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.
507
datasets available to search
ShareScore release 0.9.0
Dataset results
507 results for “symbionts”
Heterologous Microarray Hybridization Between Vesicomyid Symbionts
GEO Series GSE13447. Calyptogena magnifica symbiont; Calyptogena pacifica gill symbiont; Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica); Calyptogena kilmeri gill symbiont. 8 samples. Type: Genome variation profiling by array.
A consolidated analysis of the physiological and molecular responses induced under acid stress in the legume symbiont model soil bacterium Sinorhizobium meliloti
GEO Series GSE74449. Sinorhizobium meliloti; Sinorhizobium meliloti 1021. 1 samples. Type: Expression profiling by array.
Honey bee (Apis mellifera) queen quality: Host-microbial transcriptomes exploring the influence of age and hindgut symbiont Commensalibacter melissae
GEO Series GSE286382. Apis mellifera. 39 samples. Type: Expression profiling by high throughput sequencing.
Biofilm transcriptional pathways in the model symbiont Vibrio fischeri
GEO Series GSE237189. Aliivibrio fischeri. 15 samples. Type: Expression profiling by high throughput sequencing.
Metatranscriptomics provides insight into the physiologies of the digestive tract symbionts within the medicinal leech, Hirudo verbana
GEO Series GSE23786. Hirudo verbana; gut metagenome. 2 samples. Type: Expression profiling by high throughput sequencing.
Symbiont-host interactome mapping reveals effector-targeted modulation of hormone networks and activation of host benefits
GEO Series GSE222356. Arabidopsis thaliana. 8 samples. Type: Expression profiling by high throughput sequencing.
A dual-genome microarray for the pea aphid, and its obligate bacterial symbiont
GEO Series GSE3742. Buchnera aphidicola; Acyrthosiphon pisum. 1 samples. Type: Expression profiling by array.
The Host Modulates Transcriptional Profile and Phenotypic Heterogeneity in Symbionts
GEO Series GSE232484. Serratia marcescens. 10 samples. Type: Expression profiling by high throughput sequencing.
Identifying genetic determinants needed to establish a human gut symbiont in its habitat
GEO Series GSE17712. Bacteroides thetaiotaomicron. 59 samples. Type: Other.
Host genotype and stable differences in algal symbiont communities explain patterns of thermal stress response of Montipora capitata following thermal pre-exposure and across multiple bleaching events
<p>Data and script supporting "Stable symbiont communities and host genotype underpin complex differences in thermal stress response in <em>Montipora capitata</em>".</p> <p>"Data_MASTER.xlsx" contains raw water temperature, PAM fluorometry F<sub>v</sub>/F<sub>M</sub>, and qPCR data, as well as fragment identification information.</p> <p>"data_processing.R" contains the R script used to clean up, analyze, and visualize the data.</p> <p><strong>Abstract:</strong></p> <p>As sea surface temperatures increase worldwide due to climate change, coral bleaching events are becoming more frequent and severe, resulting in reef degradation. Leveraging the inherent ability of reef-building corals to acclimatize to thermal stress via pre-exposure to protective temperature treatments may become an important tool in improving the resilience of coral reefs to rapid environmental change. We investigated whether historical bleaching phenotype, coral host genotype, and exposure to protective temperature treatments would affect the response of the Hawaiian coral <em>Montipora capitata</em> to natural thermal stress. Fragments were collected from colonies that demonstrated different bleaching responses during the 2014-2015 event in Kāne‘ohe Bay (O‘ahu, Hawai‘i) and exposed to four different artificial temperature pre-treatments (and a control at ambient temperature). After recovery, fragments experienced a natural thermal stress event either in laboratory conditions or their native reef environment. Response to thermal stress was quantified by measuring changes in the algal symbionts’ photochemical efficiency, community composition, and relative density. Historical bleaching phenotype was reflected in stable differences in symbiont community composition, with historically bleached corals containing only <em>Cladocopium</em> symbionts and historically non-bleached corals having mixed symbiont communities dominated by <em>Durusdinium</em>. Mixed-community corals lost more <em>Cladocopium</em> than <em>Cladocopium</em>-only corals during the natural thermal stress event, and preferentially recovered with <em>Durusdinium</em>. Laboratory pre-treatments exposed corals to more thermal stress than anticipated, causing photochemical damage that varied significantly by genotype. While none of the treatments had a protective effect, temperature variation during treatments had a significant detrimental effect on photochemical efficiency during the thermal stress event. These results show that acclimatization potential is affected by fine-scale differences in temperature regime, host genotype, and relatively stable differences in symbiont community composition that underpin historical bleaching phenotypes in <em>M. capitata</em>.</p> <p> </p>
