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1,765 results for “Fungal”
Lab disease outcomes data evaluating how antibiotic tolerant vs. non-tolerant cell-free supernatant from Pseudomonas aeruginosa affects the interaction between a fungal pathogen (Batrachochytrium dendrobatidis) and amphibian (Rana sylvaticus), 2022.
Microbes living on hosts and in the environment can play a key role in helping hosts to combat pathogens. However, antibiotic-induced alterations to microbial metabolite production could disrupt this dynamic. Here, we investigated whether antibiotic tolerance influences the anti-pathogenic properties of host-associated (living on the host; biofilms) and environmental (living in the soil of water column; planktonic) microbes in vitro and in vivo. For our model host and pathogen, we used the amphibian (Rana sylvatica)-Batrachochytrium dendrobatidis (Bd) system. For our model host-associated (biofilm) and environmental (planktonic) microbes, we used four strains of Pseudomonas aeruginosa that vary in their tolerance to antibiotics and their biofilm-forming capabilities: Planktonic, non-antibiotic tolerant (ΔsagS/VC); Planktonic, antibiotic tolerant (ΔsagS::sagS_L154A); Biofilm, non-antibiotic tolerant (ΔsagS::sagS_D105A); Biofilm, antibiotic tolerant (ΔsagS::sagS). We collected cell-free supernatants (CFS) from each strain to examine the effects of metabolites. We conducted four experiments. In our pathogen-only exposures to test direct effects of metabolites on Bd, we exposed Bd zoospores to each P. aeruginosa CFS at six concentrations. After 11 days of growth, we measured relative abundance of Bd across each treatment. In our host-only exposures to test effects of metabolites on host disease outcomes, we placed R. sylvatica tadpoles in individual units containing each P. aeruginosa CFS. After 48 hours, water was changed into clean well water (no CFS). Bd zoospores were immediately added to each experimental unit following the water change. After 5 days of Bd exposure, we measured snout-vent length (SVL), mass, developmental stage, and Bd quantification in the mouthparts using qPCR for each tadpole. In our host-pathogen exposures to test interactive effects of metabolites on hosts in the presence of the pathogen, we conducted the same experiment as above. However, ins
Fungal Diversity in Sarracenia Purpurea Pitchers at Harvard Forest 2009-2010
The carnivorous pitcher plant Sarracenia purpurea is widely distributed in the United States and Canada, and is host to a variety of symbiotic organisms, including symbiotic fungi. Culturing of S. purpurea pitcher contents in its native range uncovers diverse single-celled (yeast) communities; these yeast communities are dominated by the ascomycete yeast Candida pseudoglaebosa. We set out to understand how fungal diversity in S. purpurea pitchers changes over space and time, and how C. pseudoglaebosa might influence this diversity. In the summer of 2009, we assayed S. purpurea pitcher water fungal succession in Tom Swamp in Harvard Forest. We sequenced fungal DNA barcodes from 43 pitchers at different times throughout the growing season, and found that C. pseudoglaebosa has a strong impact on fungal diversity. It generally appears in pitchers early in succession, and once it arrives, it often becomes dominant quickly and decreases community evenness. We also identified two other culturable yeasts, Rhodotorula babjevae and Moesziomyces aphidis, which are common but not dominant in pitchers. In laboratory experiments, C. pseudoglaebosa outcompetes these two yeasts, but only if it is inoculated in large numbers, suggesting that C. pseudoglaebosa’s dominance is a consequence of early arrival during pitcher succession. The following summer (2010), we collected water from pitchers at five distant sites in the United States and Canada, and assayed fungal community diversity and C. pseudoglaebosa genetic diversity. We sampled pitcher plants from Tom Swamp in Harvard Forest, plus four other sites in British Columbia, Newfoundland, Georgia, and Florida (Floridian plants were Sarracenia rosea, a close relative of S. purpurea). Fungal communities tended to be structured geographically, with close communities resembling each other more than distant communities. In contrast, C. pseudoglaebosa exhibited three populations: one well-mixed population including isolates from Harvard F
Mycorrhizal fungal communities identified from seedlings planted in the Taylor, Dalton, and Boundary fire complexes which burned in 2004
This dataset contains the operational taxonomic unit table and taxonomic assignments for fungi that were associated with the roots of seedlings planted into the 2004 burn sites. There were 458 seedlings from 22 of the 32 established intensive sites (Johnstone and Hollingsworth 2019) consistenting of black spruce, white spruce, aspen, and lodgepole pine.
