Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
3,415
datasets available to search
ShareScore release 0.7.1
Dataset results
3,415 results for “Gut”
Figure. Comparison of longest primary feather, tail length, and chest circumference in male and female common snipe (* = p <0.05; **= p <0.01). Table 3. Weight of gut variables in male and female common snipe. in Revision of common snipe, Gallinago gallinago in morphometric analysis and building the standard reference haematological values for further studies
Figure. Comparison of longest primary feather, tail length, and chest circumference in male and female common snipe (* = p <0.05; **= p <0.01). Table 3. Weight of gut variables in male and female common snipe.
Figure 4. Smittium aggregatum. a in A NEW ASSOCIATION BETWEEN HARPELLALES, INSECT-GUT INHABITING FUNGI, AND CHIRONOMIDAE IN JAPAN WITH AN UPDATED LIST OF HARPELLALES DOCUMENTED FROM CHIRONOMIDAE Abstract
Figure 4. Smittium aggregatum. a. Thallus in the hindgut. Arrow: Hindgut cuticle (folded when dissected). Arrowheads: spores. Hyphal aggregation at the basal area of the thallus is the feature of this species. b. Detached spore. Arrowhead: Collar. Appendage is not reported in this species. c. Spore production. Arrowhead: The youngest spore. Scales. a: 20 μm. b–c: 5μm. Specimen ID. a: TNS-F-89237. b and c: TNS-F-89234. National Museum of Nature and Science, Tokyo. Host: larvae of Tanytarsini collected at Enzan Takahashi, Yamanashi, 1300m above sea level. a: water-mounted. b and c: Lactophenol-mounted.
Figure 3. Stachylina pedifer. a in A NEW ASSOCIATION BETWEEN HARPELLALES, INSECT-GUT INHABITING FUNGI, AND CHIRONOMIDAE IN JAPAN WITH AN UPDATED LIST OF HARPELLALES DOCUMENTED FROM CHIRONOMIDAE Abstract
Figure 3. Stachylina pedifer. a. Mature thalli in the peritrophic membrane. Arrows: foot-like shaped basal part penetrating the peritrophic membrane. Arrowheads: folding peritrophic membrane. Also, the same symbols mean the same meaning in figs b, c, and d. b. Higher magnification of the basal part of a thallus. c. Young thallus producing spores. Double arrowheads: spore initial. d. Almost mature thallus with eight spores. *: Spores of adjacent thallus. e. Detached spore. Arrowhead: appendage. Scales. a: 20 μm. b–e: 10μm. Specimen ID. a and b: 140224-1. e: 140225-4. Photos c and d are taken from temporary slides. a, c and d: water-mounted. b and e: Lactophenol-mounted.
Figure 2 in A NEW ASSOCIATION BETWEEN HARPELLALES, INSECT-GUT INHABITING FUNGI, AND CHIRONOMIDAE IN JAPAN WITH AN UPDATED LIST OF HARPELLALES DOCUMENTED FROM CHIRONOMIDAE Abstract
Figure 2. The species number in the two major genera of Harpellales described from Chironomidae (N=139 species)
Figure 1 in A NEW ASSOCIATION BETWEEN HARPELLALES, INSECT-GUT INHABITING FUNGI, AND CHIRONOMIDAE IN JAPAN WITH AN UPDATED LIST OF HARPELLALES DOCUMENTED FROM CHIRONOMIDAE Abstract
Figure 1. Total number of species in Harpellales described from Chironomidae and other hosts (N=270 species.)
Figure 3 in Isolation and characterization of bacteria associated with silkworm gut under antibiotic-treated larval feeding
Figure 3. Phylogenetic relationship of bacterial strains isolated in this study with each other based on 16S rRNA gene sequence through Neighbor-Joining method using 1000 bootstrap replicates.
Figure 1 in Isolation and characterization of bacteria associated with silkworm gut under antibiotic-treated larval feeding
Figure 1. Amplification of 16S rRNA gene (1500 bp) of isolated bacterial strains; lane 1 = HG1, lane 2 = HG2, lane 3 = HG3, lane 4 = DG1, lane 5 = DG2, lane 6 = DG3, -ve = negative control, +ve = positive control, M = 1kb DNA marker.
