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.
290
datasets available to search
ShareScore release 0.9.0
Dataset results
290 results for “phages”
Data from: Phage selection for bacterial cheats leads to population decline
While predators and parasites are known for their effects on bacterial population biology, their impact on the dynamics of bacterial social evolution remains largely unclear. Siderophores are iron-chelating molecules that are key to the survival of certain bacterial species in iron-limited environments, but their production can be subject to cheating by non-producing phenotypes. In a selection experiment conducted over c 20 bacterial generations and involving 140 populations of the pathogenic bacterium Pseudomonas aeruginosa PAO1, we assessed the impact of a lytic phage on competition between siderophore producers and non-producers. We show that the presence of lytic phages favours the non-producing genotype in competition, regardless of whether iron use relies on siderophores. Interestingly, phage pressure resulted in higher siderophore production, which constitutes a cost to the producers and may explain why they were outcompeted by non-producers. At the end of the experiment, however, cheating load reduced the fitness of mixed populations relative to producer monocultures, and only monocultures of producers managed to grow in the presence of phage in situations where siderophores were necessary to access iron. These results suggest that public goods production may be modulated in the presence of natural enemies with consequences for the evolution of social strategies.
Data from: Lytic phages obscure the cost of antibiotic resistance in Escherichia coli
The long-term persistence of antibiotic-resistant bacteria depends on their fitness relative to other genotypes in the absence of drugs. Outside the laboratory, viruses that parasitize bacteria (phages) are ubiquitous, but costs of antibiotic resistance are typically studied in phage-free experimental conditions. We used a mathematical model and experiments with Escherichia coli to show that lytic phages strongly affect the incidence of antibiotic resistance in drug-free conditions. Under phage parasitism, the likelihood that antibiotic-resistant genetic backgrounds spread depends on their initial frequency, mutation rate and intrinsic growth rate relative to drug-susceptible genotypes, because these parameters determine relative rates of phage-resistance evolution on different genetic backgrounds. Moreover, the average cost of antibiotic resistance in terms of intrinsic growth in the antibiotic-free experimental environment was small relative to the benefits of an increased mutation rate in the presence of phages. This is consistent with our theoretical work indicating that, under phage selection, typical costs of antibiotic resistance can be outweighed by realistic increases in mutability if drug resistance and hypermutability are genetically linked, as is frequently observed in clinical isolates. This suggests the long-term distribution of antibiotic resistance depends on the relative rates at which different lineages adapt to other types of selection, which in the case of phage parasitism is probably extremely common, as well as costs of resistance inferred by classical in vitro methods.
Data from: Exposure to phages has little impact on the evolution of bacterial antibiotic resistance on drug concentration gradients
The use of phages for treating bacterial pathogens has recently been advocated as an alternative to antibiotic therapy. Here we test a hypothesis that bacteria treated with phages may show more limited evolution of antibiotic resistance as the fitness costs of resistance to phages may add to those of antibiotic resistance, further reducing the growth performance of antibiotic-resistant bacteria. We did this by studying the evolution of phage-exposed and phage-free Pseudomonas fluorescens cultures on concentration gradients of single drugs, including cefotaxime, chloramphenicol, and kanamycin. During drug treatment, the level of bacterial antibiotic resistance increased through time, and was not affected by the phage treatment. Exposure to phages did not cause slower growth in antibiotic-resistant bacteria, although it did so in antibiotic-susceptible bacteria. We observed significant reversion of antibiotic resistance after drug use being terminated, and the rate of reversion was not affected by the phage treatment. The results suggest that the fitness costs caused by resistance to phages are unlikely to be an important constraint on the evolution of bacterial antibiotic resistance in heterogeneous drug environments. Further studies are needed for the interaction of fitness costs of antibiotic resistance with other factors.
Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations
Herd immunity, a process in which resistant individuals limit the spread of a pathogen among susceptible hosts has been extensively studied in eukaryotes. Even though bacteria have evolved multiple immune systems against their phage pathogens, herd immunity in bacteria remains unexplored. Here we experimentally demonstrate that herd immunity arises during phage epidemics in structured and unstructured Escherichia coli populations consisting of differing frequencies of susceptible and resistant cells harboring CRISPR immunity. In addition, we develop a mathematical model that quantifies how herd immunity is affected by spatial population structure, bacterial growth rate, and phage replication rate. Using our model we infer a general epidemiological rule describing the relative speed of an epidemic in partially resistant spatially structured populations. Our experimental and theoretical findings indicate that herd immunity may be important in bacterial communities, allowing for stable coexistence of bacteria and their phages and the maintenance of polymorphism in bacterial immunity.
