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287 results for “Bacterial communities”
Catalog of metagenome-assembled bacterial genomes from Antarctic endolithic communities
<p>The dataset consists of 2 rar archives and 2 files ( tab-separated values ). Here is a brief summary of their contents:</p> <ul> <li><strong>MAGs_taxonomy: </strong>GTDB classification for each MAG.</li> <li><strong>MAGs_genome_info: </strong>genome size, completeness, contamination, length, N50.</li> <li><strong>MAGs - candidate species: </strong>high quality (HQ) and medium quality (MQ) bacterial metagenome assembled genomes.</li> <li><strong>MAGs_Annotation: </strong>EggNOG annotation files. For each MAG, the following files are included: <ul> <li>eggnog.emapper.annotations: the final EggNOG annotation;</li> <li>eggnog.emapper.hmm_hits: list of significant hits to eggNOG Orthologous Groups</li> <li>eggnog.emapper.seed_orthologs: best match of each query within the best Orthologous Group (OG) reported in the eggnog.emapper.hmm_hits file<strong>.</strong></li> </ul> </li> </ul>
Data for: Heavy metal pollution impacts soil bacterial community structure and antimicrobial resistance at the Birmingham 35th Avenue Superfund Site
<p>The data in this archive are the results of a study on the impact of heavy metals (HMs) on the soil microbiota of an urban Superfund site in Alabama. HMs are known to modify bacterial communities both in the laboratory and in situ. Consequently, soils in HM-contaminated sites such as the U.S. Environmental Protection Agency (EPA) Superfund sites are predicted to have altered ecosystem functioning, with potential ramifications for the health of organisms, including humans, that live nearby. Further, several studies have shown that heavy metal-resistant (HMR) bacteria often also display antimicrobial resistance (AMR), and therefore HM-contaminated soils could potentially act as reservoirs that could disseminate AMR genes into human-associated pathogenic bacteria. To explore this possibility, topsoil samples were collected from six public locations in the zip code 35207 (the home of the North Birmingham 35th Avenue Superfund Site) and in six public areas in the neighboring zip code, 35214. 35027 soils had significantly elevated levels of the HMs As, Mn, Pb, and Zn, and sequencing of the V4 region of the bacterial 16S rRNA gene revealed that elevated HM concentrations correlated with reduced microbial diversity and altered community structure. While there was no difference between zip codes in the proportion of total culturable HMR bacteria, bacterial isolates with HMR almost always also exhibited AMR. Metagenomes inferred using PICRUSt2 also predicted significantly higher mean relative frequencies in 35207 for several AMR genes related to both specific and broad-spectrum AMR phenotypes. Together, these results support the hypothesis that chronic HM pollution alters the soil bacterial community structure in ecologically meaningful ways and may also select for bacteria with increased potential to contribute to AMR in human disease.</p>
Data from: Subtle responses of soil bacterial communities to corn-soybean-wheat rotation
<p>Crop rotational diversity can improve crop productivity and soil health and boost soil microbial diversity. This research hypothesized that a three-year rotation of corn-soybean-wheat (CSW), compared to a two-year corn-soybean (CS) rotation, would result in a more diverse and more complex soil bacterial community, together with a greater abundance of beneficial bacteria. This was evaluated in a replicated experiment established in 2013 at two locations in Ohio (USA). The soil bacterial communities under soybean were compared between CS and CSW, at both studied sites, in 2018 and 2019, through 16S rDNA amplicon metabarcoding. </p>
Supplement: Extensive diversity and rapid turnover of phage defense repertoires in cheese-associated bacterial communities
<p>Background<br> Phages are key drivers of genomic diversity in bacterial populations as they impose strong selective pressure on the evolution of bacterial defense mechanisms across closely related strains. The pan-immunity model suggests that such diversity is maintained because the effective immune system of a bacterial species is the one distributed across all strains present in the community. However, only few studies have analyzed the distribution of bacterial defense systems at the community-level, mostly focusing on CRISPR and comparing samples from complex environments. Here, we studied 2778 bacterial genomes and 188 metagenomes from cheese-associated communities, which are dominated by a few bacterial taxa and occur in relatively stable environments.</p> <p>Results<br> We corroborate previous laboratory findings that in cheese-associated communities nearly identical strains contain diverse and highly variable arsenals of innate and adaptive (i.e., CRISPR-Cas) immunity systems suggesting rapid turnover. CRISPR spacer abundance correlated with the abundance of matching target sequences across the metagenomes providing evidence that the identified defense repertoires are functional and under selection. While these characteristics align with the pan-immunity model, the detected CRISPR spacers only covered a subset of the phages previously identified in cheese, providing evidence that CRISPR does not enable complete immunity against all phages, and that the innate immune mechanisms may have complementary roles.</p> <p>Conclusions<br> Our findings show that the evolution of bacterial defense mechanisms is a highly dynamic process and highlight that experimentally tractable, low complexity communities such as those found in cheese, can help to understand ecological and molecular processes underlying phage-defense system relationships. These findings can have implications for the design of robust synthetic communities used in biotechnology and the food industry.</p>