Hubbard Brook Experimental Forest: Soil Fungal Communities, 2021-2023
Sporocarp (fungal fruiting body) observational data and fungal eDNA data extracted from soil samples collected primarily by Farrar Ransom in the summers of 2021, 2022, and 2023. Also included: detailed site metadata, soil moisture measurements, sample processing metadata, and R code used in publication analysis. Data are still being uploaded as of January 2026. The majority of these data were collected in study plots established around 2016 by Dr. Elizabeth Studer for her dissertation work. This factorial study design consists of approximately 60 plots on two hydropedological soil types beneath four canopy tree species. The four tree species we considered were white ash (Fraxinus americana), sugar maple (Acer saccharum), American beech (Fagus grandifolia), and yellow birch (Betula alleghaniensis). Some of these plots are now part of the ongoing Ash Protection Experiment. The following data tables and other entities were used in the analysis for the publication: Unique soil fungal communities are associated with disappearing ash trees in a northern temperate hardwood forest. Site_Metadata; eDNA_Abun_Table; eDNA_Taxa_Metadata; eDNA_Extraction_Metadata; iNext_Format_eDNA; Sporocarp_Count_Table; Sporocarp_Prop_Table; Soil_Moisture_Measurements; PCR_Plate_Gel_Photos; FR_DADA2_PlusFilter_CodePub; FR_eDNA_CodePub; FR_Sporocarp_CodePub; These data were gathered as part of the Hubbard Brook Ecosystem Study (HBES). The HBES is a collaborative effort at the Hubbard Brook Experimental Forest, which is operated and maintained by the USDA Forest Service, Northern Research Station.
Tree-Associated Fungal and Bacterial Communities at Harvard Forest 2021
Cities are investing in tree-planting initiatives to protect their citizens from climate change-related heat and pollution exposure, yet Boston’s street trees are growing nearly four times as fast and dying twice as young as Massachusetts’ rural forest trees. Our research aims to characterize the belowground variables and microbial community composition that might explain the differences in growth and mortality rates observed between urban and rural trees. In 2021, soil, leaf, and root samples were taken from 25 trees in Harvard Forest to use as a rural comparison to Boston’s street trees and trees in other forests along an urban-to-rural gradient from Boston into Western Massachusetts. At each tree, three 12” deep, 2.4-centimeter radius soil cores were taken within the drip line, and soil cores were divided into the top 6” and lower 6” of soil. Fine roots were picked from each soil core. Six leaf samples were taken from the mid-canopy of each tree, where possible. Soil variables including temperature, moisture, percent organic matter, soluble nitrogen availability, bulk density, and root biomass were measured. Thus far, we have found that urban trees have fewer roots than Harvard Forest trees (F1,252) = 10.88, p = 0.0011), and that urban trees establish more root biomass deeper into the soil than Harvard Forest trees (p = 4.84e-5).
Peat characteristics, microbial PLFA, and fungal and actinobacterial sequences from Lakkasuo peatland drainage experiment, year 2004
<p>We analysed the response of microbial communities, characterized by phospholipid fatty acids (PLFAs), and fungal and actinobacterial communities, characterized by PCR-DGGE fingerprinting and direct sequencing, to changing hydrological conditions at three different sites in the boreal peatland complex Lakkasuo in southern Finland. Additionally, several peat characteristics were measured. The experimental design involved undrained controls as well as short-term (3 years) and long-term (43 years) water-level drawdown. The sites were, in their undrained state, a herb-rich sedge fen, a sedge fen, and a bog with hummock-lawn-hollow microtopography.</p> <p>Codes are explained in the Notes sheets of the Excel files. The contents of the csv files are identical to the corresponding Excel file data sheets.</p> <p>Please check the decimal separator! Comma is used in Finland, and that may have been carried over. All commas in data columns are decimal separators.</p>
Effects of factorial nitrogen, phosphorus, and potassium with micronutrient addition and Host Community on Fungal Endophyte Diversity at Cedar Creek Ecosystem Reserve, Minnesota, USA, 2014
The microbes contained within free-living organisms can alter host growth, reproduction, and interactions with the environment. In turn, processes occurring at larger scales determine the local biotic and abiotic environment of each host that may affect the diversity and composition of the microbiome community. Here, we examine variation in the diversity and composition of the foliar fungal microbiome in the grass host, Andropogon gerardii, across a factorial nitrogen, phosphorus, and potassium addition experiment in Minnesota, USA. We found limited evidence of direct effects of nutrients on endophyte diversity. Instead, the effects of nutrients on endophyte diversity appeared to be mediated by accumulation of plant litter and plant diversity loss. Specifically, nitrogen addition is associated with a 40% decrease in plant diversity and an 11% decrease in endophyte richness. Although nitrogen, phosphorus, and potassium addition increased aboveground live biomass and decreased relative Andropogon cover, endophyte diversity did not covary with live plant biomass or Andropogon cover. Our results suggest that fungal endophyte diversity within this focal host is determined in part by the diversity of the surrounding plant community and its potential impact on immigrant propagules and dispersal dynamics. Our results suggest that elemental nutrients reduce endophyte diversity indirectly via impacts on the local plant community, not direct response to nutrient addition.
