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.
2,708
datasets available to search
ShareScore release 0.7.1
Dataset results
2,708 results for “microbiota”
Data from: Structure and function of the bacterial and fungal gut microbiota of Neotropical butterflies
Open the record for dataset details and reuse information.
Thonningianin A ameliorated renal interstitial fibrosis in diabetic nephropathy mice by modulating gut microbiota dysbiosis and repressing inflammation
Open the record for dataset details and reuse information.
Dietary vitamin A modifies the gut microbiota and intestinal tissue transcriptome, impacting intestinal permeability and the release of inflammatory factors, thereby influencing Aβ pathology
Open the record for dataset details and reuse information.
The airway microbiota and exacerbations of COPD
Open the record for dataset details and reuse information.
Gut microbiota sequences of the long-tailed dwarf hamster (Cricetulus longicaudatus) using 16S rDNA
Open the record for dataset details and reuse information.
Something in the water: Aquatic microbial communities influence the larval amphibian gut microbiota, neurodevelopment, and behavior
Open the record for dataset details and reuse information.
Inflammatory responses induced by the monophasic variant of Salmonella typhimurium in pigs play a role in the high shedder phenotype and fecal microbiota composition
Open the record for dataset details and reuse information.
With or without you: Gut microbiota does not predict aggregation behavior in European earwig females
Open the record for dataset details and reuse information.
Fecal microbiota transplants (FMT) of three distinct human communities to germ-free mice exacerbated inflammation and decreased lung function in their offspring
Open the record for dataset details and reuse information.
The impact of Rhodiola Rosea on biomarkers of diabetes, inflammation, and microbiota in a leptin receptor-knockout mouse model
Open the record for dataset details and reuse information.
Effects of Lactobacillus plantarum Q180 on blood lipid levels and intestinal microbiota : a double-blind, randomized, placebo-controlled, parallel trial
<p>Probiotics can improve the intestinal environment by enhancing beneficial bacteria to potentially regulate lipid levels; however, the underlying mechanisms remain unclear. The aim of this study was to investigate the effect of <em>Lactobacillus plantarum</em> Q180 (LPQ180) on blood lipid levels and the intestinal microbiome environment from a clinical perspective. A double-blind, randomized, placebo-controlled study was conducted including 70 participants of both sexes, 20 years of age and older, with blood triacylglyceride (TG) levels below 200 mg/dL. Treatment with LPQ180 for 12 weeks significantly decreased LDL-cholesterol (<em>p</em> = 0.042) and apolipoprotein (Apo)B-100 (<em>p</em> = 0.003) levels, and decreased postprandial maximum concentrations (C<sub>max</sub>) and areas under the curve (AUC) of TG, chylomicron TG, ApoB-48, and ApoB-100. LPQ180 treatment significantly decreased total indole and phenol levels (<em>p</em> = 0.019). In addition, there was a negative correlation between baseline microbiota abundance and lipid marker change, which was negatively correlated with metabolites related to harmful bacteria. LPQ180 treatment may help prevent hypertriglyceridemia by improving fasting and postprandial blood lipid levels. In addition, LPQ180 effectively prevented the growth of harmful bacteria, particularly in subjects with higher baseline levels of harmful gut microbiota. Probiotics can improve the intestinal environment by enhancing beneficial bacteria to potentially regulate lipid levels; however, the underlying mechanisms remain unclear. The aim of this study was to investigate the effect of <em>Lactobacillus plantarum</em> Q180 (LPQ180) on blood lipid levels and the intestinal microbiome environment from a clinical perspective. A double-blind, randomized, placebo-controlled study was conducted including 70 participants of both sexes, 20 years of age and older, with blood triacylglyceride (TG) levels below 200 mg/dL. Treatment with LPQ180 for 12 weeks significantly decreased LDL-cholesterol (<em>p</em> = 0.042) and apolipoprotein (Apo)B-100 (<em>p</em> = 0.003) levels, and decreased postprandial maximum concentrations (C<sub>max</sub>) and areas under the curve (AUC) of TG, chylomicron TG, ApoB-48, and ApoB-100. LPQ180 treatment significantly decreased total indole and phenol levels (<em>p</em> = 0.019). In addition, there was a negative correlation between baseline microbiota abundance and lipid marker change, which was negatively correlated with metabolites related to harmful bacteria. LPQ180 treatment may help prevent hypertriglyceridemia by improving fasting and postprandial blood lipid levels. In addition, LPQ180 effectively prevented the growth of harmful bacteria, particularly in subjects with higher baseline levels of harmful gut microbiota.</p>
