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PeerJ 2024Urban forests are essential for maintaining urban ecological stability. As decomposers, soil microorganisms play an indispensable role in the stability of urban forest...
Urban forests are essential for maintaining urban ecological stability. As decomposers, soil microorganisms play an indispensable role in the stability of urban forest ecosystems, promoting the material cycle of the ecosystems. This study used high-throughput sequencing technology to explore the bacteria in six forest stands, including (ZL), (SSL), (SZY), mixed broad-leaved shrub forest (ZKG), mixed pine and cypress forest (SBL), and mixed broad-leaved tree forest (ZKQ). Meanwhile, the differences in fungal communities were investigated. The results show that ZL has the highest alpha diversity of bacterial communities, while its fungal community is the lowest; Proteobacteria is the most abundant bacterial phylum in the six forest stands; ZKQ has the highest fungal diversity. In addition, soil microbial communities are affected by environmental factors. Soil pH, organic matter (SOM), and available phosphorus (AP) significantly influence the compositions of urban forest soil microbial communities. This study revealed the differences in bulk soil (BS) microbial community structures among six forest stands and the relationship between environmental factors and soil microbial communities, which has important guiding significance for creating healthy and stable urban forests with profound ecological benefits.
Topics: Forests; Microbiota; Mycobiome; Trees; Soil
PubMed: 38444615
DOI: 10.7717/peerj.16987 -
Molecular Ecology May 2022The development of high-throughput sequencing (HTS) technologies has greatly improved our capacity to identify fungi and unveil their ecological roles across a variety... (Review)
Review
The development of high-throughput sequencing (HTS) technologies has greatly improved our capacity to identify fungi and unveil their ecological roles across a variety of ecosystems. Here we provide an overview of current best practices in metabarcoding analysis of fungal communities, from experimental design through molecular and computational analyses. By reanalysing published data sets, we demonstrate that operational taxonomic units (OTUs) outperform amplified sequence variants (ASVs) in recovering fungal diversity, a finding that is particularly evident for long markers. Additionally, analysis of the full-length ITS region allows more accurate taxonomic placement of fungi and other eukaryotes compared to the ITS2 subregion. Finally, we show that specific methods for compositional data analyses provide more reliable estimates of shifts in community structure. We conclude that metabarcoding analyses of fungi are especially promising for integrating fungi into the full microbiome and broader ecosystem functioning context, recovery of novel fungal lineages and ancient organisms as well as barcoding of old specimens including type material.
Topics: Biodiversity; DNA Barcoding, Taxonomic; Fungi; Microbiota; Mycobiome; Research Design
PubMed: 35395127
DOI: 10.1111/mec.16460 -
Molecular Nutrition & Food Research May 2024Gut fungi are important parts of intestinal microbes. Dietary ingredients have the potential to regulate the structure of gut fungi in different directions and modulate... (Review)
Review
Gut fungi are important parts of intestinal microbes. Dietary ingredients have the potential to regulate the structure of gut fungi in different directions and modulate mycobiome composition by changing dietary patterns, which have been applied to neurological disorders. Emerging pieces of evidence have revealed the regulatory functions of gut mycobiome in gastrointestinal diseases, but the relationships between gut fungi and functional gastrointestinal disorders (FGIDs) are ignored in the past. This review discusses the impact of dietary nutrients and patterns on mycobiome, and the possible ways in which gut fungi are involved in the pathogenesis of FGIDs. Besides affecting host immunity, intestinal fungi can be involved in the pathogenesis of FGIDs by endosymbiosis or bidirectional regulation with gut bacteria as well. In addition, the Mediterranean diet may be the most appropriate dietary pattern for subjects with FGIDs. A full understanding of these associations may have important implications for the pathogenesis and treatment of FGIDs.
Topics: Humans; Gastrointestinal Diseases; Gastrointestinal Microbiome; Diet; Mycobiome; Fungi; Diet, Mediterranean; Animals
PubMed: 38659179
DOI: 10.1002/mnfr.202300382 -
Microbiome Nov 2021Children spend considerable time in daycare centers in parts of the world and are exposed to the indoor micro- and mycobiomes of these facilities. The level of exposure...
BACKGROUND
Children spend considerable time in daycare centers in parts of the world and are exposed to the indoor micro- and mycobiomes of these facilities. The level of exposure to microorganisms varies within and between buildings, depending on occupancy, climate, and season. In order to evaluate indoor air quality, and the effect of usage and seasonality, we investigated the spatiotemporal variation in the indoor mycobiomes of two daycare centers. We collected dust samples from different rooms throughout a year and analyzed their mycobiomes using DNA metabarcoding.
RESULTS
The fungal community composition in rooms with limited occupancy (auxiliary rooms) was similar to the outdoor samples, and clearly different from the rooms with higher occupancy (main rooms). The main rooms had higher abundance of Ascomycota, while the auxiliary rooms contained comparably more Basidiomycota. We observed a strong seasonal pattern in the mycobiome composition, mainly structured by the outdoor climate. Most markedly, basidiomycetes of the orders Agaricales and Polyporales, mainly reflecting typical outdoor fungi, were more abundant during summer and fall. In contrast, ascomycetes of the orders Saccharomycetales and Capnodiales were dominant during winter and spring.
