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.
492
datasets available to search
ShareScore release 0.7.1
Dataset results
492 results for “microbial communities”
Automated design of synthetic microbial communities
<p>In naturally occurring microbial systems, species rarely exist in isolation. There is strong ecological evidence for a positive relationship between species diversity and the functional output of communities. The pervasiveness of these communities in nature highlights that there may be advantages for engineered strains to exist in cocultures as well. Building synthetic microbial communities allows us to create distributed systems that mitigates issues often found in engineering a monoculture, especially when functional complexity is increasing. Here, we demonstrate a methodology for designing robust synthetic communities that use quorum sensing to control amensal bacteriocin interactions in a chemostat environment. We explore model spaces for two and three strain systems, using Bayesian methods to perform model selection, and identify the most robust candidates for producing stable steady state communities. Our findings highlight important interaction motifs that provide stability, and identify requirements for selecting genetic parts and tuning the community composition.</p>
Dataset - Spatio-temporal modeling of the crowding conditions and metabolic variability in microbial communities
<p><strong>Dataset simulated for the manuscript "Spatio-temporal modeling of the crowding conditions and metabolic variability in microbial communities" by Angeles-Martinez and Hatzimanikatis.</strong></p>
Impact of viruses on microbial communities and biogeochemical processes in agricultural soils
<p>The source data of microcosm experiment.</p>
Dataset and R code used in "Environmental filtering governs consistent vertical zonation in sedimentary microbial communities across disconnected mountain lakes"
<p>Dataset and R code used for the manuscript:</p> <p>Von Eggers, J. M., Wisnoski, N. I., Calder, J. W., Capo, E., Groff, D. V., Krist, A. C., & Shuman, B. (2024). Environmental filtering governs consistent vertical zonation in sedimentary microbial communities across disconnected mountain lakes. <em>Environmental Microbiology</em>, 26(3), e16607.</p> <p>This dataset and code are also available on GitHub (<a href="https://github.com/jvoneggers/WYLakeSedMicrobes">https://github.com/jvoneggers/WYLakeSedMicrobes</a>).</p>
UV radiation accelerates litter decomposition in a valley-type savanna by enhancing microbial community diversity and function
<p><span>We present the data of the study by Gao et al. (202</span><span>4</span><span>): <a name="_Hlk179470571"></a><a name="OLE_LINK42"></a><strong><span>UV radiation accelerates litter decomposition in a valley-type savanna by enhancing microbial community diversity and function</span></strong></span><span>.</span><span> The excel file (Raw Data) includes the following sheets: 1- Radiation (w·m<sup>-2</sup>) variation of UV-A and UV-B during the experimental period. 2- Decay constants (<em>K</em>, yr<sup>−1</sup>) and changes in the mass loss rate of litter under different UV conditions during the experimental period<span>. 3- </span>The content of lignin, cellulose, C, N and P of litter under different UV conditions during the experimental period<span>. 4-</span></span><span> </span><span>16S ASVs under different UV conditions<span>. 5-</span></span><span> </span><span>ITS ASVs under different UV conditions.</span></p>
Viroplant Project - Microcosm studies on the effect of bacteriophages used as plant protection products on soil microbial communities
<p>This file contains the description, data and DNA analyses on the effect of bacteriophages with a potential to be used as plant protecction products on the structure and function of soil microbial communities. The objective was to evaluate two different microcsom incubation systems with phages and microbial cells from soil, or soil itself and to analyses in a time dependent manner how the phages affect the natural soil microbiomes. The microbial communities were quantified with qPCR and their diversity analyzed with PCR amplified 16S rRNA gene sequences. Bioinformatic analyses were used to evaluate microbial community responses</p>
Individual dietary specialization in a generalist bee varies across populations but has no effect on the richness of associated microbial communities
<p><span></span></p> <p>Despite the increasingly documented occurrence of individual specialization, the relationship between individual consumer interactions and diet-related microbial communities in wild populations is still unclear. Using data from nests of the bee <em>Ceratina australensis</em> from three different wild populations, we combine metabarcoding and network approaches to explore the existence of individual variation in resource use within and across populations, and whether dietary specialization affects the richness of pollen-associated microbes. We reveal the existence of marked dietary specialization. In the most specialized population, we also show that individuals' diet breadth was positively related to the richness of fungi, but not bacteria. Overall, individual specialization appeared to have a weak or negligible effect on the microbial richness of nests, suggesting that different mechanisms beyond environmental transmission may be at play regarding microbial acquisition in wild bees.</p>