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>
Data from: The microbiota influences the Drosophila melanogaster life history strategy
<p class="CxSpFirst">Organisms are locally adapted when members of a population have a fitness advantage in one location relative to conspecifics in other geographies. For example, across latitudinal gradients, some organisms may trade off between traits that maximize fitness components in one, but not both, of somatic maintenance or reproductive output. Latitudinal gradients in life history strategies are traditionally attributed to environmental selection on an animal's genotype, without any consideration of the possible impact of associated microorganisms ("microbiota") on life history traits. Here, we show in Drosophila melanogaster, a key model for studying local adaptation and life history strategy, that excluding the microbiota from definitions of local adaptation is a major shortfall. First, we reveal that an isogenic fly line reared with different bacteria varies the investment in early reproduction versus somatic maintenance. Next, we show that in wild fruit flies, the abundance of these same bacteria was correlated with the latitude and life history strategy of the flies, suggesting geographic specificity of the microbiota composition. Variation in microbiota composition of locally adapted D. melanogaster could be attributed to both the wild environment and host genetic selection. Finally, by eliminating or manipulating the microbiota of fly lines collected across a latitudinal gradient, we reveal that host genotype contributes to latitude-specific life history traits independent of the microbiota and that variation in the microbiota can suppress or reverse the differences between locally adapted fly lines. Together, these findings establish the microbiota composition of a model animal as an essential consideration in local adaptation.</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>
Data from: Quorum-sensing signaling by chironomid egg masses' microbiota affects haemagglutinin/protease (HAP) production by Vibrio cholerae
<p><i>Vibrio cholerae</i>, the causative agent of cholera, is commonly isolated, along with other bacterial species, from chironomid insects (<i>Diptera: Chironomide</i>). Nevertheless, its prevalence in the chironomid egg masses' microbiota is less than 0.5%. <i>V. cholerae</i> secretes haemagglutinin/protease (HAP) that degrades the gelatinous matrix of chironomid egg masses and prevents hatching. Quorum sensing (QS) activates HAP production in response to accumulation of bacterial autoinducers (AIs). Our aim was to define the impact of chironomid microbiota on HAP production by <i>V. cholerae</i>. To study QS signaling, we used<i> V. cholerae</i> bioluminescence reporter strains (QS-proficient O1 El-Tor wild type and QS-deficient mutants) and different bacterial species that we isolated from chironomid egg masses. These egg mass isolates, as well as a synthetic AI-2, caused an enhancement in <i>lux</i> expression by a <i>V. cholerae</i> QS-deficient mutant. The addition of the egg mass bacterial isolate supernatant to the QS-deficient mutant also enhanced HAP production and egg mass degradation activities. Moreover, the <i>V. cholerae</i> wild type strain was able to proliferate using egg masses as their sole carbon source while the QS-deficient was not. The results demonstrate that members of the chironomid bacterial consortium produce external chemical cues that, like AI-2, induce expression of the<i> hapA </i>gene in <i>V. cholerae</i>. Understanding the interactions between <i>V. cholerae</i> and the insects' microbiota may help uncover the interactions between this pathogen and the human gut microbiota.</p>
Gut microbiota in reintroduction of Giant Panda