CONCLUSIONS
Our findings provide clear evidences that the indoor mycobiomes in daycare centers are structured by occupancy as well as outdoor seasonality. We conclude that the temporal variability should be accounted for in indoor mycobiome studies and in the evaluation of indoor air quality of buildings. Video abstract.
Topics: Air Microbiology; Air Pollution, Indoor; Child; Dust; Environmental Monitoring; Fungi; Humans; Mycobiome; Seasons
PubMed: 34753520
DOI: 10.1186/s40168-021-01167-x -
Metabolism: Clinical and Experimental Aug 2017Human gut microbiome is defined as the gene complement of the gut microbial community, measured via laboratory metagenomic techniques. It includes bacteriome, virome and... (Review)
Review
Human gut microbiome is defined as the gene complement of the gut microbial community, measured via laboratory metagenomic techniques. It includes bacteriome, virome and mycobiome, which represent, respectively, the assemblages of bacteria, viruses and fungi, living in the human gut. Gut microbiota function as a living "organ" that interacts with the gastro-intestinal environment, provides nutrients and vitamins to the organism and transduces hormonal messages, essentially influencing the main metabolic pathways, including drug metabolism. A clear association between gut, and glucose metabolism disorders has recently emerged. Medications acting on glucose absorption in the gut, or enhancing gut hormone activity are already extensively employed in the therapy of diabetes. Moreover, the gut is characterized by immune, and autonomous neuronal features, which play a critical role in maintaining glucose metabolism homeostasis. Gut microbes respond to neuroendocrine, and immune biochemical messages, affecting the health, and behavior of the host. There is vast heterogeneity in the studies included in this review, hence a meta-analysis, or a systematic review were not applicable. In this article, we attempt to reveal the interplay between human gut microbiota physiology, and hyperglycemic states, synthesizing, and interpreting findings from human studies.
Topics: Animals; Gastrointestinal Microbiome; Glucose Metabolism Disorders; Humans; Hyperglycemia; Microbiota; Mycobiome
PubMed: 28732571
DOI: 10.1016/j.metabol.2017.04.014 -
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 -
Environmental Microbiology Aug 2022The factors shaping the composition of the tree mycobiome are still under investigation. We tested the effects of host genotype, site, host phenotypic traits, and air...
The factors shaping the composition of the tree mycobiome are still under investigation. We tested the effects of host genotype, site, host phenotypic traits, and air fungal spore communities on the assembly of the fungi inhabiting Norway spruce needles. We used Norway spruce clones and spore traps within the collection sites and characterized both needle and air mycobiome communities by high-throughput sequencing of the ITS2 region. The composition of the needle mycobiome differed between Norway spruce clones, and clones with high genetic similarity had a more similar mycobiome. The needle mycobiome also varied across sites and was associated with the composition of the local air mycobiome and climate. Phenotypic traits such as diameter at breast height or crown health influenced the needle mycobiome to a lesser extent than host genotype and air mycobiome. Altogether, our results suggest that the needle mycobiome is mainly driven by the host genotype in combination with the composition of the local air spore communities. Our work highlights the role of host intraspecific variation in shaping the mycobiome of trees and provides new insights on the ecological processes structuring fungal communities inhabiting woody plants.
Topics: Fungi; Genotype; Mycobiome; Picea; Spores, Fungal; Trees
PubMed: 35315253
DOI: 10.1111/1462-2920.15974 -
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 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 -
Clinical and Experimental Allergy :... Dec 2021Major allergen sources Dermatophagoides farinae, Dermatophagoides pteronyssinus and Tyrophagus putrescentiae have been reported to have distinct microbiomes. The purpose...
BACKGROUND
Major allergen sources Dermatophagoides farinae, Dermatophagoides pteronyssinus and Tyrophagus putrescentiae have been reported to have distinct microbiomes. The purpose of this study was to investigate the effect of each mite on airway epithelial cells as a model of airway allergic disease.
METHODS
Transcriptomic analysis (RNA-seq) of an airway epithelial cell line (BEAS-2B) was performed to compare gene expression patterns after treatment with extracts of three mite species (D. farinae, D. pteronyssinus and T. putrescentiae). In addition, mycobiome deep sequencing of mites was employed to identify fungal species that interact with the microbiomes of the mites.
RESULTS
Immune responses to bacteria were enriched only in the D. farinae-treated group as this species harboured larger numbers of bacteria than the other mites, and the high level of LPS in D. farinae caused proinflammatory cytokine production in airway epithelial cells. In addition, antibiotic metabolism pathways were enriched in D. pteronyssinus-treated cells but not in D. farinae -treated cells. Subsequent experiments revealed that D. pteronyssinus had a high fungal load that inhibited bacterial survival in this mite species.
CONCLUSION
The large amount of bacteria in D. farinae causes airway epithelial cells to produce more allergy-related cytokines than D. pteronyssinus, since fungi present in D. pteronyssinus suppress the abundance of mite-associated bacteria.
Topics: Allergens; Animals; Dust; Humans; Hypersensitivity; Microbiota; Mites; Mycobiome; Pyroglyphidae
PubMed: 34087033
DOI: 10.1111/cea.13962