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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 -
Frontiers in Cellular and Infection... 2023
Topics: Mycobiome; Microbiota; Fungi
PubMed: 37457964
DOI: 10.3389/fcimb.2023.1240657 -
Virulence Apr 2017Skin constantly encounters external elements, including microbes. Culture-based studies have identified fungi present on human skin and have linked some species with... (Review)
Review
Skin constantly encounters external elements, including microbes. Culture-based studies have identified fungi present on human skin and have linked some species with certain skin diseases. Moreover, modern medical treatments, especially immunosuppressants, have increased the population at risk for cutaneous and invasive fungal infections, emphasizing the need to understand skin fungal communities in health and disease. A major hurdle for studying fungal flora at a community level has been the heterogeneous culture conditions required by skin fungi. Recent advances in DNA sequencing technologies have dramatically expanded our knowledge of the skin microbiome through culture-free methods. This review discusses historical and recent research on skin fungal communities - the mycobiome - in health and disease, and challenges associated with sequencing-based mycobiome research.
Topics: Fungi; Health; Humans; Microbiota; Mycobiome; Mycoses; Skin
PubMed: 27754756
DOI: 10.1080/21505594.2016.1249093 -
Virulence Apr 2017Many species of fungi have been detected in the healthy human gut; however, nearly half of all taxa reported have only been found in one sample or one study. Fungi... (Review)
Review
Many species of fungi have been detected in the healthy human gut; however, nearly half of all taxa reported have only been found in one sample or one study. Fungi capable of growing in and colonizing the gut are limited to a small number of species, mostly Candida yeasts and yeasts in the family Dipodascaceae (Galactomyces, Geotrichum, Saprochaete). Malassezia and the filamentous fungus Cladosporium are potential colonizers; more work is needed to clarify their role. Other commonly-detected fungi come from the diet or environment but either cannot or do not colonize (Penicillium and Debaryomyces species, which are common on fermented foods but cannot grow at human body temperature), while still others have dietary or environmental sources (Saccharomyces cerevisiae, a fermentation agent and sometime probiotic; Aspergillus species, ubiquitous molds) yet are likely to impact gut ecology. The gut mycobiome appears less stable than the bacterial microbiome, and is likely subject to environmental factors.
Topics: Diet; Environmental Exposure; Fungi; Gastrointestinal Microbiome; Gastrointestinal Tract; Humans; Microbiota; Mycobiome
PubMed: 27736307
DOI: 10.1080/21505594.2016.1247140 -
Nature Aug 2023
Topics: Humans; Mycobiome; Pancreatic Neoplasms; Fungi
PubMed: 37532815
DOI: 10.1038/s41586-023-06293-0 -
Cell Sep 2022Distinct fungal communities or "mycobiomes" have been found in individual tumor types and are known to contribute to carcinogenesis. Two new studies present a...
Distinct fungal communities or "mycobiomes" have been found in individual tumor types and are known to contribute to carcinogenesis. Two new studies present a comprehensive picture of the tumor-associated mycobiomes from a variety of human cancers. These studies reveal that fungi, although in low abundance, are ubiquitous across all major human cancers and that specific mycobiome types can be predictive of survival.