Metaproteomics reveals age-specific alterations of gut microbiome in hamsters with SARS-CoV-2 infection
<p><span>The gut microbiome's pivotal role in health and disease is well-established. SARS-CoV-2 infection often causes gastrointestinal symptoms and is associated with changes of the microbiome in both human and animal studies. While hamsters serve as important animal models for coronavirus research, there exists a notable void in functional characterization of their microbiomes with metaproteomics. In this study, we present a workflow for analyzing the hamster gut microbiome, including a metagenomics-derived hamster gut microbial protein database and a data-independent acquisition metaproteomics method. Using this workflow, we identified 32419 protein groups from the fecal microbiomes of young and old hamsters infected with SARS-CoV-2 . We showed age-specific changes in the expressions of microbiome functions and host proteins associated with microbiomes, providing further functional insight into the dysbiosis and aberrant cross-talks between the microbiome and host in SARS-CoV-2 infection. Altogether this study established and demonstrated the capability of metaproteomics for the study of hamster microbiomes.<span> </span></span></p>
German beaver gut metagenome
<p>This dataset is part of research study:</p> <p> </p> <p>Pratama R, Schneider D, Böer T and Daniel R (2019) First Insights Into Bacterial Gastrointestinal Tract Communities of the Eurasian Beaver (<em>Castor fiber</em>). <em>Front. Microbiol.</em> 10:1646. doi: 10.3389/fmicb.2019.01646</p>
A human gut Faecalibacterium prausnitzii fatty acid amide hydrolase- Genome Annotation
<p>Genome annotation for <em>F. prausnitzii </em>Bg7063</p> <p><em>Science </em><strong>386</strong>, eado6828 (2024)</p> <p>DOI: 10.1126/science.ado6828</p> <p>Undernutrition in Bangladeshi children is associated with disruption of postnatal gut microbiota assembly; compared with standard therapy, a microbiota-directed complementary food (MDCF) substantially improved their ponderal and linear growth. Here, we characterize a fatty acid amide hydrolase (FAAH) from a growth-associated intestinal strain of Faecalibacterium prausnitzii cultured from these children. This enzyme, expressed and purified from Escherichia coli, hydrolyzes a variety of N-acylamides, including oleoylethanolamide (OEA), neurotransmitters, and quorum sensing N-acyl homoserine lactones; it also synthesizes a range of N-acylamides, notably N-acyl amino acids. Treating germ-free mice with N-oleoylarginine and N-oleolyhistidine, major products of FAAH OEA metabolism, markedly affected expression of intestinal immune function pathways. Administering MDCF to Bangladeshi children considerably reduced fecal OEA, a satiety factor whose levels were negatively correlated with abundance and expression of their F. prausnitzii FAAH. This enzyme, structurally and catalytically distinct from mammalian FAAH, is positioned to regulate levels of a variety of bioactive molecules.</p> <p> </p>
The influence of the gut microbiome on BCG-induced trained immunity
<p>This repository contains the code to reproduce the analysis in the study investigating the effects of gut microbiota on Bacillus Calmette-Guerin (BCG) vaccination of 321 healthy Dutch individuals. The results are presented in the paper</p> <p><em>The influence of the gut microbiome on BCG-induced trained immunity</em></p> <p>by</p> <p>Martin Stražar, Vera P. Mourits, Valerie A.C.M. Koeken, L. Charlotte J. de Bree, Simone J.C.F.M. Moorlag, Leo A.B. Joosten, Reinout van Crevel, Hera Vlamakis, Mihai G. Netea, Ramnik J. Xavier</p> <p>(2021)</p> <p> </p> <p>The bacillus Calmette-Guérin (BCG) vaccine protects against tuberculosis and heterologous infections but elicits high interindividual variation in specific and nonspecific (trained) immune responses. While the gut microbiome is increasingly recognized as an important modulator of vaccine responses and immunity in general, its potential role in BCG-induced protection is largely unknown. </p> <p>Stool and blood were collected from 321 healthy adults before BCG vaccination, followed by blood sampling two weeks and three months afterwards. Metagenomics based on de novo genome assembly revealed 43 immunomodulatory taxa. The nonspecific, trained immune response was detected by altered production of cytokines IL-6, IL-1β, and TNF-α upon ex vivo blood restimulation with Staphylococcus aureus and negatively correlated with abundance of Roseburia. The specific