubMed: 33837008
DOI: 10.1128/AEM.02795-20 -
The primate gut mycobiome-bacteriome interface is impacted by environmental and subsistence factors.NPJ Biofilms and Microbiomes Mar 2022The gut microbiome of primates is known to be influenced by both host genetic background and subsistence strategy. However, these inferences have been made mainly based...
The gut microbiome of primates is known to be influenced by both host genetic background and subsistence strategy. However, these inferences have been made mainly based on adaptations in bacterial composition - the bacteriome and have commonly overlooked the fungal fraction - the mycobiome. To further understand the factors that shape the gut mycobiome of primates and mycobiome-bacteriome interactions, we sequenced 16 S rRNA and ITS2 markers in fecal samples of four different nonhuman primate species and three human groups under different subsistence patterns (n = 149). The results show that gut mycobiome composition in primates is still largely unknown but highly plastic and weakly structured by primate phylogeny, compared with the bacteriome. We find significant gut mycobiome overlap between captive apes and human populations living under industrialized subsistence contexts; this is in contrast with contemporary hunter-gatherers and agriculturalists, who share more mycobiome traits with diverse wild-ranging nonhuman primates. In addition, mycobiome-bacteriome interactions were specific to each population, revealing that individual, lifestyle and intrinsic ecological factors affect structural correspondence, number, and kind of interactions between gut bacteria and fungi in primates. Our findings indicate a dominant effect of ecological niche, environmental factors, and diet over the phylogenetic background of the host, in shaping gut mycobiome composition and mycobiome-bacteriome interactions in primates.
Topics: Animals; Bacteria; Gastrointestinal Microbiome; Mycobiome; Phylogeny; Primates
PubMed: 35301322
DOI: 10.1038/s41522-022-00274-3 -
MSphere Oct 2023The glassy-winged sharpshooter, Germar, is an invasive xylem-feeding leafhopper with a devastating economic impact on California agriculture through transmission of the...
The glassy-winged sharpshooter, Germar, is an invasive xylem-feeding leafhopper with a devastating economic impact on California agriculture through transmission of the plant pathogen, . While studies have focused on or known symbionts of , little work has been done at the scale of the microbiome (the bacterial community) or mycobiome (the fungal community). Here, we characterize the mycobiome and the microbiome of across Southern California and explore correlations with captivity and host insecticide resistance status. Using high-throughput sequencing of the ribosomal internal transcribed spacer 1 region and the 16S rRNA gene to profile the mycobiome and microbiome, respectively, we found that while the mycobiome significantly varied across Southern California, the microbiome did not. We also observed a significant difference in both the mycobiome and microbiome between captive and wild . Finally, we found that the mycobiome, but not the microbiome, was correlated with insecticide resistance status in wild . This study serves as a foundational look at the mycobiome and microbiome across Southern California. Future work should explore the putative link between microbes and insecticide resistance status and investigate whether microbial communities should be considered in management practices. IMPORTANCE The glassy-winged sharpshooter is an invasive leafhopper that feeds on the xylem of plants and transmits the devastating pathogen, , resulting in significant economic damage to California's agricultural system. While studies have focused on this pathogen or obligate symbionts of the glassy-winged sharpshooter, there is limited knowledge of the bacterial and fungal communities that make up its microbiome and mycobiome. To address this knowledge gap, we explored the composition of the mycobiome and the microbiome of the glassy-winged sharpshooter across Southern California and identified differences associated with geography, captivity, and host insecticide resistance status. Understanding sources of variation in the microbial communities associated with the glassy-winged sharpshooter is an important consideration for developing management strategies to control this invasive insect. This study is a first step toward understanding the role microbes may play in the glassy-winged sharpshooter's resistance to insecticides.
Topics: Animals; Mycobiome; RNA, Ribosomal, 16S; Microbiota; Hemiptera; Geography
PubMed: 37800904
DOI: 10.1128/msphere.00267-23 -
Virulence Apr 2017
Topics: Fungi; Gastrointestinal Microbiome; Gastrointestinal Tract; Humans; Mycobiome
PubMed: 28102762
DOI: 10.1080/21505594.2017.1279780