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38 results for “Mycobiome”
Dryland soil mycobiome response to long-term precipitation variability at the Jornada Basin LTER site, 2013-2019
This dataset contains data and code for the paper "Dryland soil mycobiome response to long-term precipitation variability depends on host type" published in Journal of Ecology in 2022. Data were collected at the Jornada Basin LTER site in southern New Mexico, USA. Soil samples were sent to the University of Georgia, for DNA extraction and sequencing, performed at the Georgia Genomics and Bioinformatics Core in Athens, GA. Sequencing data are archived at NCBI under project identifier PRJNA884111.
The mycobiome of the gut of willow wood borer, Xiphydria prolongata (Hymenoptera: Xiphydriidae): a rich source of rare yeasts
<p>A high-throughput amplicon sequencing as a culture-independent approach was used to identify the gut mycobiome of the willow wood borer <em>Xiphydria prolongata</em>. The findings of this study are significance in terms of the insect-fungal interactions and indicate the unexpected richness of the mycobiome and the presence of many rare yeast species in the wood borer gut. A total of 40 fungal genera were found, and among them, only one endophytic fungi, <em>Daldinia</em> (Hypoxylaceae), has been previously reported in <em>Xiphydria.</em> <em>Zygosaccharomyces siamensis</em> is the most prevalent ascomycete species, while <em>Rhodosporidiobolus colostri</em> is the most abundant basidiomycetous yeast in <em>X. prolongata</em>. Some of the species identified in here was known as very rare fungus such as <em>Skoua fertilis</em>, <em>Chaetomium nepalense, R. colostri </em>and<em> Vustinia terrae</em>. This study is also the first report to <em>S. fertilis </em>and<em> V. terrae</em> in the insect gut flora. These funguses most likely aid in the digestion of lignocellulose in the gut of wood borer. Therefore, further researches are required to know the source of acquisition and functional role of these yeast and their industrial potential.</p>
Annual plant competition experiment results and associated mycobiome ASV tables
<p>Major theories regarding microbe-mediated plant community dynamics assume that plant species cultivate distinct microbial communities. However, few studies empirically assess the role of species-associated microbial community dissimilarity in plant competitive dynamics. In this study, we paired a competition experiment between eight annual forbs with a characterization of species-associated fungal communities to assess whether mycobiome dissimilarity is associated with pairwise competitive dynamics. Using a quantitative approach informed by modern coexistence theory, we found that fungal dissimilarity was correlated with both increased stabilizing niche differences and fitness inequalities. Additionally, we found that the probability of coexistence increased with mycobiome dissimilarity. When subsetting the community into different fungal functional groups (pathotrophs, saprotrophs, symbiotrophs), overall relationships between dissimilarity and competitive dynamics were independent of these functional groups. </p> <p>Synthesis: These results suggest that fungal community divergence may play an important role in mediating plant competitive dynamics. Although fungal community dissimilarity is associated with both niche and fitness differences, complex biotic and/or abiotic interactions belowground may result in an observed correlation between fungal community dissimilarity and plant coexistence. Ultimately, this study suggests a novel approach to better understanding how microbiome dissimilarity may impact host community dynamics.</p>
Annual plant competition experiment results and associated mycobiome ASV tables
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Impact of nitrogen and phosphorus addition on resident soil and root mycobiomes in beech forests
<p>The aim of the study was to investigate the influence of fertilizers on root-associated and soil residing fungi in beech forests. We report data from a fertilization experiment in three temperate beech forest with contrasting soil phosphorus concentrations. We used soil cores and the fractions of the organic layer and mineral topsoil separately of spring and fall 2018. We collected bulk soil and roots. We provide data on soil for pH, mineral elements, ammonium, nitrate, carbon, nitrogen. We provide data on root mineral nutrients, carbon and nitrogen. Illumina sequencing in soil and roots provides fungal amplicon sequence variant (ASV) and morphotyping of beech fine roots the active colonizing ectomycorrhizal fungi, including diversity parameters.</p>
Control samples for ITS1 Metabarcoding of the Cynomolgus Macaque Intestinal Mycobiome
<p>Library and Sequencing controls used for the Metabarcoding ITS1 analysis of intestinal content of the Cynomolgus Macaque</p> <p> </p>
Earth Microbiome Project and Global Soil Mycobiome Data Subsets
<p>These are subsets of the publicly available Earth Microbiome Project (<a href="https://earthmicrobiome.org/">https://earthmicrobiome.org/</a>, <a href="../records/890000">https://zenodo.org/records/890000</a>) [1] and Global Soil Mycobiome project datasets (<a href="https://doi.org/10.15156/BIO/2263453"><span>https://doi.org/10.15156/BIO/2263453</span></a>) [2,3], provided for benchmarking and testing purposes. These are re-released with attribution under a CC-BY-4.0 license, following the license of the original source creators. If you use this resource, please cite the original references as given below:</p> <p>1. Thompson, L. R., <em>et al.</em> (2017). A communal catalogue reveals Earth’s multiscale microbial diversity. <em>Nature</em>, 551:457-463. <a href="http://doi.org/10.1038/nature24621" target="_blank" rel="noopener noreferrer">doi:10.1038/nature24621</a>.</p> <p>2. Tedersoo, L., <em>et al.</em> The Global Soil Mycobiome consortium dataset for boosting fungal diversity research. <em>Fungal Diversity</em> <strong>111</strong>, 573–588 (2021). https://doi.org/10.1007/s13225-021-00493-7</p> <p>3. Tedersoo, L. (2021): The Global Soil Mycobiome consortium dataset for boosting fungal diversity research v2. University of Tartu. 10.15156/BIO/2263453</p>