<p>Reintroduction is a key approach in the conservation of endangered species. In recent decades many reintroduction projects have been conducted for conservation purposes, but the rate of success has been low. Given the important role of gut microbiota in health and diseases, we questioned whether gut microbiota <a name="_Hlk522007838">would play a crucial role in giant panda's wild training process</a>. The wild procedure is when -captive-born babies live with their mothers in a wilderness enclosure and learn wilderness survival skills from their mothers. During the wild training process, the baby pandas undergo wilderness survival tests and regular physical examinations. Based on their performance through these tests, the top subjects (age 2-3 years old) are released into the wild while the others are translocated to captivity. <a name="_Hlk17030785">After release, we tracked one released panda (Zhangxiang) and collected its fecal samples for 5 months (Jan 16<sup>th</sup> 2013 to Mar 29<sup>th</sup> 2014). </a>Here, we analyzed the Illumina HiSeq sequencing data (V4 region of 16S rRNA gene) from captive pandas (n=24) , wild-training baby pandas (n=8) of which 6 were released and 2 were unreleased, wild-training mother pandas (n=8), one released panda (Zhangxiang), and wild giant pandas (n=18). Our results showed that <a name="_Hlk10634744">the gut microbiota of wild-training pandas is significantly different from that of wild pandas but similar to that of captive ones. </a><a name="_Hlk522008735">The gut microbiota of the released panda Zhangxiang gradually changed to become similar to those of wild pandas after release. In addition, </a><a name="_Hlk16625538">we identified several bacteria that were enriched in the released baby pandas before release</a>, compared with the unreleased baby pandas. These bacteria include several known gut-health related beneficial taxa such as <i>Roseburia</i>, <i>Coprococcus</i>, <i>Sutterella, Dorea,</i> and <i>Ruminococcus</i>.<i> </i><a name="_Hlk10634845">Therefore, our results suggest that certain members of the gut microbiota may be important in panda reintroduction. </a></p>
Roundup causes embryonic development failure, alters metabolic pathways and gut microbiota functionality in non-target species
<p><b>Background: </b>Research around the weedkiller Roundup is among the most contentious of the 21<sup>st</sup> century. Scientists have provided inconclusive evidence that the weedkiller causes cancer and other life-threatening diseases, while industry-paid research reports that the weedkiller has no adverse effect on humans or animals. Much of the controversial evidence on Roundup is rooted in the approach used to determine safe use of chemicals, defined by outdated toxicity tests.We apply a system biology approach to the biomedical and ecological model species <i>Daphnia</i> to quantify the impact of Glyphosate and of its commercial formula, Roundup, on fitness, genome-wide transcription and gut microbiota, taking full advantage of clonal reproduction in <i>Daphnia. </i>We then <span>apply </span>machine learning-based statistical analysis to identify and prioritize correlations between genome-wide transcriptional and microbiota changes.</p> <p><b>Results: </b>We demonstrate that chronic exposure to ecologically relevant concentrations of Glyphosate and Roundup at the approved regulatory threshold for drinking water in the US induce embryonic developmental failure, significant DNA damage (genotoxicity), and interfere with signaling. Furthermore, chronic exposure to the weedkiller alters the gut microbiota functionality and composition interfering with carbon and fat metabolism, as well as homeostasis. Using the 'Reactome', we identify conserved pathways across the Tree of Life, which are potential targets for Roundup in other species, including liver metabolism, inflammation pathways and collagen degradation, responsible for the repair of wounds and tissue remodeling.</p> <p><b>Conclusions: </b>Our results show that chronic exposure to concentrations of Roundup and Glyphosate at the approved regulatory threshold for drinking water causes embryonic development failure, and alteration of key metabolic functions via direct effect on the host molecular processes and indirect effect on the gut microbiota. The ecological model species <i>Daphnia</i> occupies a central position in the food web of aquatic ecosystems, being the preferred food of small vertebrates and invertebrates as well as a grazer of algae and bacteria. The impact of the weedkiller on this keystone species has cascading effects on aquatic food webs, affecting their ability to deliver critical ecosystem services.</p>
Gut microbiota in non-obese adolescent girls with polycystic ovary syndrome: effects of randomized treatments