Plant management but not fertilization mediates soil carbon emission and microbial community composition in subtropical Eucalyptus plantations
<p><span>The diversity of </span><span>plant functional group</span><span>s</span><span> in plantations affects soil carbon, but we have limited understanding of the underlying mechanisms for how plant management affects soil carbon dynamics. Here, we conducted a 3-year manipulation experiment of plant functional groups that included understory removal, tree root trenching, and fertilization treatments in 2-year-old and 6-year-old <em>Eucalyptus</em> plantations in the subtropical region. The results showed that soil respiration was significantly suppressed by understory removal (-38%), tree root trenching (-41%), and their interactions (-54%), but that fertilization alone and in interactions had no significant effect. The Chao1 indices for soil bacterial and fungal diversity significantly decreased with understory removal in the 2-year-old plantation and with tree root trenching in the 6-year-old plantation. Soil bacterial and fungal communities were also affected by understory removal and tree root trenching. Soil respiration, physicochemical characteristics, microbial diversity, and community composition were significantly affected by plantation age. Reductions in soil carbon emissions were associated with reductions in plant functional groups and soil microbial groups, while increases in soil respiration were associated with soil physicochemical factors, soil temperature, and plantation age. Our findings highlight that plant managements are of great significance to the soil carbon emission processes in afforested plantations.</span></p>
Assessing the importance of interspecific interactions in the evolution of microbial communities
<p>These data and script are related to the article entitled "Assessing the importance of interspecific interactions in the evolution of microbial communities". This study reports the results of an experiment that aimed at understanding the role of interactions between bacterial species in the evolutionary responses of bacterial communities. The phenotype (optical density) of eight communities composed of two bacterial strains was assessed before and after an experimental evolution of five months (with a transfer each 3.5 days) and compared to the phenotype of communities rebuilt from the same strains that evolved in isolation. The phenotype of the bacterial strains of the study grown in isolation under the three evolutionary treatments (ancestor, evolved in isolation, evolved in community) was also assessed. All the data and codes needed to reproduce the figures and tables presented in the manuscript are provided.</p>
Figure 3 in Microbial source tracking and antimicrobial resistance in one river system of a rural community in Bahia, Brazil
Figure 3. Locations and copy numbers for human- and ruminant-indicative Bacteroides spp. DNA extracted from the material retained from filtration of 500 ml was used for qPCR determination of rDNA copy number. The size of the indicated shapes in the figure is proportional to the copy number/ml at that point as indicated in the legend. Inset shows points 12 and 13 at the same scale as the main figure.
Figure 2 in Microbial source tracking and antimicrobial resistance in one river system of a rural community in Bahia, Brazil
Figure 2. Locations and concentrations of coliforms and E. coli at water collection points. A volume of water (100 µl – 1 ml) collected mid-stream was plated using the Coliscan culture system. Colonies were identified and counted at 48h. The size of the indicated shapes in the figure is proportional to the number of colonies/ml cultured as indicated in the legend. Inset shows points 12 and 13 at the same scale as the main figure.
Figure 1 in Microbial source tracking and antimicrobial resistance in one river system of a rural community in Bahia, Brazil
Figure 1. Study area, rivers and water collection sites. The collection points on the Jiquiriçá River are P1-5; collection points on the Brejões P6-8. P3 is at the junction of the 2 rivers, and P9 and P10 are from the water treatment plant and an outside faucet, respectively. Left inset – Location of Bahia state, Salvador and Jenipapo within Brazil based on Wikimedia Commons (2011). Right inset – relationship of P12 and P13 to Jenipapo. These 2 points represent the source of piped water for the community and the furthest point upstream for collection on the Brejões River, respectively. Inset modified from Wikimedia Commons (2011).