Data for: The indoor mycobiomes of daycare centers are affected by occupancy and climate
<p>With an alarming increase in chronic diseases like childhood asthma and allergies, there is an increased focus on the exposure of young children to indoor biological and chemical air pollutants. Our study of 125 daycares throughout Norway demonstrates that the indoor mycobiome not only reflects cooccurring outdoor fungi but also includes a high abundance of yeast and mold fungi with an affinity for indoor environments.</p>
Analysing indoor mycobiomes through a large‐scale citizen science study in Norway
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The avian mycobiome: Phylogenetic trees and alignments for key fungal groups
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Data from: Assemblies of leaf and root mycobiomes in a temperate grassland: Dispersal limitation overpowers selection
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Impact of nitrogen and phosphorus addition on resident soil and root mycobiomes in beech forests
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Data for: The indoor mycobiomes of daycare centers are affected by occupancy and climate
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Data from: Host genotype is an important determinant of the cereal phyllosphere mycobiome
The phyllosphere mycobiome in cereals is an important determinant of crop health. However, an understanding of the factors shaping this community is lacking. Fungal diversity in leaves from a range of cultivars of winter wheat (Triticum aestivum), winter and spring barley (Hordeum vulgare) and a smaller number of samples from oat (Avena sativa), rye (Secale cereale) and triticale (Triticum × Secale) was studied using next-generation sequencing. The effects of host genotype, fungicide treatment and location on fungal communities were explored. In total, 635 251 fungal internal transcribed spacer (ITS) reads were obtained from 210 leaf samples. Visual disease assessments and relative read abundance of Zymoseptoria tritici and Ramularia collo-cygni were strongly positively related. Crop genotype at the species level explained 43% of the variance in the total dataset, followed by fungicide treatment (13%) and location (4%). Indicator species, including plant pathogens, responding to factors such as crop species, location and treatment were identified. Host genotype at both the species and cultivar level is important in shaping phyllosphere fungal communities, whereas fungicide treatment and location have minor effects. We found many host-specific fungal pathogens, but also a large diversity of fungi that were relatively insensitive to host genetic background, indicating that host-specific pathogens live in a 'sea' of nonspecific fungi.
A genomic compendium of cultivated human gut fungi characterizes the gut mycobiome and its relevance to common diseases
<p><span>Morphological and scanning electron microscopy images of 206 fungal species cultivated from human feces. </span></p>
Effects of the fungicide penconazole on the leaf litter associated aquatic mycobiome in artificial stream channel and flask experiments
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Spatiotemporal variation of the indoor mycobiome in daycare centers
Abstract 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.
Infant mode of delivery shapes the skin mycobiome of prepubescent children
<p>STORMS checklist for <strong>Infant mode of delivery shapes the skin mycobiome of prepubescent children</strong>.</p>
A longitudinal study of the pulmonary mycobiome in subjects with and without chronic obstructive pulmonary disease
Background <p>Few studies have examined the stability of the pulmonary mycobiome. We report longitudinal changes in the oral and pulmonary mycobiome of participants with and without COPD in a large-scale bronchoscopy study (MicroCOPD).</p> <div class="section toc-section"> Methods <p>Repeated sampling was performed in 30 participants with and 21 without COPD. We collected an oral wash (OW) and a bronchoalveolar lavage (BAL) sample from each participant at two time points. The internal transcribed spacer 1 region of the ribosomal RNA gene cluster was PCR amplified and sequenced on an Illumina HiSeq sequencer. Differences in taxonomy, alpha diversity, and beta diversity between the two time points were compared, and we examined the effect of intercurrent antibiotic use.</p> </div> <div class="section toc-section"> Results <p>Sample pairs were dominated by <em>Candida</em>. We observed less stability in the pulmonary taxonomy compared to the oral taxonomy, additionally emphasised by a higher Yue-Clayton measure in BAL compared to OW (0.69 vs 0.22). No apparent effect was visually seen on taxonomy from intercurrent antibiotic use or participant category. We found no systematic variation in alpha diversity by time either in BAL (p-value 0.16) or in OW (p-value 0.97), and no obvious clusters on bronchoscopy number in PCoA plots. Pairwise distance analyses showed that OW samples from repeated sampling appeared more stable compared to BAL samples using the Bray-Curtis distance metric (p-value 0.0012), but not for Jaccard.</p> </div> <div class="section toc-section"> Conclusion <p>Results from the current study propose that the pulmonary mycobiome is less stable than the oral mycobiome, and neither COPD diagnosis nor intercurrent antibiotic use seemed to influence the stability.</p> </div>
Gut Mycobiome Profile in Alcoholic Liver Disease.
ClinicalTrials.gov study NCT05793190. IPD Sharing: NO. Countries: 1. Publications: 5.
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
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