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.
18
datasets available to search
ShareScore release 0.9.0
Dataset results
18 results for “Microbial evolution”
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>
Microbial warfare and the evolution of symbiosis
<p>Cooperative symbionts enable their hosts to exploit a diversity of environments. A low genetic diversity (high relatedness) between the symbionts within a host is thought to favour cooperation by reducing conflict within the host. However, hosts will not be favoured to transmit their symbionts in costly ways that increase relatedness, unless this also provides an immediate fitness benefit to the host. We suggest that costly antimicrobial warfare, with compounds such as bacteriocins, could provide a relatively universal reason for why hosts would gain a benefit from increasing the relatedness between bacterial symbionts. We theoretically test this hypothesis with a simple illustrative model that examines whether hosts should manipulate relatedness, and an individual-based simulation, where host control evolves in a structured population. We find that hosts can be favoured to manipulate relatedness, to reduce conflict between symbionts via this immediate reduction in symbiont warfare.</p>
Evolution in interacting species alters predator life history traits, behavior and morphology in experimental microbial communities
Open the record for dataset details and reuse information.
Microbial warfare and the evolution of symbiosis
Open the record for dataset details and reuse information.
Data from: Microbial solutions to dietary stress: Experimental evolution reveals host-microbiome interplay in Drosophila melanogaster
Open the record for dataset details and reuse information.
Evolution and regulation of microbial secondary metabolism
Microbes have disproportionate impacts on the macroscopic world. This is in part due to their ability to grow to large groups and cooperatively secrete massive amounts of secondary metabolites that impact their environment. Yet, the conditions enabling secondary metabolism without compromising primary needs remain unclear. Here we investigated the biosynthesis of thamnolipids, a secondary metabolite that Pseudomonas aeruginosa makes to decrease the surface tension of surrounding liquid. Using a combination of genomics, metabolomics, transcriptomics, and mathematical modeling we show that biosynthesis of rhamnolipids from glycerol varies inconsistently across the phylogenetic tree; instead, non-producer lineages are also those worse at reducing the oxidative stress of primary glycerol metabolism. The link to oxidative stress explains the inconsistent distribution across the P. aeruginosa tree, adding a new layer to the regulation of rhamnolipids—a microbial secondary metabolite important for fitness in natural and clinical settings.
Evolution and regulation of microbial secondary metabolism
Open the record for dataset details and reuse information.
Evolution of specialization in a plant-microbial mutualism is explained by the oscillation theory of speciation
Open the record for dataset details and reuse information.
Data from: Experimental evolution with a multicellular host causes diversification within and between microbial parasite populations – differences in emerging phenotypes of two different parasite strains
Host-parasite coevolution is predicted to have complex evolutionary consequences, potentially leading to the emergence of genetic and phenotypic diversity for both antagonists. However, little is known about variation in phenotypic responses to coevolution between different parasite strains exposed to the same experimental conditions. We infected Caenorhabditis elegans with one of two strains of Bacillus thuringiensis and either allowed the host and the parasite to experimentally coevolve (coevolution treatment) or allowed only the parasite to adapt to the host (one-sided parasite adaptation). By isolating single parasite clones from evolved populations, we found phenotypic diversification of the ancestral strain into distinct clones, which varied in virulence towards ancestral hosts and competitive ability against other parasite genotypes. Parasite phenotypes differed remarkably not only between the two strains, but also between and within different replicate populations, indicating diversification of the clonal population caused by selection. This study highlights that the evolutionary selection pressure mediated by a multicellular host causes phenotypic diversification, but not necessarily with the same phenotypic outcome for different parasite strains.
Data from: The effects of spatial structure, frequency dependence and resistance evolution on the dynamics of toxin-mediated microbial invasions
Recent evidence suggests that interference competition between bacteria shapes the distribution of the opportunistic pathogen Staphylococcus aureus in the lower nasal airway of humans, either by preventing colonization or by driving displacement. This competition within the nasal microbial community would add to known host factors that affect colonization. We tested the role of toxin-mediated interference competition in both structured and unstructured environments, by culturing S. aureus with toxin-producing or nonproducing Staphylococcus epidermidis nasal isolates. Toxin-producing S. epidermidis invaded S. aureus populations more successfully than nonproducers, and invasion was promoted by spatial structure. Complete displacement of S. aureus was prevented by the evolution of toxin resistance. Conversely, toxin-producing S. epidermidis restricted S. aureus invasion. Invasion of toxin-producing S. epidermidis populations by S. aureus resulted from the evolution of toxin resistance, which was favoured by high initial frequency and low spatial structure. Enhanced toxin production also evolved in some invading populations of S. epidermidis. Toxin production therefore promoted invasion by, and constrained invasion into, populations of producers. Spatial structure enhanced both of these invasion effects. Our findings suggest that manipulation of the nasal microbial community could be used to limit colonization by S. aureus, which might limit transmission and infection rates.
Effect of mutation supply on population dynamics and trait evolution in experimental microbial community
<p>Mutation supply can influence eco-evolutionary dynamics in important ways which have received little attention. Mutation supply determines key features of population genetics, such as the pool of adaptive mutations, evolutionary pathways available, and importance of processes such as clonal interference. The resultant trait evolutionary dynamics, in turn, can alter population size and species interactions. However, controlled experiments testing for the importance of mutation supply on rapid adaptation and thereby population and community dynamics are lacking. To close this knowledge gap, we performed a serial passage experiment with wild-type Pseudomonas fluorescens and an isogenic xerD mutant with reduced mutation rate. Bacteria were grown at two resource levels in combination with the presence of a ciliate predator. We found that a higher mutation supply enabled faster adaptation to the low-resource environment and anti-predatory defense. This was associated with higher population size at the ecological level and better access to high-recurrence mutational targets at the genomic level for the strain with higher mutation supply. In contrast, mutation rate did not affect growth under high-resource level, possibly because of more permissive conditions or high population size saturated in mutations. Our results demonstrate that intrinsic mutation rate influences population dynamics and trait evolution particularly when population size is constrained by extrinsic conditions.</p>
Data from: Experimental evolution with a multicellular host causes diversification within and between microbial parasite populations – differences in emerging phenotypes of two different parasite strains
Open the record for dataset details and reuse information.
Data from: The effects of spatial structure, frequency dependence and resistance evolution on the dynamics of toxin-mediated microbial invasions
Open the record for dataset details and reuse information.
Data from: Rapid evolution of adaptive niche construction in experimental microbial populations
Open the record for dataset details and reuse information.
Effect of mutation supply on population dynamics and trait evolution in experimental microbial community
Open the record for dataset details and reuse information.
Data from: Resident microbial communities inhibit growth and antibiotic resistance evolution of Escherichia coli in human gut microbiome samples
Open the record for dataset details and reuse information.
Microbial Colonization Distribution and Adaptive Evolution of Lower Respiratory Tract in Bronchiectasis Patients.
ClinicalTrials.gov study NCT04966793. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Microbial adaptation to environmental niches can be reproduced by experimental evolution
GEO Series GSE20373. Lactococcus lactis subsp. lactis. 16 samples. Type: Expression profiling by array.
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.