Fig. 6 in Toxocara canis-induced changes in host intestinal microbial communities
Fig. 6 Correlation networks of the microbiome. a Heatmap of correlation coefficients in the CI, II and Tc groups. b Network map between species. Each node in the graph represents a species, with the color of the dot representing the highest relative abundance observed within these subgroups.The size of the dot corresponds to the average relative abundance of the species, with larger dots indicating higher abundance.The species are connected to each other through straight lines, with the color pink indicating a positive correlation and blue indicating a negative correlation. The thickness of the lines reflects the magnitude of the correlation, with only correlation coefficients> 0.2 between species being displayed
Fig. 3 in Toxocara canis-induced changes in host intestinal microbial communities
Fig. 3 Comparison of beta diversity indicator of flora among CI, II and Tc groups. a Unweighted uniFrac analysis, b Weighted uniFrac analysis, c Partial least-squares discriminant analysis. CI, Intestine samples of dogs in control group; II, intestine samples of dogs in infected group; plsda, partial least-squares discriminant analysis; Tc, Toxocara canis samples
Fig. 5 in Toxocara canis-induced changes in host intestinal microbial communities
Fig. 5 Differences in species composition of flora in the CI, II and Tc group at the genus level. The horizontal coordinate is the sample name and the vertical coordinate is the relative abundance of the species annotated. Species not annotated at this taxonomic level and whose abundance was <0.5% of the sample were combined as "Others" (a). b The top 10 species at the genus level in the CI, II and TI group. Note that the significance of the test of difference was marked with an asterisk at the top of the bar graph if available. CI, Intestine samples of dogs in control group; II, intestine samples of dogs in infected group; Tc, Toxocara canis samples
Fig. 2 in Toxocara canis-induced changes in host intestinal microbial communities
Fig. 2 Boxplots showing comparisons of the alpha diversity indicators of flora among the three experimental groups. a Coverage index, b Chao index, c Shannon index, d Ace index. CI, Intestine samples of dogs in control group; II, intestine samples of dogs in infected group; Tc, Toxocara canis samples
Fig. 1 in Toxocara canis-induced changes in host intestinal microbial communities
Fig. 1 OTU cluster analysis. OTUs were generated according to 97% sequence similarity clustering. a Venn diagram of the unique and common OTUs among the three groups. b Rank-abundance curves. c Rarefaction curve. d Species accumulation curve. CI, Intestine samples of dogs in control group; II, intestine samples of dogs in infected group; OTU, operational taxonomic unit; Tc, Toxocara canis samples
Dataset for "The Role of Microbial Communities in Biogeochemical Cycles and Greenhouse Gas Emissions within Tropical Soda Lakes"
<p>Here, we make available 27 raw metagenomic files in fastq.gz associated to the article: "The Role of Microbial Communities in Biogeochemical Cycles and Greenhouse Gas Emissions within Tropical Soda Lakes". This files is not paired, with forward as _1.fastq.gz and reverse as _2.fastq.gz. The abstract of manuscript is described below:<br><br></p> <p>Abstract</p> <p>Although anthropogenic activities are the primary drivers of increased greenhouse gas (GHG) emissions, it is crucial to acknowledge that wetlands are a significant source of these gases. Brazil's Pantanal, the largest tropical inland wetland, includes numerous lacustrine systems with freshwater and soda lakes. This study focuses on soda lakes to explore potential biogeochemical cycling and the contribution of biogenic GHG emissions from the water column, particularly methane. Both seasonal variations and the eutrophic status of each examined lake significantly influenced GHG emissions. Eutrophic turbid lakes (ET) showed remarkable methane emissions, likely due to cyanobacterial blooms. The decomposition of cyanobacterial cells, along with the influx of organic carbon through photosynthesis, accelerated the degradation of high organic matter content in the water column by the heterotrophic community. This process released byproducts that were subsequently metabolized in the sediment leading to methane production, more pronounced during periods of increased drought. In contrast, oligotrophic turbid lakes (OT) avoided methane emissions due to high sulfate levels in the water, though they did emit CO2 and N2O. Clear vegetated oligotrophic turbid lakes (CVO) also emitted methane, possibly from organic matter input during plant detritus decomposition, albeit at lower levels than ET. Over the years, a concerning trend has emerged in the Nhecolândia subregion of Brazil's Pantanal, where the prevalence of lakes with cyanobacterial blooms is increasing. This indicates the potential for these areas to become significant GHG emitters in the future. The study highlights the critical role of microbial communities in regulating GHG emissions in soda lakes, emphasizing their broader implications for global GHG inventories. Thus, it advocates for sustained research efforts and conservation initiatives in this environmentally critical habitat.</p> <p><strong> </strong></p>
Dataset for microbial community and carbon use efficiency determined under SPP project- CueNosc
<p>This dataset encapsulates molecular and biothermal data derived from the CueNosc sub-project, which operates under the umbrella of the German research initiative "SoilSystems: Systems Ecology of Soils – Energy Discharge Modulated by Microbiome and Boundary Conditions." This initiative is supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) as part of the priority program 2322.</p> <p>We carried out a microcosm incubation experiment utilizing both intact soil samples and soil-free microbial cell extracts (SFCE). The primary aim was to assess the impact of various carbon substrates—including glucose, glutamine, glycerol, and citric acid—on microbial communities' dynamic and their carbon use efficiency (CUE). The data collected includes detailed analyses of microbial community composition at the phylum level and CUE values. Carbon use efficiency was obtained by calculating the calorespirometric ratio (metabolic heat production to respiration).</p> <p> </p>
Fig. 1 in Eukaryotic Microbial Communities Associated with Rock-dwelling Foliose Lichens: A Functional Morphological and Microecological Analysis
Fig. 1. Photograph of a portion of a Flavoparmelia thallus showing an example of a radially oriented lobe with three segments sampled in analyzing the microbial communities: A – inner, B – middle, and C – outer. Scale bar: 5 mm.
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.