Exploring the Roles of Ribosomal Peptides in Prokaryote-Phage Interactions through Deep Learning-Enabled Metagenome Mining
<ol> <li><a href="../api/records/10202404/draft/files/OVD.fa.gz/content">OVD.fa.gz: The Ocean Virus Database containing the identified viral sequences</a></li> </ol> <p><a href="../api/records/8138131/draft/files/OVD_taxonomy.upload.txt/content">2. OVD_taxonomy.upload.txt: The taxonomic information of the OVD.</a></p> <p>3. <a href="../api/records/8138131/draft/files/host_phage_pair_summary.upload.txt/content">host_phage_pair_summary.upload.txt: The phage-host relationships.</a></p> <p>4. <a href="../api/records/8138131/draft/files/RiPP_vpf_host_phage_summary.upload.txt/content">RiPP_vpf_host_phage_summary.upload.txt: The RiPP-involving phage-host interaction network.</a></p> <p>5. virus_db_checkv_quality_summary_upload.tsv: The quality assessment of GOV2 and the identified phages in this study using CheckV.</p>
Selection for phage resistance reduces virulence of Shigella flexneri
<p>There is increasing interest in phage therapy as an alternative to chemical antibiotics for treating bacterial infections, especially using phages that select for evolutionary trade-offs between increased phage resistance and decreased fitness traits such as virulence in target bacteria. A vast repertoire of virulence factors allows the opportunistic bacterial pathogen, <i>Shigella flexneri</i>, to invade human gut epithelial cells, to replicate intracellularly, and to evade host immunity through intercellular spread; the latter is an infection stage that causes tissue damage, contributing to host mortality. It is previously shown that outer membrane porin OmpA of <i>S. flexneri</i> is necessary for polar localization of virulence factor IcsA, which polymerizes host actin and results in bacterial motility within infected cells. We hypothesized that a phage which uses OmpA as a receptor to recognize, bind and infect <i>S. flexneri</i>, should select for phage-resistant mutants with attenuated intercellular spread. Here we show that a naturally-isolated <i>Myoviridae</i> virus, phage A1-1, requires OmpA as a receptor, and selects for reduced virulence in <i>S. flexneri</i>. We characterized five phage-resistant mutants by measuring their phenotypic changes relative to wildtype bacteria in various traits: cell-membrane permeability, total lipopolysaccharide (LPS), sensitivity to four antibiotics, and susceptibility to infection by phages T7 and 60B. Results separated the mutants into two groups: R1 and R2 phenotypically resembled <i>ompA</i> knockouts, whereas R3, R4 and R5 were similar to LPS-deficient strains. Whole genome sequencing confirmed that R1 and R2 had mutations in <i>ompA</i>, while R3, R4 and R5 showed mutations in LPS inner-core biosynthesis genes <i>gmhA</i> and <i>gmhC</i>. Bacterial plaque assays in Vero cells confirmed that all five phage-resistant mutants were incapable of intercellular spread. We concluded that selection for <i>S. flexneri</i> resistance to phage A1-1 generally reduced the virulence trait intercellular spread, but this trade-off could be mediated either by mutations in <i>ompA</i> or those in LPS-core genes that likely altered OmpA conformation.</p>
Jumbo phages possess independent synthesis and utilization systems of NAD+
Open the record for dataset details and reuse information.
Some data for phage protein annotation AI pipeline
Open the record for dataset details and reuse information.
Fig. 2. Maximum likelihood 16S in Molecular Identification of a Phage-infected Protochlamydia Strain Naturally Harboured by Non-Encysting Naegleria
Fig. 2. Maximum likelihood 16S rDNA tree of Parachlamydiaceae, showing the major lineages and sublineages, and all the phylotypes assigned to Protochlamydia naegleriophila. The Pcb1 strain recovered here and the reference strain KNic (in bold) are both natural endosymbionts of Naegleria spp. The tree was rooted on members of Criblamydiaceae and Waddliaceae. Bootstrap values (BV) after 1,000 replicates for ML/NJ/MP were indicated at nodes. Filled circle – node 100% supported with all three methods; asterisk – node supported but BV <40%; hyphen – node not supported. Scale bar represents substitution/site.
Fig. 1 in Molecular Identification of a Phage-infected Protochlamydia Strain Naturally Harboured by Non-Encysting Naegleria
Fig. 1. Light microscopy of Pcb-infected Vero cells monolayer at 3 days p.i., showing multiple vacuoles. Scale bar: 20 µm.