response, measured by IFN-γ production upon Mycobacterium tuberculosis stimulation, was associated positively with Ruminococcus and Eggerthella lenta. The immunomodulatory taxa identified also had the strongest effects on circulating metabolites, with Roseburia predominantly affecting phenylalanine metabolism. This was corroborated by abundances of relevant enzymes, suggesting alternate phenylalanine metabolism modules are activated in a Roseburia species-dependent manner. </p> <p><br> Variability in cytokine production after BCG vaccination was associated with the abundance of microbial genomes, which in turn affect or produce metabolites in circulation. Roseburia was found to alter both trained immune responses and phenylalanine metabolism, revealing microbes and microbial products that may alter BCG-induced immunity. Together, our findings contribute to the understanding of specific and trained immune responses after BCG vaccination.</p> <p>The analysis and dataset details are further described in README.md and <a href="https://gitlab.com/xavier-lab-computation/public/bcg300">https://gitlab.com/xavier-lab-computation/public/bcg300</a> .</p>
Data for "Unravelling the collateral damage of antibiotics on gut bacteria"
<p>This dataset encompasses all data needed to reproduce the analyses presented in the paper "Unravelling the collateral damage of antibiotics on gut bacteria", available here: https://doi.org/10.1038/s41586-021-03986-2</p> <p>You can also check the GitLab repository: https://git.embl.de/maier/abxbug/</p>
Data for: Context-dependent effects of glucocorticoids on the lizard gut microbiome
<p><strong>Data from: Context-dependent effects of glucocorticoids on the lizard gut microbiome </strong>(provisionally accepted, Molecular Ecology 2021) </p> <p>Metadata is in Sheet 2. Address queries to kirstyjmacleod@gmail.com.</p> <p><strong>Publication abstract:</strong> The vertebrate gut microbiota (bacterial, archaeal, and fungal communities of the gastrointestinal tract) can have profound effects on physiological processes of their hosts. Although relatively stable, changes in microbiome structure and composition occur due to changes in the environment, including exposure to stressors and associated increases in glucocorticoid hormones. Although a growing number of studies have linked stressor exposure to microbiome changes, few studies have experimentally explored the specific influence of glucocorticoids on the microbiome in wild animals, or across ecologically-important processes (e.g., reproductive stages). Here we tested the response of the gut microbiota of adult female Sceloporus undulatus across gestation to ecologically relevant elevations of a stress-relevant glucocorticoid hormone (CORT) in order to determine a) how experimentally elevated CORT influenced microbiome characteristics, and b) whether this relationship was dependent on reproductive context (i.e. whether females were gravid or not, and in those that were gravid, gestational stage). We show that the effects of CORT on gut microbiota are complex and depend on both gestational state and stage. CORT treatment altered microbial community membership and resulted in an increase in microbiome diversity in late-gestation females, and microbial community membership varied according to treatment. In non-gravid females, CORT treatment resulted in inter-individual variation in microbial communities, but this effect was not observed in late-gestation females. Our results highlight the need for a more holistic understanding of the downstream physiological effects of glucocorticoids, as well as the importance of context (here, gestational state and stage) in interpreting stress effects in ecology.</p>
Visual Tracking of Entire Bumblebee Colonies Using Novel Pipeline Finds No Evidence of Gut-Brain Axis (Replicates 1, 2)
<p>This archive contains raw data processed from video files taken of bumblebee colonies during replicates 1 and 2 of a study on the effect of the gut microbiome on social behaviour. Files ending with "_raw.csv" contain data on read tags, while ones ending with "_noID.csv" contain data on potential tags. Files are named as follows: R[replicate number][Baseline/Data][Day]R[recording session][HiveID][VideoID]</p>
Fig. 2 in The Impact Of Gut Passage By Binturongs (Arctictis Binturong) On Seed Germination
Fig. 2. Germination time of papaya, longan, and chiku seeds ingested by binturongs and non-ingested controls. Sample sizes, from left to right, are 799, 181, 742, 191, 28, and 23 seeds.
