-
Signal Transduction and Targeted Therapy Feb 2023
Topics: Humans; Mycobiome; Neoplasms
PubMed: 36725834
DOI: 10.1038/s41392-023-01334-6 -
Frontiers in Immunology 2022Mounting evidence suggests that bacterial dysbiosis and immunity disorder are associated with patients with chronic kidney disease (CKD), but the mycobiome is beginning...
OBJECTIVES
Mounting evidence suggests that bacterial dysbiosis and immunity disorder are associated with patients with chronic kidney disease (CKD), but the mycobiome is beginning to gain recognition as a fundamental part of our microbiome. We aim to characterize the profile of the mycobiome in the gut of CKD patients and its correlation to serum immunological profiles.
METHODS AND MATERIALS
Ninety-two CKD patients and sex-age-body mass index (BMI)-matched healthy controls (HCs) were recruited. Fresh samples were collected using sterile containers. ITS transcribed spacer ribosomal RNA gene sequencing was performed on the samples. An immunoturbidimetric test was used to assess the serum levels of immunological features.
RESULTS
The CKD cohort displayed a different microbial community from that in the HC cohort according to principal coordinate analysis (PCoA). (=0.001). The comparison of the two cohorts showed that the CKD cohort had significantly higher gut microbial richness and diversity (<0.05). The CKD cohort had lower abundances of , , , and compared to the HC cohort, while it had higher (<0.05). However, the microbial community alteration was inconsistent with the severity of kidney damage in patients, as only patients in CKD stage 1~3 had differed microbial community concerning for HCs based on PCoA (<0.05). The serum concentration of the kappa light chain in CKD patients was positively associated with , whereas the it was negatively associated with (<0.05).
CONCLUSIONS
Not only was gut mycobiome dysbiosis observed in CKD patients, but the dysbiosis was also associated with the immunological disorder. These findings suggest that therapeutic strategies targeting gut mycobiome might be effective.
Topics: Dysbiosis; Humans; Immunoglobulin kappa-Chains; Microbiota; Mycobiome; Renal Insufficiency, Chronic; Saccharomyces
PubMed: 35784313
DOI: 10.3389/fimmu.2022.843695 -
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 -
Nature Genetics Jun 2024
Topics: Humans; Metagenomics; Gastrointestinal Microbiome; Mycobiome; Fungi; Metagenome
PubMed: 38871865
DOI: 10.1038/s41588-024-01817-4 -
Medical Mycology Jan 2022Analysis of mycobiome from formalin-fixed, paraffin-embedded (FFPE) biopsies should preferentially detect only fungi which are actually present in the intestine wall, in...
UNLABELLED
Analysis of mycobiome from formalin-fixed, paraffin-embedded (FFPE) biopsies should preferentially detect only fungi which are actually present in the intestine wall, in contrast to stool samples, which are limited by the diet composition. Next generation sequencing provides the advantage of analyzing many species from a single sample. Consequently, canonical correspondence analysis divided fungal genera present in FFPE intestinal tissues into three well-defined experimental groups (negative controls - NC, Crohn's disease - CD, ulcerative colitis - UC). Simultaneously, the analysis showed that particular fungal genera are associated with these experimental groups and several fungal genera occurred in all experimental groups equally. Our results also showed a noticeable increase of Ascomycota proportion from NC, through CD to UC. Fungal genera Malassezia, Cladosporium and Toninia occurred in all experimental groups assuming that they are common components of the intestinal mycobiome. Other fungal genera found only in the NC experimental group were non-pathogenic and might bring some benefits. In contrast, CD and UC samples were characterized by an accumulation of genera with inhibitive effects on growth of other fungal genera and the presence of opportunistic pathogens. Furthermore, a decrease in the fungal genus Malassezia in inflammatory tissues was observed; Specifically, the UC experimental group showed a connection between the presence of Candida and seven time's lower amounts of Malassezia (compared to amounts found in NC). The CD experimental group was characterized by the simultaneous presence of Engyodontium album with Lecanicillium, and indicates a possible pathogenic effect of Ramularia in disease development.
LAY SUMMARY
Mycobiome analysis of formalin-fixed and paraffin-embedded biopsies may highlight actual fungal genera composition in the intestinal wall. Interestingly, experimental groups of Crohn's disease and ulcerative colitis clearly differed by structure of their mycobiomes.
Topics: Adult; Aged; Ascomycota; Biopsy; Female; Humans; Inflammatory Bowel Diseases; Intestines; Male; Middle Aged; Mycobiome; Young Adult
PubMed: 34850076
DOI: 10.1093/mmy/myab076 -
Nature Communications Jun 2023Despite their role in host nutrition, the anaerobic gut fungal (AGF) component of the herbivorous gut microbiome remains poorly characterized. Here, to examine global...