Comparison of Control and Phage-treated Groups in Mouse Model
<p>Control mice (left) became lethargic at ~36 hours after intraperitoneal injection with <em>P. aeruginosa </em>PAO1. Phage-treated mice (right) showed increased vitality. Further analysis revealed phage-treated mice had completely cleared infection thanks to phage cocktail application.</p>
crAss-like phage
Open the record for dataset details and reuse information.
Data from: Plasmid carriage can limit bacteria-phage coevolution
Coevolution with bacteriophages is a major selective force shaping bacterial populations and communities. A variety of both environmental and genetic factors has been shown to influence the mode and tempo of bacteria–phage coevolution. Here, we test the effects that carriage of a large conjugative plasmid, pQBR103, had on antagonistic coevolution between the bacterium Pseudomonas fluorescens and its phage, SBW25ϕ2. Plasmid carriage limited bacteria–phage coevolution; bacteria evolved lower phage-resistance and phages evolved lower infectivity in plasmid-carrying compared with plasmid-free populations. These differences were not explained by effects of plasmid carriage on the costs of phage resistance mutations. Surprisingly, in the presence of phages, plasmid carriage resulted in the evolution of high frequencies of mucoid bacterial colonies. Mucoidy can provide weak partial resistance against SBW25ϕ2, which may have limited selection for qualitative resistance mutations in our experiments. Taken together, our results suggest that plasmids can have evolutionary consequences for bacteria that go beyond the direct phenotypic effects of their accessory gene cargo.
Orbitrap LC-MS/MS data for phage nucleosides
<p>These are files containing LC-MS/MS data for phage T4 and phage SPO1 nucleosides. Phage SPO1 data are in files prefixed ORB59709, and T4 data are in files prefixed with ORB59710. The .RAW files are Thermo .raw files obtained after tandem mass spectrometry, and were converted to .mgf format using MSConvert 3.0.22031 (a component of the Proteowizard open source mass spectrometry bioinformatics software package) under generic default presets for .mgf file extraction.</p> <p>Also included are our mass and charge lists for known nucleosides, known charged adducts, and known neutral adducts.</p> <p>File list: </p> <p>ORB59709.RAW = Raw SPO1 data<br> ORB59709.mgf = Processed SPO1 data<br> ORB59710.RAW = Raw T4 data<br> ORB59710.mgf = Processed T4 data</p> <p>Mass_lists_Nucleosides.csv = Masses and charges of known nucleosides<br> Mass_lists_Charged_adducts.csv = Masses and charges of common charged adducts<br> Mass_lists_Neutral_adducts.csv = Masses of common neutral adducts</p> <p> </p>
An efficient, scarless, selection-free technology for phage engineering
<p>Most recently developed phage engineering technologies are based on the CRISPR-Cas system. Here we present a non-CRISPR-based method for genetically engineering the Escherichia coli phages T5, T7, and P1 by adapting a technology, called pORTMAGE, which was developed for engineering bacterial genomes. The technology comprises E. coli harboring a plasmid encoding a potent recombinase and a gene transiently silencing a repair system. Oligonucleotides with the desired phage mutation are electroporated into E. coli followed by infection of the target bacteriophage. The high efficiency of this technology, which yields 1-14% of desired recombinants, allows low-throughput screening for the desired mutant. We have demonstrated the use of this technology for single-base substitutions, for deletions of 50 bases, for insertions of 20 bases, and for three different phages. However, the technology may also be readily modified for use across many additional bacterial and phage strains.</p>
Study to Evaluate the Safety, Phage Kinetics, and Efficacy of Inhaled AP-PA02 in Subjects With Non-Cystic Fibrosis Bronchiectasis and Chronic Pulmonary Pseudomonas Aeruginosa Infection
ClinicalTrials.gov study NCT05616221. IPD Sharing: NO. Countries: 1. Publications: 0.
Biomarkers of Phage Treatment Response in NTM and Other Infections
ClinicalTrials.gov study NCT07076238. IPD Sharing: YES. Countries: 1. Publications: 0.
PHAGE Study: Bacteriophages as Novel Prebiotics
ClinicalTrials.gov study NCT03269617. IPD Sharing: NO. Countries: 0. Publications: 2.
Data from: Analysis of spounaviruses as a case study for the overdue reclassification of tailed phages
Open the record for dataset details and reuse information.
Data from: The cost of phage resistance in a plant pathogenic bacterium is context-dependent
Open the record for dataset details and reuse information.
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.