Fig. 1 in The Impact Of Gut Passage By Binturongs (Arctictis Binturong) On Seed Germination
Fig. 1. Germination rate of longan, papaya, and chiku seeds ingested by binturongs (red) and non-ingested controls (yellow). Sample sizes, from left to right, are 742, 191, 799, 181, 28, and 23 seeds.
Gut microbiota of wild arboreal and ground-feeding tropical primates
<p>16S rRNA gene and ITS sequences from fecal samples of 12 groups of Udzungwa (Tanzania) red colobus Procolobus gordonorum (total number of samples: 89), and five groups of yellow baboon Papio cynocephalus (total number of samples: 69).</p> <p>The dataset consists of the following files:</p> <ul> <li><strong>16S_raw.tar</strong>: raw 16S rRNA gene sequences;</li> <li><strong>16S_filtered.fasta.gz</strong>: merged, adapter trimmed and quality filtered 16S rRNA gene sequences;</li> <li><strong>16S_ID.txt</strong>: 16S file ID to sample ID mapping;</li> <li><strong>ITS_raw.tar</strong>: raw ITS sequences;</li> <li><strong>ITS_filtered.fasta.gz</strong>: merged, adapter trimmed and quality filtered ITS sequences;</li> <li><strong>ITS_ID.txt</strong>: ITS file ID to sample ID mapping;</li> <li><strong>Metadata.tsv</strong>: sample metadata;</li> <li><strong>Accessions.tsv</strong>: ENA project and sample accessions;</li> <li><strong>Helminths.tsv</strong>: helminths abundances table.</li> </ul> <p> </p>
NGS Data Accompanying "Deep Learning Enables Design of Multifunctional Synthetic Human Gut Microbiome Dynamics"
<p>NGS Data Accompanying "Deep Learning Enables Design of Multifunctional Synthetic Human Gut Microbiome Dynamics", currently in review.</p>
A field experiment reveals seasonal variation in the Daphnia gut microbiome
<p>The gut microbiome is increasingly recognized for its impact on host fitness, but it remains poorly understood how naturally variable environments influence gut microbiome diversity and composition. We studied changes in the gut microbiome of ten genotypes of water fleas (<em>Daphnia magna</em>) in submerged mesocosm enclosures in a eutrophic lake over a period of 16 weeks, from early summer to autumn. The microbial diversity increased when <em>Daphnia</em> were reintroduced from the laboratory to the lake, and the composition of gut microbes drastically changed. Both gut microbiome diversity and composition continued to change over the 16-week period, with alpha diversity peaking in late summer. The gut microbiome community was clearly distinct from that of the surrounding water, and temporal changes in the two communities were independent of each other. There were no consistent differences in the gut microbiomes among <em>Daphnia</em> genotypes in the lake environment. The change in gut microbiome over the season was accompanied by a decline in reproductive output and survival. There were weak, but statistically supported, effects of microbiota composition on<em> Daphnia </em>fitness, but there was no evidence that natural variation in microbiome diversity or composition was associated with tolerance to the cyanotoxin microcystin. We conclude that the gut microbiome of <em>Daphnia</em> is highly dynamic in a natural lake environment, but that host genetic effects on microbiome diversity and composition between genotypes within a population can be vanishingly small. These results emphasize that establishing the ecological effects of gut microbiota will require largescale experiments under natural conditions.</p>
Low molecular weight seaweed–derived polysaccharides lead to increased faecal bulk but do not alter human gut health markers
<p>Differential analysis of taxa before and after the consumption of either agar, alginate or maltodextrin showed no significant change at phylum or family level (<strong>Supplementary tables 1-2</strong>). </p> <p><em>Supplementary Table 1: Differential abundance analysis with ALDEX2 on family level</em></p> <p><em>Supplementary Table 2: Differential abundance analysis with ALDEX2 on phylum level</em></p>
ScienceDex guides
Understand access before you commit
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.