-
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 -
PloS One 2021The fungal part of the pulmonary microbiome (mycobiome) is understudied. We report the composition of the oral and pulmonary mycobiome in participants with COPD compared... (Observational Study)
Observational Study
BACKGROUND
The fungal part of the pulmonary microbiome (mycobiome) is understudied. We report the composition of the oral and pulmonary mycobiome in participants with COPD compared to controls in a large-scale single-centre bronchoscopy study (MicroCOPD).
METHODS
Oral wash and bronchoalveolar lavage (BAL) was collected from 93 participants with COPD and 100 controls. Fungal DNA was extracted before sequencing of the internal transcribed spacer 1 (ITS1) region of the fungal ribosomal RNA gene cluster. Taxonomic barplots were generated, and we compared taxonomic composition, Shannon index, and beta diversity between study groups, and by use of inhaled steroids.
RESULTS
The oral and pulmonary mycobiomes from controls and participants with COPD were dominated by Candida, and there were more Candida in oral samples compared to BAL for both study groups. Malassezia and Sarocladium were also frequently found in pulmonary samples. No consistent differences were found between study groups in terms of differential abundance/distribution. Alpha and beta diversity did not differ between study groups in pulmonary samples, but beta diversity varied with sample type. The mycobiomes did not seem to be affected by use of inhaled steroids.
CONCLUSION
Oral and pulmonary samples differed in taxonomic composition and diversity, possibly indicating the existence of a pulmonary mycobiome.
Topics: Aged; Case-Control Studies; DNA, Fungal; Female; Fungi; Humans; Lung; Male; Middle Aged; Mouth; Mycobiome; Norway; Pulmonary Disease, Chronic Obstructive
PubMed: 33826639
DOI: 10.1371/journal.pone.0248967 -
Frontiers in Immunology 2022Human gut microbiome has gained great attention for its proposed roles in the development of hypertension. The fungal microbiome in the human gut (i.e. the mycobiome) is...
OBJECTIVES
Human gut microbiome has gained great attention for its proposed roles in the development of hypertension. The fungal microbiome in the human gut (i.e. the mycobiome) is beginning to gain recognition as a fundamental part of our microbiome. However, the existing knowledge of human mycobiome has never revealed the association between gut mycobiome and hypertension. It is known that inflammation and immunity contribute to human hypertension. Here, we sought to investigate whether gut mycobiome could predict the development of hypertension and its association with immunoglobulin light chains.
METHODS AND MATERIALS
Participants were classified into three cohorts: prehypertension (pre-HTN), hypertension (HTN), and normal-tension (NT) based on their blood pressure. Fresh samples were collected, and the ITS transcribed spacer ribosomal RNA gene sequence was performed. An immunoturbidimetric test was used to examine the serum levels of immunological light chains.
RESULTS
Subjects in both of the states of pre-HTN and HTN had different fungal microbiome community compared to the NT group (FDR<0.05). Slightly higher levels of fungal richness and diversity were observed in the groups of pre-HTN and HTN. The relative abundance of increased in the HTN group compared to that in the NT group, and the relative abundance of enriched in the NT group. For the pre-HTN group, the relative abundance of was positively associated with serum the concentration of light chain (LC) κ (r=0.510, P=0.044); for the HTN group, the relative abundance of was positively associated with the serum concentration of LC κ (P<0.05), the relative abundance of was positively associated with both the serum concentrations of LC κ and LC λ (r>0.30, P<0.05).
CONCLUSIONS
Our present study demonstrated that gut fungal dysbiosis occurred in the state of prehypertension, and fungal dysbiosis can predict the dysregulation of serum light chains in hypertension patients. Further study on modulating gut fungal community should be focused on balancing the immunological features in hypertension.
Topics: Humans; Mycobiome; Immunoglobulin Light Chains; Prehypertension; Dysbiosis; Hypertension
PubMed: 36643913
DOI: 10.3389/fimmu.2022.1089295 -
Pediatric Research Aug 2023The composition of the gut fungal microbiome, mycobiome, is likely associated with human health. Yet, the development of gut mycobiome is poorly understood in infants...
BACKGROUND
The composition of the gut fungal microbiome, mycobiome, is likely associated with human health. Yet, the development of gut mycobiome is poorly understood in infants and children. Here we investigate how perinatal events influence the development of gut mycobiome.
METHODS
In this prospective cohort study of 140 infants, we used ITS gene sequencing of fecal samples from birth to the age of 18 months. We compared gut mycobiome composition according to delivery mode and exposure to intrapartum antibiotics during vaginal delivery.
RESULTS
At birth, gut mycobiome were dominated by the genus Candida, at 6-month stool samples by Malassezia and Cystofilobasidium, and the 18-month stool samples by Trichosporon and unidentified fungi. Perinatal factors altered mycobiome. At 18 months, gut mycobiome of infants born vaginally consisted mostly of Trichosporon (32%) and unidentified fungi (31%), while those born via Cesarean section delivery samples had mycobiome dominated by Saccharomyces (50%). At the age of 18 months, those exposed to intrapartum antibiotics had mycobiome dominated by Trichosporon (66%) not seen in those unexposed to antibiotics.
CONCLUSIONS
Delivery mode and exposure to intrapartum antibiotic prophylaxis were markedly associated with gut mycobiome composition from birth to 18 months of age.
IMPACT
The composition of the gut mycobiome is likely associated with human health. Yet, the development of gut mycobiome is poorly understood in infants and children. In this prospective cohort study, delivery mode and exposure to intrapartum antibiotic prophylaxis were markedly associated with gut mycobiome composition from birth to 18 months of age. The impact of intrapartum antibiotic prophylaxis on fungal microbiome in vaginally born infants, previously shown to influence gut bacteriome composition, may be explained by the interaction between bacteria and fungi. Gut mycobiome composition likely deserves further investigation in relation to gut microbiome and health in children.