Dataset for Phosphite as an Engineered Niche for Pseudomonas veronii in a Synthetic Soil Bacterial Community
<p>Files containing the source data and analyses used in the manuscript "Phosphite as an Engineered Niche for <em>Pseudomonas veronii </em>in a Synthetic Soil Bacterial Community".</p> <p> </p> <p>Clara Bailey (1), Philip Gwyther (2), Senka Čaušević (2), Brandon L. Greene (1), and Jan Roelof van der Meer (2)</p> <p>1) Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California, United States</p> <p>2) Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland</p> <p> </p> <p>This dataset contains 16S rRNA gene amplicon sequencing data (in the form of an abundance table, "abund.csv" and combined with CFU counts in "abund_cfu.csv"), toluene quantification data, and CFU counts. All data analysis, statistical tests, and generated figures are contained in the relevant .R script. Refer to README files for data tables as well as the README section at the header of the R script. The dataset has been updated from version 1 to include manuscript revisions, and updated calculations and figures. </p> <p> </p>
Metagenomics data of the bacterial community in Bemisia tabaci from Burkina Faso
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Different facets of bacterial and fungal communities drive soil multifunctionality in grasslands spanning a 3,500 km transect
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Siderophores drive invasion dynamics in bacterial communities through their dual role as public good versus public bad
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Data for: Heavy metal pollution impacts soil bacterial community structure and antimicrobial resistance at the Birmingham 35th Avenue Superfund Site
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Simulation data from: Dynamics of immune memory and learning in bacterial communities
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Data from: Fungal communities are important determinants of bacterial community composition in deadwood
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Data from: Subtle responses of soil bacterial communities to corn-soybean-wheat rotation
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Different approaches to processing environmental DNA samples in turbid waters have distinct effects for fish, bacterial and archaea communities
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Data from: Spatio-temporal trends in richness and persistence of bacterial communities in decline-phase water vole populations
<p><strong>ABSTRACT</strong><br> Understanding the driving forces that control vole population dynamics requires identifying bacterial parasites hosted by the voles and describing their dynamics at the community level. To this end, we used high-throughput DNA sequencing to identify bacterial parasites in cyclic populations of montane water voles that exhibited a population outbreak and decline in 2014-2018. An unexpectedly large number of 155 Operational Taxonomic Units (OTUs) representing at least 13 genera in 11 families was detected. Individual bacterial richness was higher during declines, and vole body condition was lower. Richness as estimated by Chao2 at the local population scale did not exhibit clear seasonal or cycle phase-related patterns, but at the vole meta-population scale, exhibited seasonal and phase-related patterns. Moreover, bacterial OTUs that were detected in the low density phase were geographically widespread and detected earlier in the outbreak; some were associated with each other. Our results demonstrate the complexity of bacterial community patterns with regard to host density variations, and indicate that investigations about how parasites interact with host populations must be conducted at several temporal and spatial scales: multiple times per year over multiple years, and at both local and long-distance dispersal scales for the host(s) under consideration.</p> <p><strong>FILE DESCRIPTION:</strong></p> <p><strong>Trapping, physical, and demographic data for the 1376 <em>Arvicola terrestris</em> included in sequencing runs 1 to 8</strong></p> <p>This XLSX file contains the following information concerning the 1376 animals included in the eight sequencing runs: location, session numbering, animal_id, trap_name, capture_date, species, sex (1=male, 2=female), weight (g), length_body (mm), length_tail (mm, testes (0=abdominal, 1=scrotal), testes_length (mm), testes_width (mm), nipples (0=small, 1=lactating), vagina (0=not perforate, 1=perforate), pub_symph (0=closed, 1=open), uterus_scars (#), embryos(#), lens_weight (g), lens_weight2 (g) and sequencing labels</p> <p>File name: Animal_details.xlsx</p> <p> </p> <p><strong>Information concerning the <em>Arvicola terrestris</em> samples and the positive and negative controls multiplexed in the 16Sv4 MiSeq sequencing runs 1 to 8</strong></p> <p>This XLSX file contains the Run IDs, Sample IDs, Sample types, Dates & Site names, DNA extraction kit, PCR IDs, PCR replicate numbers, numbers of reads before and after filtering and the fastq file names for the 6615 PCR products multiplexed in the eight different Illumina MiSeq runs.