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1,065 results for “Gut microbiota”
Evidence supporting the microbiota-gut-brain axis in a songbird
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Data from: No evidence that gut microbiota impose a net cost on their butterfly host
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Sexual dimorphism of the gut microbiota in the Chinese alligator and its convergence in the wild environment
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The gut microbiota in chronic obstructive pulmonary disease varies by CT-verified emphysema status
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Data from: Gut microbiota provide co-existing strategies for two species of symmetrically distributed rodents in competition for food
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Data from: Host-associated beneficial gut microbiota boosts induced immunity and limits immune deployment costs in bumblebees
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Does ivermectin treatment for endemic hookworm infection alter the gut microbiota of endangered Australian sea lion pups?
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Phylogenies related to: Codiversification of gut microbiota with humans
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Direct and indirect effects of pesticide exposure on farmland raptor gut microbiota
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Immune stimulation induced changes to the native gut microbiota of bumble bees
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Data from: Association between gut health and gut microbiota in a polluted environment
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Data from: Structure and function of the bacterial and fungal gut microbiota of Neotropical butterflies
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Thonningianin A ameliorated renal interstitial fibrosis in diabetic nephropathy mice by modulating gut microbiota dysbiosis and repressing inflammation
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Dietary vitamin A modifies the gut microbiota and intestinal tissue transcriptome, impacting intestinal permeability and the release of inflammatory factors, thereby influencing Aβ pathology
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Gut microbiota sequences of the long-tailed dwarf hamster (Cricetulus longicaudatus) using 16S rDNA
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Something in the water: Aquatic microbial communities influence the larval amphibian gut microbiota, neurodevelopment, and behavior
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With or without you: Gut microbiota does not predict aggregation behavior in European earwig females
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Bioinformatic pipeline: Vast differences in strain-level diversity in the gut microbiota of two closely related honey bee species
<p>This data-set contains the full bioinformatic pipeline used to analyze metagenomic samples in the study "Vast differences in strain-level diversity in the gut microbiota of two closely related honey bee species" (Ellegaard et al. 2020, Current Biology). </p> <p>New metagenomic samples were generated for the study, for which the raw data is available on the NCBI Sequence Read Achive, under accession: PRJNA59809.</p> <p>The data of this submission consist of 9 tar-balls, as further described here below. Download and unpack to view the contents (tar -zxvf filename.tar.gz). For each tarball, all directories contain README.txt files, describing the contents of the directory. Due to size constraints, some intermediate files have been omitted, and some workflows are demonstrated for a subset of the data. However, the full analysis can be reproduced from the raw data, using the provided scripts.</p> <p>All scripts are included within the directories where they were applied. Perl-scripts contain documentation, which can be viewed by typing: "perl script_name.pl -h". For R scripts, the usage is indicated as a comment in the top lines of each script. Note that many of the scripts require specific input-files to be present in the run-directory. Their usage is demonstrated within the workflow directories in bash-scripts (*.sh). Commands used for generating plots and some statistics are given within workflow directories in text-files "R.commands" when applicable.</p> <p>Aside from custom code, the pipeline also utilizes various open-source Software packages, which are detailed in the file "software_dependencies.txt". Note, while many of the scripts will run fast on any computer, some steps of the pipeline are computationally demanding, and will require significant computing time, as well as storage space. When scripts are known to be time-consuming, this is indicated in the script help message.</p> <p>Description of tarballs.</p> <p>raw_data_processing.tar.gz: Describes the quality-control and trimming of raw data, and includes info on the sequencing run.</p> <p>databases.tar.gz: Contains all databases used for analysis, in addition to relevant meta-data.