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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 -
EBioMedicine Sep 2021The mycobiome is the fungal component of the gut microbiome and is implicated in several autoimmune diseases. However, its role in MS has not been studied.
BACKGROUND
The mycobiome is the fungal component of the gut microbiome and is implicated in several autoimmune diseases. However, its role in MS has not been studied.
METHODS
In this case-control observational study, we performed ITS sequencing and characterised the gut mycobiome in people with MS (pwMS) and healthy controls at baseline and after six months.
FINDINGS
The mycobiome had significantly higher alpha diversity and inter-subject variation in pwMS than controls. Saccharomyces and Aspergillus were over-represented in pwMS. Saccharomyces was positively correlated with circulating basophils and negatively correlated with regulatory B cells, while Aspergillus was positively correlated with activated CD16 dendritic cells in pwMS. Different mycobiome profiles, defined as mycotypes, were associated with different bacterial microbiome and immune cell subsets in the blood. Initial treatment with dimethyl fumarate, a common immunomodulatory therapy which also has fungicidal activity, did not cause uniform gut mycobiome changes across all pwMS.
INTERPRETATION
There is an alteration of the gut mycobiome in pwMS, compared to healthy controls. Further study is required to assess any causal association of the mycobiome with MS and its direct or indirect interactions with bacteria and autoimmunity.
FUNDING
This work was supported by the Washington University in St. Louis Institute of Clinical and Translational Sciences, funded, in part, by Grant Number # UL1 TR000448 from the National Institutes of Health, National Center for Advancing Translational Sciences, Clinical and Translational Sciences Award (Zhou Y, Piccio, L, Lovett-Racke A and Tarr PI); R01 NS102633-04 (Zhou Y, Piccio L); the Leon and Harriet Felman Fund for Human MS Research (Piccio L and Cross AH). Cantoni C. was supported by the National MS Society Career Transition Fellowship (TA-1805-31003) and by donations from Whitelaw Terry, Jr. / Valerie Terry Fund. Ghezzi L. was supported by the Italian Multiple Sclerosis Society research fellowship (FISM 2018/B/1) and the National Multiple Sclerosis Society Post-Doctoral Fellowship (FG- 1907-34474). Anne Cross was supported by The Manny & Rosalyn Rosenthal-Dr. John L. Trotter MS Center Chair in Neuroimmunology of the Barnes-Jewish Hospital Foundation. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.
Topics: Biomarkers; Body Mass Index; Case-Control Studies; Computational Biology; Diet; Disease Susceptibility; Dysbiosis; Feces; Gastrointestinal Microbiome; Host Microbial Interactions; Humans; Metagenome; Metagenomics; Multiple Sclerosis; Mycobiome
PubMed: 34455391
DOI: 10.1016/j.ebiom.2021.103557 -
Frontiers in Cellular and Infection... 2021Reports on alterations in the oral mycobiome of HIV-infected patients are still limited. This study was designed to compare the salivary mycobiome between 30 human...
Reports on alterations in the oral mycobiome of HIV-infected patients are still limited. This study was designed to compare the salivary mycobiome between 30 human immunodeficiency virus (HIV) infections and 30 healthy controls and explore the effect of antiretroviral therapy (ART) administration on the oral mycobiome of HIV infections. Results showed that the diversity and richness of salivary mycobiome in HIV-infected individuals were higher than those of controls ( < 0.05). After ART, the diversity and richness of salivary mycobiome in HIV-infected patients were reduced significantly ( < 0.05). , , , , and were significantly enriched in the HIV group and dramatically decreased after ART. While the relative abundance of , , and significantly increased in patients with HIV after ART. Correlation analysis revealed that , , , and were positively correlated with viral load (VL), whereas and were negatively related to VL and positively related to CD4 T-cell counts. All results showed that HIV infection and ART administration affected the composition of salivary mycobiome communities. Furthermore, differences of salivary mycobiome in HIV infections after ART were complex and might mirror the immune state of the body.