Data from: Superparasitism drives heritable symbiont epidemiology and host sex ratio in a wasp
Heritable microbial symbionts have profound impacts upon the biology of their arthropod hosts. Whilst our current understanding of the dynamics of these symbionts is typically cast within a framework of vertical transmission only, horizontal transmission has been observed in a number of cases. For instance, several symbionts can transmit horizontally when their parasitoid hosts share oviposition patches with uninfected conspecifics, a phenomenon called superparasitism. Despite this, horizontal transmission, and the host contact structures that facilitates it, have not been considered in heritable symbiont epidemiology. Here, we tested for the importance of host contact, and resulting horizontal transmission, for the epidemiology of a male-killing heritable symbiont (Arsenophonus nasoniae) in parasitoid wasp hosts. We observed that host contact through superparasitism is necessary for this symbiont's spread in populations of its primary host Nasonia vitripennis, such that when superparasitism rates are high, A. nasoniae almost reaches fixation, causes highly female biased population sex ratios and consequently causes local host extinction. We further tested if natural interspecific variation in superparasitism behaviours predicted symbiont dynamics among parasitoid species. We found that A. nasoniae was maintained in laboratory populations of a closely related set of Nasonia species, but declined in other, more distantly related pteromalid hosts. The natural proclivity of a species to superparasitise was the primary factor determining symbiont persistence. Our results thus indicate that host contact behaviour is a key factor for heritable microbe dynamics when horizontal transmission is possible, and that 'reproductive parasite' phenotypes, such as male-killing, may be of secondary importance in the dynamics of such symbiont infections.
Data from: Shared genes but not shared genetic variation: legume colonization by two belowground symbionts
Mutualisms between hosts and multiple symbionts can generate diffuse coevolution if genetic covariance exists between host traits governing multiple interactions. Rhizobia and arbuscular mycorrhizal fungi (AMF) both interact with legume hosts, providing complementary nutrients (nitrogen and phosphorous). Molecular approaches have revealed extensive pleiotropy in the plant genetic pathways required for colonization of both symbionts; however, a quantitative genetic approach is required to understand whether this pleiotropy shapes evolution in natural populations. In a greenhouse experiment with 75 families of Chamaecrista fasciculata grown in two phosphorous environments (fertilized and unfertilized), positive covariance between nodule number and plant aboveground biomass within and across environments indicates selection for increased allocation to rhizobia. Genetic variation for host restriction of AMF colonization in response to P suggests that this aspect of context-dependency can evolve in host populations, and that selection in this mutualism varies with P. Despite the existence of gene-level pleiotropy during rhizobium and AMF infection, we find no evidence for genetic covariance in symbiont colonization or its response to phosphorous - suggesting that genetic variation at other, non-pleiotropic loci govern variation in colonization and thus that these traits likely evolve independently in plant populations.
Data from: Development, feeding, and sex shape the relative quantity of the nutritionnal obligatory symbiont Wolbachia in bed bugs
<p>Datasets and scripts (statistical analyses and graphs) from "Development, feeding, and sex shape the relative quantity of the nutritionnal obligatory symbiont <em>Wolbachia</em> in bed bugs" by Poulain <em>et al.</em>, <em>Frontiers in Microbiology</em>, 15:1386458.</p> <p>doi: 10.3389/fmicb.2024.1386458</p>
ANI values for alphaproteobacterial gutless oligochaete symbionts
<p>ANI values for alphaproteobacterial gutless oligochaete symbionts.</p> <p>Tool used to acquire the matrices: http://enve-omics.ce.gatech.edu/g-matrix/.</p>
Three phylogenetically distinct and culturable diazotrophs are perennial symbionts of leaf-cutting ants