</p> <p>File name: Sample_and_sequencing_informations.xlsx</p> <p> </p> <p><strong>MiSeq raw sequences of the 16Sv4 rRNA gene from <em>Arvicola terrestris</em> samples (Run1)</strong></p> <p>This ZIP file contains the Run1 FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each <em>Arvicola terrestris</em> sample using the MiSeq platform. The 1570 multiplexed PCR products were indexed using both forward and reverse indices. The list of the multiplexed samples and positive & negative controls are provided in the following XLSX file titled: Sample_and_sequencing_informations.xlsx.</p> <p>File name: MiSeq_Reads_16S_Arvicola_terrestris_Run1.zip</p> <p> </p> <p><strong>MiSeq raw sequences of the 16Sv4 rRNA gene from <em>Arvicola terrestris</em> samples (Run2)</strong></p> <p>This ZIP file contains the Run2 FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each <em>Arvicola terrestris</em> sample using the MiSeq platform. The 1668 multiplexed PCR products were indexed using both forward and reverse indices. The list of the multiplexed samples and positive & negative controls are provided in the following XLSX file titled: Sample_and_sequencing_informations.xlsx.</p> <p>File name: MiSeq_Reads_16S_Arvicola_terrestris_Run2.zip</p> <p> </p> <p><strong>MiSeq raw sequences of the 16Sv4 rRNA gene from <em>Arvicola terrestris</em> samples (Run3)</strong></p> <p>This ZIP file contains the Run3 FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each <em>Arvicola terrestris</em> sample using the MiSeq platform. The 1646 multiplexed PCR products were indexed using both forward and reverse indices. The list of the multiplexed samples and positive & negative controls are provided in the following XLSX file titled: Sample_and_sequencing_informations.xlsx.</p> <p>File name: MiSeq_Reads_16S_Arvicola_terrestris_Run3.zip</p> <p> </p> <p><strong>MiSeq raw sequences of the 16Sv4 rRNA gene from <em>Arvicola terrestris</em> samples (Run4)</strong></p> <p>This ZIP file contains the Run4 FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each <em>Arvicola terrestris</em> sample using the MiSeq platform. The 1712 multiplexed PCR products were indexed using both forward and reverse indices. The list of the multiplexed samples and positive & negative controls are provided in the following XLSX file titled: Sample_and_sequencing_informations.xlsx.</p> <p>File name: MiSeq_Reads_16S_Arvicola_terrestris_Run4.zip</p> <p> </p> <p><strong>MiSeq raw sequences of the 16Sv4 rRNA gene from <em>Arvicola terrestris</em> samples (Run5)</strong></p> <p>This ZIP file contains the Run5 FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each <em>Arvicola terrestris</em> sample using the MiSeq platform. The 1680 multiplexed PCR products were indexed using both forward and reverse indices. The list of the multiplexed samples and positive & negative controls are provided in the following XLSX file titled: Sample_and_sequencing_informations.xlsx.</p> <p>File name: MiSeq_Reads_16S_Arvicola_terrestris_Run5.zip</p> <p> </p> <p><strong>MiSeq raw sequences of the 16Sv4 rRNA gene from <em>Arvicola terrestris</em> samples (Run6)</strong></p> <p>This ZIP file contains the Run6 FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each <em>Arvicola terrestris</em> sample using the MiSeq platform. The 1704 multiplexed PCR products were indexed using both forward and reverse indices. The list of the multiplexed samples and positive & negative controls are provided in the following XLSX file titled: Sample_and_sequencing_informations.xlsx.</p> <p>File name: MiSeq_Reads_16S_Arvicola_terrestris_Run6.zip</p> <p> </p> <p><strong>MiSeq raw sequences of the 16Sv4 rRNA gene from <em>Arvicola terrestris</em> samples (Run7)</strong></p> <p>This ZIP file contains the Run7 FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each <em>Arvicola terrestris</em> sample using the MiSeq platform. The 1620 multiplexed PCR products were indexed using both forward and reverse indices. The list of the multiplexed samples and positive & negative controls are provided in the following XLSX file titled: Sample_and_sequencing_informations.xlsx.</p> <p>File name: MiSeq_Reads_16S_Arvicola_terrestris_Run7.zip</p> <p> </p> <p><strong>MiSeq raw sequences of the 16Sv4 rRNA gene from <em>Arvicola terrestris</em> samples (Run8)</strong></p> <p>This ZIP file contains the Run8 FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each <em>Arvicola terrestris</em> sample using the MiSeq platform. The 1630 multiplexed PCR products were indexed using both forward and reverse indices. The list of the multiplexed samples and positive & negative controls are provided in the following XLSX file titled: Sample_and_sequencing_informations.xlsx.