Topics: Infant, Newborn; Humans; Infant; Child; Pregnancy; Female; Child, Preschool; Mycobiome; Cesarean Section; Prospective Studies; Parturition; Anti-Bacterial Agents
PubMed: 36670159
DOI: 10.1038/s41390-023-02471-y -
Scientific Reports Jul 2021Microplastic (MP) is a pervasive pollutant in nature that is colonised by diverse groups of microbes, including potentially pathogenic species. Fungi have been largely...
Microplastic (MP) is a pervasive pollutant in nature that is colonised by diverse groups of microbes, including potentially pathogenic species. Fungi have been largely neglected in this context, despite their affinity for plastics and their impact as pathogens. To unravel the role of MP as a carrier of fungal pathogens in terrestrial ecosystems and the immediate human environment, epiplastic mycobiomes from municipal plastic waste from Kenya were deciphered using ITS metabarcoding as well as a comprehensive meta-analysis, and visualised via scanning electron as well as confocal laser scanning microscopy. Metagenomic and microscopic findings provided complementary evidence that the terrestrial plastisphere is a suitable ecological niche for a variety of fungal organisms, including important animal and plant pathogens, which formed the plastisphere core mycobiome. We show that MPs serve as selective artificial microhabitats that not only attract distinct fungal communities, but also accumulate certain opportunistic human pathogens, such as cryptococcal and Phoma-like species. Therefore, MP must be regarded a persistent reservoir and potential vector for fungal pathogens in soil environments. Given the increasing amount of plastic waste in terrestrial ecosystems worldwide, this interrelation may have severe consequences for the trans-kingdom and multi-organismal epidemiology of fungal infections on a global scale.
Topics: Ecosystem; Environmental Monitoring; Fungi; Microplastics; Mycobiome
PubMed: 34267241
DOI: 10.1038/s41598-021-92405-7 -
Journal of Dental Research Feb 2021Recent efforts to understand the oral microbiome have focused on its fungal component. Since fungi occupy a low proportion of the oral microbiome biomass, mycobiome... (Review)
Review
Recent efforts to understand the oral microbiome have focused on its fungal component. Since fungi occupy a low proportion of the oral microbiome biomass, mycobiome studies rely on sequencing of internal transcribed spacer (ITS) amplicons. ITS-based studies usually detect hundreds of fungi in oral samples. Here, we review the oral mycobiome, critically appraising the significance of such large fungal diversity. When harsh lysis methods are used to extract DNA, 2 oral mycobiome community types (mycotypes) are evident, each dominated by only 1 genus, either or . The rest of the diversity in ITS surveys represents low-abundance fungi possibly acquired from the environment and ingested food. So far, is the only genus demonstrated to reach a significant biomass in the oral cavity and clearly shown to be associated with a distinct oral ecology. thrives in the presence of lower oral pH and is enriched in caries, with mechanistic studies in animal models suggesting it participates in the disease process by synergistically interacting with acidogenic bacteria. serves as the main etiological agent of oral mucosal candidiasis, in which a -bacteriome partnership plays a key role. The function of other potential oral colonizers, such as lipid-dependent , is still unclear, with further studies needed to establish whether are metabolically active oral commensals. Low-abundance oral mycobiome members acquired from the environment may be viable in the oral cavity, and although they may not play a significant role in microbiome communities, they could serve as opportunistic pathogens in immunocompromised hosts. We suggest that further work is needed to ascertain the significance of oral mycobiome members beyond . ITS-based surveys should be complemented with other methods to determine the in situ biomass and metabolic state of fungi thought to play a role in the oral environment.
Topics: Bacteria; Fungi; Microbiota; Mouth; Mycobiome
PubMed: 32924741
DOI: 10.1177/0022034520956975 -
International Journal of Oral Science Jul 2019The biodiversity of the mycobiome, an important component of the oral microbial community, and the roles of fungal-bacterial and fungal-immune system interactions in...
The biodiversity of the mycobiome, an important component of the oral microbial community, and the roles of fungal-bacterial and fungal-immune system interactions in the pathogenesis of oral lichen planus (OLP) remain largely uncharacterized. In this study, we sequenced the salivary mycobiome and bacteriome associated with OLP. First, we described the dysbiosis of the microbiome in OLP patients, which exhibits lower levels of fungi and higher levels of bacteria. Significantly higher abundances of the fungi Candida and Aspergillus in patients with reticular OLP and of Alternaria and Sclerotiniaceae_unidentified in patients with erosive OLP were observed compared to the healthy controls. Aspergillus was identified as an "OLP-associated" fungus because of its detection at a higher frequency than in the healthy controls. Second, the co-occurrence patterns of the salivary mycobiome-bacteriome demonstrated negative associations between specific fungal and bacterial taxa identified in the healthy controls, which diminished in the reticular OLP group and even became positive in the erosive OLP group. Moreover, the oral cavities of OLP patients were colonized by dysbiotic oral flora with lower ecological network complexity and decreased fungal-Firmicutes and increased fungal-Bacteroidetes sub-networks. Third, several keystone fungal genera (Bovista, Erysiphe, Psathyrella, etc.) demonstrated significant correlations with clinical scores and IL-17 levels. Thus, we established that fungal dysbiosis is associated with the aggravation of OLP. Fungal dysbiosis could alter the salivary bacteriome or may reflect a direct effect of host immunity, which participates in OLP pathogenesis.
Topics: Adult; Bacteria; Case-Control Studies; Dysbiosis; Female; Humans; Lichen Planus, Oral; Male; Microbiota; Middle Aged; Mouth Mucosa; Mycobiome; Saliva
PubMed: 31263096
DOI: 10.1038/s41368-019-0045-2