Soil and root-associated fungal response to nitrogen and phosphorus addition from grasslands worldwide: 2011-2012.
Ecosystems across the globe receive elevated inputs of nutrients, but the consequences of this for soil fungal guilds that mediate key ecosystem functions remain unclear. We found that nitrogen and phosphorus addition to 25 grasslands distributed across four continents promoted the relative abundance of fungal pathogens, suppressed mutualists, but did not affect saprotrophs. Structural equation models suggested that responses were often indirect and primarily mediated by nutrient-induced shifts in plant communities. Nutrient addition also reduced co-occurrences within and among fungal guilds, which could have important consequences for belowground interactions. Focusing only on plots that received no nutrient addition, soil properties influenced pathogen abundance globally, whereas plant community characteristics influenced mutualists, and climate influenced saprotrophs. These guild-level responses enhance our ability to predict soil functional responses to anthropogenic eutrophication and the associated longer-term responses of plant communities to this important global change factor.
Fungal litter mat cover in Cannopy Trimming Experiment (CTE) plots responses to canopy opening, hurricanes and drought
Fungi that bind leaf litter into mats and produce white-rot via degradation of lignin and other aromatic compounds influence forest nutrient cycling and soil fertility. Over three and a half years beginning in June 2014, 6 months before the second iteration of the Canopy Trimming Experiment (CTE), we measured quarterly the extent of white-rot litter mats formed by basidiomycete fungi in the Luquillo Mountains of Puerto Rico in response to disturbances – a simulated hurricane treatment executed by canopy trimming and debris addition in December 2014 (CTE0, a mid-year drought in 2015, and two hurricanes 10 days apart in September 2017. Percent fungal litter mat cover ranged from 0.4% after hurricanes Irma and Maria to a high of 53% in forest with undisturbed canopy prior to the 2017 hurricanes, with means mostly between 10 - 45% of fungal litter mat cover in undisturbed forest. Drought decreased litter mat cover in both treatments, except in one undisturbed plot dominated by a drought-resistant fungus, Marasmius crinis-equi. Percent fungal litter mat cover sharply declined after real hurricanes and the simulated hurricane treatment (CTE). We found that solar radiation had a significant treatment effect and was strongly negatively correlated with percent litter mat cover within each of the four climatic seasons. Solar radiation was also strongly negatively correlated with relative humidity, throughfall, rain and litter wetness. However, rainfall was negatively correlated with litter mat cover, possibly due to erosion or saturation during high rainfall events. Canopy opening reduced leaf litterfall rates but did not affect litter mat cover. The main negative effect on basidiomycete fungi that bind leaf litter into mats was lower litter moisture associated with increased solar radiation from canopy opening and high leaf fall during drought. Variation in drought tolerance among basidiomycete fungal litter mat formers provided some resilience to drought. \<para\> Support f
Demographic data from long-term symbiont removal experiments with grasses and Epichloë fungal endophytes
This project was designed to understand the demographic effects of vertically transmitted fungal endophytes (Epichloë spp.) on their grass hosts. The experiment includes seven host-symbiont taxonomic pairs: Agrostis perennans - E. amarillans, Elymus villosus - E. elymi, Elymus virginicus - E. elymi or EviTG-1, Festuca subverticillata - E. starrii, Poa alsodes - E. alsodes, Poa sylvestris - E. PsyTG-1, Schedonorus arundinaceus - E. coenophiala. Experimental plots were established at the Indiana University Lilly-Dickey Woods Research and Teaching Preserve in south-central Indiana, USA in 2007. For each species, 5-10 plots were planted with naturally symbiotic (S+) hosts, and 5-10 plots were plated with hosts that were disinfected of fungal endophytes by heat treatment (S-). Over 15 years (2007-2022) we collected demographic data on the survival, growth, reproduction, and recruitment of all plants in all plots. Beginning in 2018 we also collected data on the locations of all plants in every plot.