</p> <p>File name: MiSeq_Reads_16S_Arvicola_terrestris_Run8.zip</p> <p> </p> <p><strong>Raw abundance table of the 16v4 rRNA gene from <em>Arvicola terrestris samples before data filtering (Run1 to 8)</em></strong></p> <p>This CSV file contains the number of reads for each distinct variant (OTU) and each of the 6615 PCR products, including the <em>Arvicola terrestris</em> samples and the controls, sequenced in the MiSeq runs 1 to 8 before the data filtering.</p> <p>File name: Read_abundance_table_before_filtering.csv</p> <p> </p> <p><strong>Abundance table of the 16v4 rRNA gene from <em>Arvicola terrestris</em> samples after data filtering (Run1 to 8)</strong></p> <p>This CSV file contains the number of reads for each distinct variant (OTU) and each <em>Arvicola terrestris</em> sample sequenced in the MiSeq runs 1 to 8 after the data filtering.</p> <p>File name: Read_abundance_table_after_filtering.csv</p>
Data from: A temporally intensive survey of bacterial communities of Brassica napus genotypes grown in three environments
Soil bacterial communities play vital roles in nutrient cycling and plant health. Breeding staple crops to have more robust microbiomes may be a sustainable way to improve crop yield without increasing inputs, leading to better global food security. We collected root and rhizosphere soil samples from sixteen genotypes of canola weekly for ten weeks at one site in 2016 and at three time points across three sites in 2017. We sequenced the 16S ribosomal RNA gene generating a total of 127.7 million reads. The data shows that rhizosphere communities are more diverse than corresponding root communities. Beta diversity analysis demonstrates both temporal and site-to-site differences in community structure. Using this dataset, these and other aspects of the canola microbiome characterization can be explored to advance our understanding of genotype by environment interactions This is a large temporally and spatially rich dataset, which will further our understanding of bacterial communities associated with canola. These data will be used in a variety of other projects, with the goal of enhancing agricultural sustainability.
Data from: Geographic location and food availability offer differing levels of influence on the bacterial communities associated with larval sea urchins
Determining the factors underlying the assembly, structure, and diversity of symbiont communities remains a focal point of animal-microbiome research. Much of these efforts focus on taxonomic variation of microbiota within or between animal populations, but rarely test the proportional impacts of ecological components that may affect animal-associated microbiota. Using larvae from the sea urchin Strongylocentrotus droebachiensis from the Atlantic and Pacific Oceans, we test the hypothesis that, under natural conditions, inter-population differences in the composition of larval-associated bacterial communities are larger than intra-population variation due to a heterogeneous feeding environment. Despite significant differences in bacterial community structure within each S. droebachiensis larval population based on food availability, development, phenotype, and time, variation in OTU membership and community composition correlated more strongly with geographic location. Moreover, 20-30% of OTUs associated with larvae were specific to a single location while less than 10% were shared. Taken together, these results suggest that inter-populational variation in symbiont communities may be more pronounced than intra-populational variation, and that this difference may suggest that broad scale ecological variables (e.g., across ocean basins) may mask smaller scale ecological variables (e.g., food availability).
Significant changes in bacterial communities associated with Pocillopora ingestion by CoTS: an important factor affecting the coral's health state
Coral ingestion by crown-of-thorns starfish (CoTS) is an important cause of coral reef degradation, although the impacts of CoTS feeding on coral-associated communities are not well understood. Therefore, in this study, we analyzed the zooxanthellae density (ZD), bacterial community composition, and microbial-metagenomic functional capacities associated with Pocillopora corals in healthy portions and feeding scars, following CoTS feeding. The ZDs were significantly lower in the feeding scars, and the ZD-loss rate was 92.05% ± 2.12%. The relative abundances of bacterial communities associated with corals after CoTS feeding changed significantly and were almost completely reorganized at the phylum and genus levels. Analysis of the microbial metagenomic-functional capacities showed that numerous physiological functions of the coral-bacterial holobionts in the feeding scars were diminished, including amino acid metabolism, xenobiotic biodegradation and metabolism, lipid metabolism, membrane transport, signal transduction, and cell motility. Compared with the healthy portions of Pocillopora corals, the abundances of potentially pathogenic bacteria in the corals of feeding scars significantly increased, whereas those of beneficial bacteria significantly decreased. Our research showed that coral-zooxanthellae holobionts were destroyed directly by CoTS, and our findings imply that the large increase in potentially pathogenic bacteria in feeding scars could threaten the long-term health of Pocillopora corals.