Despite their role in host nutrition, the anaerobic gut fungal (AGF) component of the herbivorous gut microbiome remains poorly characterized. Here, to examine global patterns and determinants of AGF diversity, we generate and analyze an amplicon dataset from 661 fecal samples from 34 mammalian species, 9 families, and 6 continents. We identify 56 novel genera, greatly expanding AGF diversity beyond current estimates (31 genera and candidate genera). Community structure analysis indicates that host phylogenetic affiliation, not domestication status and biogeography, shapes the community rather than. Fungal-host associations are stronger and more specific in hindgut fermenters than in foregut fermenters. Transcriptomics-enabled phylogenomic and molecular clock analyses of 52 strains from 14 genera indicate that most genera with preferences for hindgut hosts evolved earlier (44-58 Mya) than those with preferences for foregut hosts (22-32 Mya). Our results greatly expand the documented scope of AGF diversity and provide an ecologically and evolutionary-grounded model to explain the observed patterns of AGF diversity in extant animal hosts.
Topics: Animals; Mycobiome; Phylogeny; Feces; Digestive System; Biological Evolution; Mammals
PubMed: 37365172
DOI: 10.1038/s41467-023-39508-z -
Medical Mycology Jul 2021The genus Malassezia is part of the normal skin mycobiota of a wide range of warm-blooded animals. In this genus, M. cuniculi is the only species described from rabbits....
UNLABELLED
The genus Malassezia is part of the normal skin mycobiota of a wide range of warm-blooded animals. In this genus, M. cuniculi is the only species described from rabbits. However, Malassezia species are rarely studied in lagomorphs. In the present study, the presence of Malassezia was assessed in samples from the external ear canal of healthy rabbits of different breeds. Cytological and culture techniques, Sanger sequencing, and Next-generation sequencing (NGS) were used to describe the ear mycobiota in the samples. Although no growth was observed in the cultured plates, cytological examination revealed the presence of round cells similar to those of Malassezia yeasts. For metagenomics analysis, the D1/D2 domain of the large subunit of the ribosomal DNA (LSU rDNA) was PCR amplified and the resulting reads were mapped against a custom-made cured database of 26S fungal sequences. NGS analysis revealed that Basidiomycota was the most abundant phylum in all the samples followed by Ascomycota. Malassezia was the most common genus presenting the highest abundance in the external ear canal. Malassezia phylotype 131 and M. cuniculi were the main sequences detected in the external auditory canal of rabbits. The study included both lop-eared and erect-eared rabbits and no differences were observed in the results when comparing both groups. This is the first attempt to study the external ear canal mycobiome of rabbits of different breeds using NGS.
LAY SUMMARY
In the present study, the presence of Malassezia was assessed in samples from the external ear canal of healthy rabbits of different breeds. Cytological and culture techniques, Sanger sequencing, and Next-generation sequencing (NGS) were used to describe the ear mycobiota in the samples.
Topics: Animals; Breeding; DNA, Ribosomal; Ear Canal; High-Throughput Nucleotide Sequencing; Malassezia; Metagenomics; Mycobiome; Rabbits
PubMed: 33369664
DOI: 10.1093/mmy/myaa097 -
Trends in Cancer May 2024The cancer mycobiome has recently become a research hotspot. While the intratumor mycobiota is implicated in cancer initiation and progression, the gut mycobiota...
The cancer mycobiome has recently become a research hotspot. While the intratumor mycobiota is implicated in cancer initiation and progression, the gut mycobiota functions as biomarkers for cancer diagnosis and treatment. In this forum article we highlight the involvement of the mycobiome in correlation-, causation-, and prediction-oriented cancer research and discuss the potential of this burgeoning field.
Topics: Humans; Neoplasms; Mycobiome; Gastrointestinal Microbiome; Biomarkers, Tumor; Biomedical Research
PubMed: 38494372
DOI: 10.1016/j.trecan.2024.02.009 -
BMC Microbiology Mar 2023As the Human Microbiome Project (HMP) progresses, the relationship between microbes and human health has been receiving increasing attention. A growing number of reports...
As the Human Microbiome Project (HMP) progresses, the relationship between microbes and human health has been receiving increasing attention. A growing number of reports support the correlation between cancer and microbes. However, most studies have focused on bacteria, rather than fungal communities. In this study, we studied the alteration in lung mycobiome in patients with non-small-cell lung cancer (NSCLC) using metagenomic sequencing and qPCR. The higher fungal diversity and more complex network were observed in the patients with NSCLC. In addition, Alternaria arborescens was found as the most relevant fungus to NSCLC, and the enrichment of it in cancerous tissue was also detected. This study proposes that the changes in fungal communities may be closely related to lung cancer, and provides insights into further exploration the relationship between lung cancer and fungi.
Topics: Humans; Mycobiome; Carcinoma, Non-Small-Cell Lung; Fungi; Lung Neoplasms; Lung
PubMed: 36966280
DOI: 10.1186/s12866-023-02790-4 -
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