<p>The obligate mutualistic basidiomycete fungus, <i>Leucocoprinus gongylophorus</i>, mediates nutrition of leaf-cutting ants with carbons from vegetal matter. In addition, diazotrophic Enterobacteriales in the fungus garden and intestinal Rhizobiales supposedly mediate assimilation of atmospheric nitrogen; and Entomoplasmatales in the genus <i>Mesoplasma</i>, as well as other yet unidentified strains, supposedly mediate ant assimilation of other compounds from vegetal matter, such as citrate, fructose and aminoacids. Together, these nutritional partners would support the production of high yields of leafcutter biomass. In the present investigation, we propose that three phylogenetically distinct and culturable diazotrophs in the genera <i>Ralstonia</i>, <i>Methylobacterium</i> and <i>Pseudomonas</i> integrate this symbiotic nutrition network, facilitating ant nutrition on nitrogen. Strains in these genera were often isolated and directly sequenced in 16S rRNA libraries from the ant abdomen, together with the non-diazotrophs <i>Acinetobacter</i> and <i>Brachybacterium</i>. These five isolates were underrepresented in libraries, suggesting that none of them is dominant <i>in vivo.</i> Libraries have been dominated by four uncultured Rhizobiales strains in the genera <i>Liberibacter</i>, <i>Terasakiella</i> and <i>Bartonella</i> and, only in <i>Acromyrmex</i> ants, by the Entomoplasmatales in the genus <i>Mesoplasma</i>. <i>Acromyrmex</i> also presented small amounts of two other uncultured Entomoplasmatales strains, <i>Entomoplasma</i> and <i>Spiroplasma</i>. The absence of Entomoplasmatales in <i>Atta</i> workers implicates that association with these bacteria is not mandatory for ant biomass production. Most of the strains that we detected in South American ants were genetically similar with strains previously described in association with leafcutters from Central and North America, indicating wide geographic dispersion, and suggesting fixed ecological services.</p>
Figure 8 in New host detection of the parasitic mite, Erythraeus pistacicus (Trombidiformes: Erythraeidae) from Iran and indication of possible infection with bacterial symbionts
Figure 8. Haplotype network of Planomicrobium spp. based on 16S rDNA sequences.
Figure 4 from: Conradi M, Bandera E, Mudrova SV, Ivanenko VN (2018) Five new coexisting species of copepod crustaceans of the genus Spaniomolgus (Poecilostomatoida: Rhynchomolgidae), symbionts of the stony coral Stylophora pistillata (Scleractinia). ZooKeys 791: 71-95. https://doi.org/10.3897/zookeys.791.28775
Figure 4 Spaniomolgusglobus sp. n., female. a Leg 1 b Leg 2 c Leg 3 d Leg 4 Scale bar: 50 µm.
Figure 11 in Basic laboratory and field manual for conducting research with the entomopathogenic nematodes, Steinernema and Heterorhabditis, and their bacterial symbionts
Figure 11. Enumeration of nematodes in Petri dishes.
Data from: Effects of diet on resource utilization by a model human gut microbiota containing Bacteroides cellulosilyticus WH2, a symbiont with an extensive glycobiome
The human gut microbiota is an important metabolic organ. However, little is known about how its individual species interact, establish dominant positions, and respond to changes in environmental factors such as diet. In the current study, gnotobiotic mice colonized with a simplified model microbiota composed of 12 sequenced human gut bacterial species were fed oscillating diets of disparate composition. Rapid, reproducible and reversible changes in community structure were observed. Time series microbial RNA-Seq analyses revealed staggered functional responses to diet shifts throughout the community that were heavily focused on carbohydrate and amino acid metabolism. High-resolution shotgun metaproteomics confirmed many of these responses at a protein level. One member, Bacteroides cellulosilyticus WH2, proved exceptionally fit regardless of diet. Its genome encoded more carbohydrate active enzymes than any known Bacteroidetes. Transcriptional profiling indicated that B. cellulosilyticus WH2 is an adaptive forager that tailors its versatile carbohydrate utilization strategy to available dietary polysaccharides, with a strong emphasis on plant-derived xylans abundant in dietary staples like cereal grains. Two highly expressed, diet-specific polysaccharide utilization loci (PULs) in B. cellulosilyticus WH2 were identified, one with characteristics of xylan utilization systems. Introduction of a B. cellulosilyticus WH2 library comprising 26,750 isogenic transposon mutants into gnotobiotic mice along with other model community members confirmed that these loci represent critical diet-specific fitness determinants. The specific carbohydrates that trigger overexpression of these two loci and many of the organism's 111 other predicted PULs were identified by RNA-Seq during in vitro growth on 31 distinct carbohydrate substrates, allowing us to better interpret in vivo RNA-Seq and proteomics data. These results offer insight into how gut microbes adapt to dietary perturbations, both at a community level and from the perspective of a well-adapted symbiont with exceptional saccharolytic capabilities, and illustrate the value of studying defined models of the human gut microbiota.
Figures 1-2 from: Kanao T, Maruyama M (2012) Two new genera and species of the termite symbiont lineage Termitohospitini (Coleoptera, Staphylinidae, Aleocharinae) from Bolivia and peninsular Malaysia. ZooKeys 254: 67-87. https://doi.org/10.3897/zookeys.254.4043
Figures 1-2 - Habitus of Neotermitosocius bolivianus. 1 dorsal view 2 ventral view.
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.