Supplementary data for draft genome of a member of the ascomycotal fungal genus Pseudopithomyces (family Didymosphaeriaceae)
<p><span lang="EN-US">We update our previous draft genome of a member of genus <em>Pseudopithomyces</em> (previously annotated as <em>Pseudopithomyces maydicus</em> strain SBW1, now reannotated as <em>Pseudopithomyces sp</em>. strain SBW1. The new draft genome is based on a hybrid assembly utilising both ONT and Illumina data. The draft genome is comprised of 43 contigs with a total length of 39.65Mbp. We predict 13,669 protein coding gene models, of which 4241 (31%) were annotated to KEGG Orthology. Taxonomic assignment to <em>Pseudopithomyces sp.</em> was supported by comparative analysis of extracted ITS regions, mitochondrial DNA sequence and whole genome comparisons using <em>k</em>-mer sketches. </span></p> <p> </p> <p><span lang="EN-US">The following items of Additional Data Files are made available in this repository:</span></p> <p><span lang="EN-US">Additional Data File 1: contigs.fasta</span></p> <p><span lang="EN-US">FASTA file of entire assembly. </span><span lang="EN-US"> </span></p> <p> </p> <p><span lang="EN-US">Additional Data File 2: draft_genome.fasta</span></p> <p><span lang="EN-US">FASTA file of draft whole genome sequence.</span></p> <p> </p> <p><span lang="EN-US">Additional Data File 3: ITS_full.fasta</span></p> <p><span lang="EN-US">FASTA file containing full length ITS sequences from contig 23 and contig 42.</span></p> <p><span lang="EN-US"> </span></p> <p><span lang="EN-US">Additional Data File 4: 2NJ47W4U013-Alignment.txt</span></p> <p><span lang="EN-US">Text file containing BLASTN alignments for ITS region contained on contig 23</span></p> <p><span lang="EN-US"> </span></p> <p><span lang="EN-US">Additional Data File 5: 2NJXH2GE013-Alignment.txt</span></p> <p><span lang="EN-US">Text file containing BLASTN alignments for ITS region contained on contig 42</span></p> <p><span lang="EN-US"> </span></p> <p><span lang="EN-US">Additional Data File 6: 2NM79EUG016-Alignment.txt</span></p> <p><span lang="EN-US">Text file containing BLASTN alignments for the mitochondrial genome from contig 40 </span></p> <p><span lang="EN-US"> </span></p> <p><span lang="EN-US">Additional Data File 6: sourmash_bc10_hy_pm1_3.txt</span></p> <p><span lang="EN-US">Text file containing the MASH similarities of the draft genome compared to 18,883 fungal genomes.</span></p>
Artisanal and farmer bread making practices differently shape fungal species community composition in French sourdoughs
<p>Datasets describing the fungal species diversity, microbial density and acidity of French sourdoughs, phenotypic variation of Kazachstania bulderi and Kazachstania humilis strains as well as the diversity of bread-making practices of 40 bakers and farmers-bakers.The data were collected, analyzed, and reported within the following publication :</p> <p>Elisa Michel, Estelle Masson, Sandrine Bubbendorf, Léocadie Lapicque, Thibault Nidelet, Diego Segond, Stéphane Guézenec, Thérèse Marlin, Hugo deVillers, Olivier Rué, Bernard Onno, Judith Legrand, Delphine Sicard and the participating bakers: <strong>Artisanal and farmer bread making practices differently shape fungal species community composition in French sourdoughs</strong>. PCI Evol. Biol.</p> <p> </p>
Data from: Shift of bacterial and fungal communities upon soil amelioration is driven by carbon degradability of organic amendments
<p>Microbial communities of bacteria and fungi have been analyzed in soil. Agricultural soil was amended with different organic amendments including straw, compost, biogas residues, and biochar, and incubated in the lab. After 6 months, DNA extracted from soil samples was analyzed via Illumia MiSeq DNA sequencing (16S V3V4 for bacteria, ITS1 for fungi) to evaluate changes to the microbial community structure.</p> <p>For details, please see the respective publication (DOI: 10.1007/s44378-024-00012-5).</p>
Arbuscular mycorrhizal fungal response to fire and urbanization in the Great Smoky Mountains National Park
