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Journal of Hepatology Apr 2023Liver and biliary diseases affect more than a billion people worldwide, with high associated morbidity and mortality. The impact of the intestinal bacterial microbiome... (Review)
Review
Liver and biliary diseases affect more than a billion people worldwide, with high associated morbidity and mortality. The impact of the intestinal bacterial microbiome on liver diseases has been well established. However, the fungal microbiome, or mycobiome, has been overlooked for a long time. Recently, several studies have shed light on the role of the mycobiome in the development and progression of hepatobiliary diseases. In particular, the fungal genus Candida has been found to be involved in the pathogenesis of multiple hepatobiliary conditions. Herein, we compare colonisation and infection, describe mycobiome findings in the healthy state and across the various hepatobiliary conditions, and point toward communalities. We detail how quantitation of immune responses to fungal antigens can be employed to predict disease severity, e.g. using antibodies to Saccharomyces cerevisiae or specific anti-Candida albicans antibodies. We also show how fungal products (e.g. beta-glucans, candidalysin) activate the host's immune system to exacerbate liver and biliary diseases. Finally, we describe how the gut mycobiome can be modulated to ameliorate hepatobiliary conditions.
Topics: Humans; Mycobiome; Candida; Mycoses; Candida albicans; Saccharomyces cerevisiae; Digestive System Diseases
PubMed: 36565724
DOI: 10.1016/j.jhep.2022.12.006 -
Cell Host & Microbe Apr 2023Candida auris and Candida albicans can result in invasive fungal diseases. And yet, these species can stably and asymptomatically colonize human skin and... (Review)
Review
Candida auris and Candida albicans can result in invasive fungal diseases. And yet, these species can stably and asymptomatically colonize human skin and gastrointestinal tracts. To consider these disparate microbial lifestyles, we first review factors shown to influence the underlying microbiome. Structured by the damage response framework, we then consider the molecular mechanisms deployed by C. albicans to switch between commensal and pathogenic lifestyles. Next, we explore this framework with C. auris to highlight how host physiology, immunity, and/or antibiotic receipt are associated with progression from colonization to infection. While treatment with antibiotics increases the risk that an individual will succumb to invasive candidiasis, the underlying mechanisms remain unclear. Here, we describe several hypotheses that may explain this phenomenon. We conclude by highlighting future directions integrating genomics with immunology to advance our understanding of invasive candidiasis and human fungal disease.
Topics: Humans; Mycobiome; Symbiosis; Host-Pathogen Interactions; Candida albicans; Candidiasis, Invasive
PubMed: 37054674
DOI: 10.1016/j.chom.2023.02.010 -
The Journal of Allergy and Clinical... Dec 2023Atopic diseases are characterized by type 2 inflammation, with high levels of allergen-specific T2 cell immune responses and elevated production of IgE. These common... (Review)
Review
Atopic diseases are characterized by type 2 inflammation, with high levels of allergen-specific T2 cell immune responses and elevated production of IgE. These common disorders have increased in incidence around the world, which is partly explained by detrimental disturbances to the early-life intestinal microbiome. Although most studies have focused exclusively on bacterial members of the microbiome, intestinal fungi have started to be recognized for their impact on host immune development and atopy pathogenesis. From this perspective, we review recent findings demonstrating the strong interactions between members of the mycobiome and the host immune system early in life, leading to immune tolerance during eubiosis or inducing sensitization and overt T2 cell responses during dysbiosis. Current evidence places intestinal fungi as central players in the development of allergic diseases and potential targets for atopy prevention and treatments.
Topics: Humans; Mycobiome; Hypersensitivity; Hypersensitivity, Immediate; Allergens; Inflammation; Fungi
PubMed: 37865199
DOI: 10.1016/j.jaci.2023.10.006 -
Critical Care (London, England) Jan 2024Sepsis and trauma are known to disrupt gut bacterial microbiome communities, but the impacts and perturbations in the fungal (mycobiome) community after severe infection...
BACKGROUND
Sepsis and trauma are known to disrupt gut bacterial microbiome communities, but the impacts and perturbations in the fungal (mycobiome) community after severe infection or injury, particularly in patients experiencing chronic critical illness (CCI), remain unstudied.
METHODS
We assess persistence of the gut mycobiome perturbation (dysbiosis) in patients experiencing CCI following sepsis or trauma for up to two-to-three weeks after intensive care unit hospitalization.
RESULTS
We show that the dysbiotic mycobiome arrays shift toward a pathobiome state, which is more susceptible to infection, in CCI patients compared to age-matched healthy subjects. The fungal community in CCI patients is largely dominated by Candida spp; while, the commensal fungal species are depleted. Additionally, these myco-pathobiome arrays correlate with alterations in micro-ecological niche involving specific gut bacteria and gut-blood metabolites.
CONCLUSIONS
The findings reveal the persistence of mycobiome dysbiosis in both sepsis and trauma settings, even up to two weeks post-sepsis and trauma, highlighting the need to assess and address the increased risk of fungal infections in CCI patients.
Topics: Humans; Mycobiome; Dysbiosis; Gastrointestinal Microbiome; Candida; Bacteria; Sepsis; Fungi
PubMed: 38212826
DOI: 10.1186/s13054-023-04780-4 -
Hua Xi Kou Qiang Yi Xue Za Zhi = Huaxi... Jun 2019The proportion of mycobiome is less than 1% of human microbiome. However, fungal community plays a key role in human health and diseases. With high-throughput sequencing...