Topics: HIV; HIV Infections; Humans; Malassezia; Mycobiome; Viral Load
PubMed: 34926323
DOI: 10.3389/fcimb.2021.781246 -
Current Opinion in Microbiology Dec 2022The mosaic ecosystems of microbes that live on our skin encompass not only bacteria but also fungi, microeukaryotes, and viruses. As the second most prevalent group,... (Review)
Review
The mosaic ecosystems of microbes that live on our skin encompass not only bacteria but also fungi, microeukaryotes, and viruses. As the second most prevalent group, unique fungal communities are found across the dry, moist, and oily microenvironments of human skin, and alterations of these communities are largely driven by changes in skin physiology throughout an individual's lifespan. Fungi have also been associated with infection and dermatological disorders, resulting from the disrupted balance between fungal-bacterial networks on the skin. Mechanisms of colonization resistance toward fungi in the skin microbiome of animals have advanced our understanding in conservation strategies, yet in the human skin, the fungal microbiome (mycobiome) remains vastly unexplored. Here, we review recent studies on the role of fungi in the skin microbiome, emphasizing how fungal-bacterial interactions at the skin surface play an important ecological function in vertebrate hosts.
Topics: Animals; Humans; Mycobiome; Fungi; Microbiota; Skin; Bacteria
PubMed: 36372041
DOI: 10.1016/j.mib.2022.102235 -
Gut Microbes 2022While the intestinal microbiome seems a major driver of persistent immune defects in people with HIV (PWH), little is known about its fungal component, the mycobiome. We...
While the intestinal microbiome seems a major driver of persistent immune defects in people with HIV (PWH), little is known about its fungal component, the mycobiome. We assessed the inter-kingdom mycobiome-bacteriome interactions, the impact of diet, and the association with the innate and adaptive immunity in PWH on antiretroviral therapy. We included 24 PWH individuals and 12 healthy controls. We sequenced the Internal Transcribed Spacer 2 amplicons, determined amplicon sequence variants, measured biomarkers of the innate and adaptive immunity in blood and relations with diet. Compared to healthy controls, PWH subjects exhibited a distinct and richer mycobiome and an enrichment for , and . In PWH, and species were strongly correlated with several bacterial genera, including genus. Regarding the links between the mycobiome and systemic immunology, we found a positive correlation between species and the levels of proinflammatory cytokines (sTNF-R2 and IL-17), interleukin 22 (a cytokine implicated in the regulation of mucosal immunity), and CD8+ T cell counts. This suggests an important role of the yeasts in systemic innate and adaptive immune responses. Finally, we identified inter-kingdom interactions implicated in fiber degradation, short-chain fatty acid production, and lipid metabolism, and an effect of vegetable and fiber intake on the mycobiome. Therefore, despite the great differences in abundance and diversity between the bacterial and fungal communities of the gut, we defined the changes associated with HIV, determined several different inter-kingdom associations, and found links between the mycobiome, nutrient metabolism, and systemic immunity.
Topics: Bacteria; Candida; Diet; Fungi; Gastrointestinal Microbiome; HIV Infections; Humans; Inflammation; Mycobiome
PubMed: 35748016
DOI: 10.1080/19490976.2022.2089002 -
Gut and Liver Jul 2023There is growing evidence of the role of fungal microbiota in the pathogenesis of inflammatory bowel disease (IBD). Fungi can exert direct pro-inflammatory effects or... (Review)
Review
There is growing evidence of the role of fungal microbiota in the pathogenesis of inflammatory bowel disease (IBD). Fungi can exert direct pro-inflammatory effects or modify the bacterial composition via interkingdom interactions. Although several studies have demonstrated alterations in the fecal fungal microbiota composition in IBD, there is a wide variation in the mycobiome in different populations, with no definite pattern that can define the mycobiome in IBD having yet been identified. Recent work has suggested that characterizing the fecal fungal composition may influence therapeutic decisions and help to predict outcomes in a subset of IBD patients. In this study, we review the current literature on the emerging role of the fecal mycobiome as a potential tool for precision medicine in IBD.
Topics: Humans; Mycobiome; Precision Medicine; Gastrointestinal Microbiome; Inflammatory Bowel Diseases; Feces
PubMed: 37305948
DOI: 10.5009/gnl220537 -
Inflammatory Bowel Diseases Mar 2023Inflammatory bowel disease (IBD), a disorder characterized by chronic inflammation of the gastrointestinal (GI) tract and a range of adverse health effects including... (Review)
Review
Inflammatory bowel disease (IBD), a disorder characterized by chronic inflammation of the gastrointestinal (GI) tract and a range of adverse health effects including diarrhea, abdominal pain, vomiting, and bloody stools, affects nearly 3.1 million genetically susceptible adults in the United States today. Although the etiology of IBD remains unclear, genetics, stress, diet, and gut microbiota dysbiosis- especially in immunocompromised individuals- have been identified as possible causes of disease. Although previous research has largely focused on the role of bacteria in IBD pathogenesis, recently observed alterations of fungal load and biodiversity in the GI tract of afflicted individuals suggest interkingdom interactions amongst different gut microbial communities, particularly between bacteria and fungi. These discoveries point to the potential utilization of treatment approaches such as antibiotics, antifungals, probiotics, and postbiotics that target both bacteria and fungi in managing IBD. In this review, we discuss the impact of specific fungi on disease pathogenesis, with a focus on the highly virulent genus Candida and how the presence of certain co-enzymes impacts its virulence. In addition, we evaluate current gut microbiome-based therapeutic approaches with the intention of better understanding the mechanisms behind novel therapies.