Wildfires are increasing in frequency and intensity as drier and warmer climates increase plant detrital fuel loads. At the same time, increases in urbanization position 9% of fire-prone land within the US at the wildland-urban interface. While rarely studied, the compounded effects of urbanization and wildfires may have unknown synergistically negative effects on ecosystems. Previous studies at the wildland-urban interface often focus on aboveground plant communities, but belowground ecosystems may also be affected by this double disturbance. In particular, it is unclear how much fire and urbanization independently or interactively affect nutritional symbioses such as those between arbuscular mycorrhizal (AM) fungi and the majority of terrestrial plants. In November 2016, extreme drought conditions and long-term fire suppression combined to create a wildfire within the Great Smoky Mountains National Park (GSMNP) and the neighboring exurban city of Gatlinburg, TN. To understand how the double disturbance of urbanization and fire affected AM fungal communities, we collected fine roots from the five dominant understory species in September 2018 at each of 18 sites spanning three burn severities in both exurban and natural sites. Despite large variation in burn severity, plant species identity had the largest influence on AM fungi. AM fungal colonization, richness, and composition all varied most among plant species. Fire and urbanization did influence some AM fungal metrics; colonization was lower in burned sites and composition was more variable among exurban locations. There were no interactions among burn severity and urbanization on AM fungi. Our results point to the large influence of plant species identity structuring this obligate nutritional symbiosis regardless of disturbance regime. Therefore, the majority of AM fungal taxa may be buffered from fire-induced ecosystem changes if plant community composition largely remains intact, plant species life history tr
Fire-severity effects on plant-fungal interactions after a novel tundra wildfire disturbance: implications for arctic shrub and tree migration
Background-Vegetation change in high latitude tundra ecosystems is expected to accelerate due to increased wildfire activity. High-severity fires increase the availability of mineral soil seedbeds, which facilitates recruitment, yet fire also alters soil microbial composition, which could significantly impact seedling establishment. Results - We investigated the effects of fire severity on soil biota and associated effects on plant performance for two plant species predicted to expand into Arctic tundra. We inoculated seedlings in a growth chamber experiment with soils collected from the largest tundra fire recorded in the Arctic and used molecular tools to characterize root-associated fungal communities. Seedling biomass was significantly related to the composition of fungal inoculum. Biomass decreased as fire severity increased and the proportion of pathogenic fungi increased. Conclusions - Our results suggest that effects of fire severity on soil biota reduces seedling performance and thus we hypothesize that in certain ecological contexts fire-severity effects on plant-fungal interactions may dampen the expected increases in tree and shrub establishment after tundra fire.
Long-term nitrogen fertilization inhibits carbon and nitrogen loss during late stage fungal necromass decomposition depending on necromass chemistry
Fungal necromass is increasingly recognized as a key component of in soil carbon (C) and nitrogen (N) cycling. However, how C and N loss from fungal necromass during decomposition are impacted by global change factors such as anthropogenic N addition and changes to soil C supply (e.g. via changing root exudation and rhizosphere priming) remains unclear and understudied relative to plant tissues. To address these gaps, we conducted a year-long decomposition experiment with four species of fungal necromass incubated across four forested sites in plots that had received inorganic N and/or labile C fertilization for decades in Minnesota, USA. We found that necromass chemistry was the primary driver of C and N loss from fungal necromass as well as response to fertilization. Specifically, N addition suppressed late-stage decomposition, but this effect was weaker in melanin-rich necromass, contrary to the hypothesis based on plant litter dynamics that N addition should suppress decomposition of more complex organic molecules. Labile C addition had no effect on either the early or late stages of necromass decomposition. Nitrogen release from necromass also varied among species, with N-poor necromass having lower N release after controlling for differences in mass loss via regression. The relatively minor effects of N fertilization on the proportion of initial necromass N released suggests that N demand by decomposers is the primary control on N loss during fungal necromass decomposition. Together, our results stress the importance of the afterlife effects of fungal chemical composition to forest soil C and N cycles. Further, they demonstrate that C and N release from this critical pool can be reduced by ongoing anthropogenic N addition.