The proportion of mycobiome is less than 1% of human microbiome. However, fungal community plays a key role in human health and diseases. With high-throughput sequencing applications, the structure and composition of mycobiome in the mouth, lung, gut, vagina, and skin have been analyzed, and the role of microbiome in diseases has been investigated. Mycobiome also influences the composition of bacteriome and includes key species that maintain the structure and function of microbial communities. Fungi also influence host immune responses. In this review, we summarized the mycobiome com-position at various sites and different diseases and the interactions between fungi-bacteria and fungi-host.
Topics: Bacteria; Disease; Female; Fungi; Humans; Microbiota; Mouth; Mycobiome
PubMed: 31218869
DOI: 10.7518/hxkq.2019.03.017 -
Current Opinion in Microbiology Dec 2023Mammalian microbiomes have coevolved with their host to establish a stable homeostatic relationship. Multifaceted commensal-host and commensal-commensal interactions... (Review)
Review
Mammalian microbiomes have coevolved with their host to establish a stable homeostatic relationship. Multifaceted commensal-host and commensal-commensal interactions contribute to the maintenance of the equilibrium with an impact on diverse host physiological processes. Despite constant exposure to physical and chemical insults from the environment, the skin harbors a surprisingly stable microbiome. The fungal compartment of the skin microbiome, the skin mycobiome, is unique in that it is dominated by a single fungus, Malassezia. The lack in diversity suggests that the skin may provide a unique niche for this fungal genus and that Malassezia may efficiently outcompete other fungi from the skin. This opinion article examines aspects in support of this hypothesis, discusses how changes in niche conditions associate with skin mycobiome dysregulation, and highlights an emerging example of Malassezia being displaced from the skin by the emerging fungal pathogen C. auris, thereby generating a predisposing situation for fatal-invasive infection.
Topics: Animals; Mycobiome; Skin; Microbiota; Malassezia; Symbiosis; Fungi; Mammals
PubMed: 37703811
DOI: 10.1016/j.mib.2023.102381 -
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 -
Signal Transduction and Targeted Therapy Apr 2023
Topics: Humans; Mycobiome; COVID-19; Cytokines; Follow-Up Studies; Gastrointestinal Microbiome
PubMed: 37069139
DOI: 10.1038/s41392-023-01417-4 -
Frontiers in Endocrinology 2022Rheumatoid arthritis (RA) is a chronic destructive autoimmune disease of the joints which causes significant pain, functional disability, and mortality. Although... (Review)
Review
Rheumatoid arthritis (RA) is a chronic destructive autoimmune disease of the joints which causes significant pain, functional disability, and mortality. Although aberrant immune cell activation induced by the imbalance between T helper Th1/Th17 and Treg cells is implicated in the RA development, its etiopathogenesis remains unclear. The presence of mucosal inflammation and systemic IgA-isotype-autoantibodies (anti-citrullinated peptide antibodies and rheumatoid factor) in pre-clinical RA supports the mucosal origin hypothesis involving altered microbiota in disease development. The gut microbiota comprises diverse bacteria, fungal and viral components, which are critical in developing host immunity. Alterations in microbial abundance are known to exacerbate or attenuate immune responses in the gut microenvironment subsequently affecting the joints. Further, these changes can provide biomarkers for disease activity and outcome in RA. Most of the research till date has been focused on describing gut bacterial components in RA. Studies on gut mycobiome and virome components in RA are relatively new and burgeoning field. Given the paucity of mycobiome or virome specific studies in RA, this review, discusses the recent findings on alterations in gut bacterial, fungal, and viral components as well as their role in regulating the spectrum of immune-pathogenic events occurring in RA which might be explored in future as a potential therapeutic target. Further, we provide an overview on inter-kingdom interactions between bacteria, fungi, and viruses in RA. The current understanding on gut microbiota modulation for managing RA is also summarised.
Topics: Humans; Mycobiome; Virome; Arthritis, Rheumatoid; Autoimmune Diseases; Gastrointestinal Microbiome; Autoantibodies; Bacteria
PubMed: 36699026
DOI: 10.3389/fendo.2022.1044673 -
Mycopathologia Apr 2020Fungal disease is an increasingly recognised global clinical challenge associated with high mortality. Early diagnosis of fungal infection remains problematic due to the... (Review)
Review
Fungal disease is an increasingly recognised global clinical challenge associated with high mortality. Early diagnosis of fungal infection remains problematic due to the poor sensitivity and specificity of current diagnostic modalities. Advances in sequencing technologies hold promise in addressing these shortcomings and for improved fungal detection and identification. To translate such emerging approaches into mainstream clinical care will require refinement of current sequencing and analytical platforms, ensuring standardisation and consistency through robust clinical benchmarking and its validation across a range of patient populations. In this state-of-the-art review, we discuss current diagnostic and therapeutic challenges associated with fungal disease and provide key examples where the application of sequencing technologies has potential diagnostic application in assessing the human 'mycobiome'. We assess how ready access to fungal sequencing may be exploited in broadening our insight into host-fungal interaction, providing scope for clinical diagnostics and the translation of emerging mycobiome research into clinical practice.
Topics: Computational Biology; Fungi; High-Throughput Nucleotide Sequencing; Host Microbial Interactions; Humans; Metagenomics; Mycobiome; Mycoses; Pathology, Molecular
PubMed: 31894501
DOI: 10.1007/s11046-019-00413-z