</p> <p>mapping_stats.tar.gz: Contains a file with the number of reads mapped to the honey bee gut microbiota database and the host genomes, for each sample. Bash-scripts are provided, detailing how the mapping was done and quantified.</p> <p>orthologs_phylogenies.tar.gz: Contains the pipeline for inferring orthologous gene-families and core genome phylogenies, as well as scripts for filtering of single-copy core gene families.</p> <p>assemblies.tar.gz: Contains the final de novo metagenome assembly files (contig fasta-files), gener<br> ated for both complete and rarefied read subsets. Bash-scripts detailing the assembly commands are also provided.</p> <p>SDP_validation.tar.gz: Contains the pipeline for metagenomic validation of candidate SDPs. Final output-files, containing the percentage identity of recruited metagenomic ORFs to database core genes, are provided for each candidate SDP. Additionally, a small example dataset is provided, where the intermediate result-files can be viewed.</p> <p>community_profiling.tar.gz: Contains the pipeline for community profiling, i.e. the quantification of individual community members (SDPs) across samples. Final output files are provided, including mapped read coverage on core gene families and corresponding plots. A small bam-file (containing data from a single subset sample), is also provided, in order to demonstrate the pipeline, together with all scripts used.</p> <p>snv_profiling.tar.gz: Contains the pipeline used for SNV profiling, including filtering and analysis. Final filtered vcf-files are provided for each SDP. Analytical output files are also provided, including data on shared SNV fractions, distance matrices, and cumulative curves.</p> <p>metagenomic_ORF_analyses.tar.gz: Contains the pipeline for analysis of metagenomic ORFs. This includes prediction of ORFs, clustering, annotation and functional characterization. ORF sequences, annotation files, and cluster-files are provided.</p>
Large-scale metabolic interaction network of the mouse and human gut microbiota
<p>The role of our gut microbiota in health and disease is largely attributed to the collective metabolic activities of the inhabitant microbes. A system-level framework of the microbial community structure, mediated through metabolite transport, would provide important insights into the complex microbe-microbe and host-microbe chemical interactions. This framework, if adaptable to both mouse and human systems, would be useful for mechanistic interpretations of the vast amounts of experimental data from gut microbiomes in murine animal models, whether humanized or not. Here, we constructed a literature-curated, interspecies network of the mammalian gut microbiota for mouse and human hosts, called NJC19. This network is an extensive data resource, encompassing 838 microbial species (766 bacteria, 53 archaea, and 19 eukaryotes) and 6 host cell types, interacting through 8,224 small-molecule transport and macromolecule degradation events. Moreover, we compiled 912 negative associations between organisms and metabolic compounds that are not transportable or degradable by those organisms. Our network may facilitate experimental and computational endeavors for the mechanistic investigations of host-associated microbial communities.</p>
Data from: Parallel and non-parallel changes of the gut microbiota during trophic diversification in repeated young adaptive radiations of sympatric cichlid fish
<p><b>Background:</b> Recent increases in understanding the ecological and evolutionary roles of microbial communities has underscored their importance for their hosts' biology. Yet, little is known about gut microbiota dynamics during early stages of ecological diversification and speciation. We sequenced the V4 region of the 16s rRNA gene to study the gut microbiota of extremely young adaptive radiations of Nicaraguan Midas cichlid fish (<i>Amphilophus</i> cf. <i>citrinellus</i>) from two crater lakes to test the hypothesis that parallel divergence in trophic ecology is associated with parallel changes of the gut microbiota.</p> <p><b>Results:</b> Bacterial communities of the water and guts were highly distinct, indicating that the gut microbiota is shaped by host-specific factors. Across individuals of the same crater lake, differentiation in trophic ecology was associated with gut microbiota differentiation, suggesting that diet, to some extent, affects the gut microbiota. However, differences in trophic ecology were much more pronounced across than within species whereas similar patterns were not observed for taxonomic and functional differences of the gut microbiota. Across two crater lakes, we could not detect evidence for parallel changes of the gut microbiota associated with trophic ecology.</p> <p><b>Conclusions:</b> Similar cases of non-parallelism have been observed in other recently diverged fish species and might be explained by a lack of clearly differentiated niches during early stages of ecological diversification.</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.