fungal interactions during tropical leaf decomposition
Fungal interactions during leaf decomposition can facilitate or inhibit other fungi. This experiment focused on whether preconditioning of leaf litter by microfungi that were confined to one leaf (Unit-Restricted) made leaf litter less likely to be colonized and decomposed by basidiomycetes that bind litter into mats (Non-Unit- Restricted) than non-preconditioned litter. Leaves of Manilkara bidentata in litterbags were preconditioned by incubating them for 0, 1, 2 or 3 months in flat litter/seed rain baskets 10 centimeters above the forest forest floor to avoid colonization by basidiomycete fungi. Preconditioned and non-preconditioned leaves were transferred to 5 replicate basidiomycete fungal mats of Gymnopus johnstonii for 6 weeks. Both attachment by basidiomycete fungi and percent mass loss after 6 weeks decreased significantly with increasing preconditioning time. In non-preconditioned leaves, gamma irradiation did not affect mass loss or percent white-rot despite having significantly increased numbers of basidiomycete fungal connections as compared to non-irradiated leaves. In non-preconditioned leaves, more basidiomycete attachments to non-irradiated than irradiated leaves suggest facilitation by phyllosphere microfungi. While basidiomycete colonization was initially facilitated by phyllosphere fungi, we inferred that degradation of resource quality led to fewer fungal attachments and less mass loss after 1-3 months of preconditioning by microfungi. There is a 1-month time window for basidiomycete fungi to incorporate fallen leaves into their litter mats. Support for this work was provided by grants BSR-8811902, DEB-9411973, DEB-9705814 , DEB-0080538, DEB-0218039 , DEB-0620910 , DEB-1239764, DEB-1546686, and DEB-1831952 from the National Science Foundation to the University of Puerto Rico as part of the Luquillo Long-Term Ecological Research Program. Additional support provided by the University of Puerto Rico and the International Institute of Tropical Forest
Context dependency of effect of fungal connections between plants and biocrusts
Conceptual context: Species interactions may couple the resource dynamics of different primary producers and may enhance productivity by reducing loss from the system. In low-resource systems, this biotic control may be especially important for maintaining productivity. In drylands, the activities of vascular plants and biological soil crusts can be decoupled in space because biocrusts grow on the soil surface but plant roots are underground, and decoupled in time due to biocrusts activating with smaller precipitation events than plants. Soil fungi are hypothesized to functionally couple the plants and biocrusts by transporting nutrients. We studied whether disrupting fungi between biocrusts and plants reduces nitrogen transfer and retention and decreases primary production as predicted by the fungal loop hypothesis. Additionally, we compared varying precipitation regimes that can drive different timing and depth of biological activities. Methodological approach: We used field mesocosms in which the potential for fungal connections between biocrusts and roots remained intact or were impeded by mesh. We imposed a precipitation regime of small, frequent or large, infrequent rain events. We used 15N to track fungal-mediated nitrogen (N) transfer. We quantified microbial carbon use efficiency and plant and biocrust production and N content.
Root-associated fungal communities exposed to experimental drought
Plant-associated fungi can ameliorate abiotic stress in their hosts, and changes in these fungal communities can alter plant productivity, species interactions, community structure and ecosystem processes. We investigated the response of root-associated fungi to experimental drought (66% reduction in growing season precipitation) across six North American grassland ecosystem types to determine how extreme drought alters root-associated fungi, and understand what abiotic factors influence root fungal community composition across grassland ecosystems. Next generation sequencing of the fungal ITS2 region demonstrated that drought primarily re-ordered fungal species’ relative abundances within host plant species, with different fungal responses depending on host identity. Grass species that declined more under drought trended toward less community re-ordering of root fungi than species less sensitive to drought. Host identity and grassland ecosystem type defined the magnitude of drought effects on community composition, diversity, and root colonization, and the most important factor affecting fungal composition was plant species identity.
BAMBI ITS - Analysis of the fungal component (via ITS amplicon sequencing) of stool samples from preterm babies
<p>Amplicon analysis of ITS amplicons from preterm babies.</p> <p>Associated GitHub repository: <a href="https://github.com/quadram-institute-bioscience/bambi-its">https://github.com/quadram-institute-bioscience/bambi-its</a></p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.