Data from: Spatially-explicit depiction of a floral epiphytic bacterial community reveals role for environmental filtering within petals
<p>The microbiome of flowers (anthosphere) is an understudied compartment of the plant microbiome. Within the flower, petals represent a heterogeneous environment for microbes in terms of resources and environmental stress. Yet little is known of drivers of structure and function of the epiphytic microbial community at the within-petal scale. We characterized the petal microbiome in two co-flowering plants that differ in pattern of ultraviolet (UV) absorption along their petals. Bacterial communities were similar between plant hosts, with only rare phylogenetically distant species contributing to differences. The epiphyte community was highly culturable (75% of families) lending confidence to the spatially-explicit isolation and characterization of bacteria. In one host, petals were heterogeneous in UV absorption along their length and in these there was a negative relationship between growth rate and position on the petal, as well as lower UV tolerance in strains isolated from the UV absorbing base than from UV reflecting tip. A similar pattern was not seen in microbes isolated from a second host whose petals had uniform patterning along their length. Across strains, variation in carbon utilization and chemical tolerance followed common phylogenetic patterns. This work highlights the value of petals for spatially-explicit explorations of bacteria of the anthosphere.</p>
Data from: Serratia marcescens Shapes Cutaneous Bacterial Communities and Influences Survival of an Amphibian Host
A changing understanding of the functional interactions between microbial communities and their associated hosts is influencing how disease is perceived and ameliorated. Of the numerous host-microbiome-disease systems of study, the emergence of chytridiomycosis in anurans (caused by Batrachochytrium dendrobatidis, hereafter Bd), has been implicated in ongoing declines and extinction events of amphibians across the planet. Interestingly, there has been differential survival among amphibians in resisting Bd infection and subsequent disease. One factor thought to contribute to this resistance is the host-associated cutaneous microbiota. This has raised the possibility of utilizing genetically modified probiotics to restructure the host-associated microbiota for desired anti-fungal outcomes. Here, we utilize a previously described strain of Serratia marcescens (Sm) for manipulation of amphibian cutaneous microbiota. Sm was genetically altered to have a dysfunctional pathway for the production of the extracellular metabolite prodigiosin. This genetically altered strain (Δpig) and the functional prodigiosin producing strain (WT-pig) were compared for their microbial community and anti-Bd effects both in vitro and in vivo. In vitro, Bd growth was significantly repressed in the presence of prodigiosin. In vivo, the inoculation of both Sm strains was shown to significantly influence amphibian microbiota diversity with the Δpig-Sm treatment showing increasing α-diversity, and the WT-pig S. marcescens having no temporal effect on diversity. Differences were also seen in host mortality with Δpig-Sm exhibiting significantly decreased survival probability as compared to a no¬-Sm control in the presence of Bd. These results are important evidence for the potential of genetic-level manipulation of bacteria in a host microbial community, which may provide a way to alter disease outcomes and address critical frontiers in disease and microbial ecology.
Disentangling the assembly mechanisms of ant cuticular bacterial communities of two Amazonian ant species sharing a common arboreal nest
<p>Bacteria living on the cuticle of ants are generally studied for their protective role against pathogens, especially in the clade of fungus-growing ants. However, little is known of the diversity of cuticular bacteria in other ant host species, as well as of the mechanisms leading to the composition of these communities. Here, we used 16S rRNA gene amplicon sequencing to study the influence of host species, species interactions, and the pool of bacteria from the environment on the assembly of cuticular bacterial communities on two phylogenetically distant Amazonian ant species that frequently nest together inside the roots system of epiphytic plant<i>s</i>, <i>Camponotus femoratus</i> and <i>Crematogaster levior</i>. Our results show that 1) the vast majority of the bacterial community on the cuticle is shared with the nest, suggesting that most bacteria on the cuticle are acquired through environmental acquisition, 2) 5.2% and 2.0% OTUs are respectively specific to <i>Camponotus femoratus</i> and <i>Crematogaster levior</i>, likely representing their respective core cuticular bacterial community, and 3) 3.6% of OTUs are shared between the two ant species. Additionally, mass spectrometry metabolomics analysis of metabolites on the cuticle of ants, which excludes the detection of cuticular hydrocarbons produced by the host, were conducted to evaluate correlations among bacterial OTUs and m/z ion mass. Although some positive and negative correlations are found, the cuticular chemical composition was weakly species specific which supports that cuticular bacterial communities are prominently environmentally acquired. Overall, our results suggest that the environment is the dominant source of bacteria found on the cuticle of ants.</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.
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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.