<p class="Paragraph"><span><span><span><span><span><span><span><span><span><span><span><b>Context:</b> Women and obese adolescent girls with polycystic ovary syndrome (PCOS) have altered gut microbiota. </span></span></span></span></span></span></span></span></span></span></span></p> <p class="Paragraph"><span><span><span><span><span><span><span><span><span><span><span><b>Objective:</b> To study the gut microbiota composition of non-obese adolescent girls with PCOS and the effects of randomized pharmacological treatments.</span></span></span></span></span></span></span></span></span></span></span></p> <p class="Paragraph"><span><span><span><span><span><span><span><span><span><span><span><b>Design:</b> Randomized, open-label, single-center controlled trial. </span></span></span></span></span></span></span></span></span></span></span></p> <p class="Paragraph"><span><span><span><span><span><span><span><span><span><span><span><b>Settings:</b> Endocrinology Department, University Hospital. </span></span></span></span></span></span></span></span></span></span></span></p> <p class="Paragraph"><span><span><span><span><span><span><span><span><span><span><span><b>Participants: </b>30 girls with PCOS [age 15.8 years; body mass index (BMI) 25 kg/ m<sup>2</sup>] and 31 controls [age 15.9 years; BMI 22 kg/ m<sup>2</sup>]. </span></span></span></span></span></span></span></span></span></span></span></p> <p class="Paragraph"><span><span><span><span><span><span><span><span><span><span><span><b>Intervention:</b> PCOS girls were randomized to receive an oral contraceptive (OC, N= 15) or spironolactone-pioglitazone-metformin (SPIOMET, N= 15) for 1 year. </span></span></span></span></span></span></span></span></span></span></span></p> <p class="Paragraph"><span><span><span><span><span><span><span><span><span><span><span><b>Outcomes: </b>16S ribosomal subunit gene amplicon sequencing was used to describe and quantify microbial diversity and taxonomic profiles in stool samples from all subjects. Samples from 23 out of 30 girls with PCOS (OC, N= 11; SPIOMET, N= 12) were available for analysis post-treatment. Correlations between bacterial results and endocrine-metabolic variables were performed before and after randomized treatments. </span></span></span></span></span></span></span></span></span></span></span></p> <p class="Paragraph"><span><span><span><span><span><span><span><span><span><span><span><b>Results:</b> Girls with PCOS had decreased diversity alpha, altered microbiota pattern and taxonomic profile with more abundance of <i>Family XI</i> (<i>P</i>= 0.002), and less abundance of family <i>Prevotellaceae</i> (<i>P</i>= 0.0006) and the genus <i>Prevotella</i> (<i>P</i>= 0.0001) and <i>Senegalimassilia</i> (<i>P</i>< 0.0001), as compared to controls. <i>Family XI</i>abundance related positively to hepato-visceral fat (R= 0.453; <i>P</i>= 0.0003). SPIOMET treatment, but not OC, normalized the abundance of <i>Family XI</i>. <i>Prevotellaceae</i>, <i>Prevotella</i> and <i>Senegalimassilia</i> abundance remained unchanged after either treatment. </span></span></span></span></span></span></span></span></span></span></span></p> <p class="Paragraph"><span><span><span><span><span><span><span><span><span><span><span><b>Conclusion:</b> SPIOMET's spectrum of normalizing effects in non-obese girls with PCOS is herewith broadened as to include <i>Family XI</i> abundance in gut microbiota. </span></span></span></span></span></span></span></span></span></span></span></p>
Supplementary files for: How can the MHC mediate social odor via the microbiota community? A deep dive into mechanisms
<p>Genes of the major histocompatibility complex (MHC) have long been linked to odor signaling and recently researchers' attention has focused on MHC structuring of microbial communities and how this may in turn impact odor. However, understanding of the mechanisms through which the MHC could affect the microbiota to produce a chemical signal that is both reliable and strong enough to ensure unambiguous transmission of behaviorally important information remains poor. This is largely because empirical studies are rare, predictions are unclear, and the underlying immunological mechanisms governing MHC-microbiota interactions are often neglected. Here we review the immunological processes involving MHC class II (MHC-II) that could affect the commensal community. Focusing on immunological and medical research, we provide background knowledge for non-immunologists by describing key players within the vertebrate immune system relating to MHC-II molecules (which present extracellular-derived peptides, and thus interact with extracellular commensal microbes). We then systematically review the literature investigating MHC-odor-microbiota interactions in animals and identify areas for future research. These insights will help to design studies that are able to explore the role of MHC-II and the microbiota in the behavior of wild populations in their natural environment and consequently propel this research area forward.</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.