Topics: Adult; Humans; Mycobiome; Inflammatory Bowel Diseases; Inflammation; Bacteria; Dysbiosis
PubMed: 35851921
DOI: 10.1093/ibd/izac156 -
Inflammatory Bowel Diseases Oct 2023Although gut fungi have been implicated in the immunopathogenesis of inflammatory bowel disease, the fungal microbiome has not been deeply explored across endohistologic...
BACKGROUND
Although gut fungi have been implicated in the immunopathogenesis of inflammatory bowel disease, the fungal microbiome has not been deeply explored across endohistologic activity and treatment exposure in ulcerative colitis.
METHODS
We analyzed data from the SPARC IBD (Study of a Prospective Adult Research Cohort with Inflammatory Bowel Disease) registry. We evaluated the fungal composition of fecal samples from 98 patients with ulcerative colitis across endoscopic activity (n = 43), endohistologic activity (n = 41), and biologic exposure (n = 82). Across all subgroups, we assessed fungal diversity and differential abundance of taxonomic groups.
RESULTS
We identified 500 unique fungal amplicon sequence variants across the cohort of 82 patients, dominated by phylum Ascomycota. Compared with endoscopic remission, patients with endoscopic activity had increased Saccharomyces (log2 fold change = 4.54; adjusted P < 5 × 10-5) and increased Candida (log2 fold change = 2.56; adjusted P < .03). After adjusting for age, sex, and biologic exposure among patients with endoscopic activity, Saccharomyces (log2 fold change = 7.76; adjusted P < 1 × 10-15) and Candida (log2 fold change = 7.28; adjusted P< 1 × 10-8) remained enriched during endoscopic activity compared with quiescence.
CONCLUSIONS
Endoscopic inflammation in ulcerative colitis is associated with an expansion of Saccharomyces and Candida compared with remission. The role of these fungal taxa as potential biomarkers and targets for personalized approaches to therapeutics in ulcerative colitis should be evaluated.
Topics: Adult; Humans; Colitis, Ulcerative; Mycobiome; Prospective Studies; Gastrointestinal Microbiome; Inflammatory Bowel Diseases; Candida; Biological Products
PubMed: 37221272
DOI: 10.1093/ibd/izad082 -
Current Opinion in Microbiology Aug 2019The human gastrointestinal tract is home to a thriving community of microbes including the fungal 'mycobiota'. Although sequencing methodology has enumerated diverse... (Review)
Review
The human gastrointestinal tract is home to a thriving community of microbes including the fungal 'mycobiota'. Although sequencing methodology has enumerated diverse fungal genera within this niche, discerning persistent symbiotic residents from contaminants and purely environmental transients remains a challenge. Recent advances in culturomics and sequencing employing metagenomics, metatranscriptomics and longitudinal studies have begun to reveal a human symbiont 'core mycobiome' that may contribute to human health and disease. Trans-kingdom interactions between the bacterial microbiota and evolution within the niche have defined C. albicans as a true symbiont, setting a bar for defining other fungi. Additionally, elegant investigations of mammalian antifungal immunity have examined mononuclear phagocytes, neutrophils, antigen-specific recognition by T cells and other mechanisms important for local and systemic effects on the host, providing further evidence supporting gut persistence. In this review we discuss current research aimed at investigating the symbiotic mycobiota and propose four criteria aiding in the differentiation of fungal symbionts from environmental transients.
Topics: Animals; Fungi; Gastrointestinal Microbiome; Gastrointestinal Tract; Humans; Metagenomics; Mice; Mycobiome; Symbiosis
PubMed: 31726316
DOI: 10.1016/j.mib.2019.09.010