Topics: Fungi; Humans; Mycobiome; Neoplasms
PubMed: 36179665
DOI: 10.1016/j.cell.2022.09.013 -
Indian Journal of Gastroenterology :... Feb 2024Inflammatory bowel disease (IBD) is an immune mediated chronic inflammatory disorder of gastrointestinal tract, which has underlying multifactorial pathogenic... (Review)
Review
Inflammatory bowel disease (IBD) is an immune mediated chronic inflammatory disorder of gastrointestinal tract, which has underlying multifactorial pathogenic determinants such as environmental factors, susceptibility genes, gut microbial dysbiosis and a dysregulated immune response. Human gut is a frequent inhabitant of complex microbial ecosystem encompassing bacteria, viruses, parasites, fungi and other microorganisms that have an undisputable role in maintaining balanced homeostasis. All of these microbes interact with immune system and affect human gut physiology either directly or indirectly with interaction of each other. Intestinal fungi represent a smaller but crucial component of the human gut microbiome. Besides interaction with bacteriome and virome, it helps in balancing homoeostasis between pathophysiological and physiological processes, which is often dysregulated in patients with IBD. Understanding of gut mycobiome and its clinical implications are still in in its infancy as opposed to bacterial component of gut microbiome, which is more often focused. Modulation of gut mycobiome represents a novel and promising strategy in the management of patients with IBD. Emerging mycobiome-based therapies such as diet interventions, fecal microbiota transplantation (FMT), probiotics (both fungal and bacterial strains) and antifungals exhibit substantial effects in calibrating the gut mycobiome and restoring dysbalanced immune homeostasis by restoring the core gut mycobiome. In this review, we summarized compositional and functional diversity of the gut mycobiome in healthy individuals and patients with IBD, gut mycobiome dysbiosis in patients with IBD, host immune-fungal interactions and therapeutic role of modulation of intestinal fungi in patients with IBD.
Topics: Humans; Mycobiome; Dysbiosis; Ecosystem; Inflammatory Bowel Diseases; Gastrointestinal Microbiome
PubMed: 38409485
DOI: 10.1007/s12664-023-01510-0 -
Food Research International (Ottawa,... May 2021Sesame (Sesamum indicum) is one of the most widely cultivated crops in Asia and Africa. The identification of the geographical origins of sesame seeds is important for...
Sesame (Sesamum indicum) is one of the most widely cultivated crops in Asia and Africa. The identification of the geographical origins of sesame seeds is important for the detection of fraudulent samples. This study was conducted to build a prediction model and suggest potential biomarkers for distinguishing the geographical origins of sesame seeds using mycobiome (fungal microbiome) analysis coupled with multivariate statistical analysis. Sesame seeds were collected from 25 cities in Korea, six cities in China, and five sites in other countries (Ethiopia, India, Nigeria, and Pakistan). According to the expression of fungal internal transcribed spacer (ITS) sequences in sesame seeds, 21 fungal genera were identified in sesame seeds from various countries. The optimal partial least squares-discriminant analysis model was established by applying two components with unit variance scaling. Based on seven-fold cross validation, the predictive model had 94.4% (Korea vs. China/other countries), 91.7% (China vs. Korea/other countries), and 88.9% (other countries vs. Korea/China) accuracy in determining the geographical origins of sesame seeds. Alternaria, Aspergillus, and Macrophomina were suggested as the potential fungal genera to differentiate the geographical origins of sesame seeds. This study demonstrated that mycobiome analysis could be used as a complementary method for distinguishing the geographical origins of raw sesame seeds.
Topics: China; Ethiopia; India; Mycobiome; Nigeria; Pakistan; Republic of Korea; Seeds; Sesamum
PubMed: 33992372
DOI: 10.1016/j.foodres.2021.110271 -
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 -
Gut Microbes 2024The role of gut fungal species in tumor-related processes remains largely unexplored, with most studies still focusing on fungal infections. This review examines the... (Review)
Review
The role of gut fungal species in tumor-related processes remains largely unexplored, with most studies still focusing on fungal infections. This review examines the accumulating evidence suggesting the involvement of commensal and pathogenic fungi in cancer biological process, including oncogenesis, progression, and treatment response. Mechanisms explored include fungal influence on host immunity, secretion of bioactive toxins/metabolites, interaction with bacterial commensals, and migration to other tissues in certain types of cancers. Attempts to utilize fungal molecular signatures for cancer diagnosis and fungal-derived products for treatment are discussed. A few studies highlight fungi's impact on the responsiveness and sensitivity to chemotherapy, radiotherapy, immunotherapy, and fecal microbiota transplant. Given the limited understanding and techniques in fungal research, the studies on gut fungi are still facing great challenges, despite having great potentials.
Topics: Humans; Mycobiome; Gastrointestinal Microbiome; Fungi; Carcinogenesis; Cell Transformation, Neoplastic
PubMed: 38485702
DOI: 10.1080/19490976.2024.2328868