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”
Partial Atomic Model of the Tailed Lactococcal Phage TP901-1 as Predicted by AlphaFold2
Open the record for dataset details and reuse information.
A domesticated phage suppresses competitors in historical and modern metapopulations of pathogenic bacteria
<p>Bacteria have repeatedly repurposed the machinery of their viruses (bacteriophage) to kill strains of neighboring bacteria. These bacteriophage (phage)-derived elements are strain-specific in their killing activity, and this specificity has been proposed to drive bacterial population dynamics. Direct evidence of the impact of phage-derived elements on natural populations over time is limited. Here we identified viral sequences in a metapopulation of wild plant-associated <em>Pseudomonas</em> spp. genomes. We discovered that the most abundant viral cluster does not encode an intact phage but instead encodes a tailocin: a phage-derived element that bacteria use to kill bacterial competitors. Each pathogenic <em>Pseudomonas</em> sp. strain carries one of a few distinct tailocin variants, which target variable polysaccharides in the outer membrane of co-occurring pathogenic strains. Analysis of historic herbarium samples from the past 170 years revealed that the same tailocin and receptor variants have persisted in the <em>Pseudomonas</em> populations for at least two centuries, suggesting the continued use of a defined set of tailocin haplotypes and receptors. These results indicate that tailocin genetic diversity can be mined to develop targeted "tailocin cocktails" for microbial control.</p>
Regulatory and Technical boundaries for phage therapy and FMT in animals - 17.10.2021 (Part B)
<p>Roundtable discussion on Fecal Microbiota Transplantation chaired by Klaus Helmann (KLIFOVET, DE).</p> <p>The roundtable participants enlisted below:</p> <ul> <li>Thomas Thymann (University of Copenhagen, DK)</li> <li>Mirja Huhtinen (Orion Pharma, FI)</li> <li>Jordi Torren (European Medicines Agency, NL)</li> <li>Alexandre Thibodeau (University of Montreal, CA)</li> <li>Lotte Dahl (Danish Medicines Agency, DK)</li> <li>Martin Bronislaw Oleksiewicz (Danish Medicines Agency, DK)</li> </ul> <p>The invited speakers and the attendees of the workshop have given their informed and explicit consent to the project consortium partners for the publication of this video according to the GDPR in the EU Regulation 2016/679.</p> <p>The video is available on YouTube: <strong><a href="http://youtu.be/0fzARCNlDg8">https://youtu.be/0fzARCNlDg8</a></strong></p> <p>The presentations and opinions disclosed in this video are only for general information purpose and do not constitute a joint declaration on behalf of the beneficiaries of the AVANT project.</p> <p>For any further questions please contact us <strong><a href="avant@rtds-group.com">avant@rtds-group.com</a></strong></p>
Regulatory and Technical boundaries for phage therapy and FMT in animals - 17.10.2021 (Part A)
<p>Roundtable discussion on Phage Therapy chaired by Klaus Helmann (KLIFOVET, DE).</p> <p>The roundtable participants enlisted below:</p> <ul> <li>Michela Gambino (University of Copenhagen, DK)</li> <li>Frenk Smrekar (JAFRAL, SI)</li> <li>Javier Pozo Gonzalez (European Medicines Agency, NL)</li> <li>Lotte Dahl (Danish Medicines Agency, DK)</li> <li>Martin Bronislaw Oleksiewicz (Danish Medicines Agency, DK)</li> </ul> <p>The invited speakers and the attendees of the workshop have given their informed and explicit consent to the project consortium partners for the publication of this video according to the GDPR in the EU Regulation 2016/679.</p> <p>The video is available on YouTube: <strong><a href="http://youtu.be/ySXKKC8CGf8">https://youtu.be/ySXKKC8CGf8</a></strong></p> <p>The presentations and opinions disclosed in this video are only for general information purpose and do not constitute a joint declaration on behalf of the beneficiaries of the AVANT project.</p> <p>For any further questions please contact us <strong><a href="avant@rtds-group.com">avant@rtds-group.com</a></strong></p>
Pivotal role of O-antigenic polysaccharide display in the sensitivity against phage tail-like particles in environmental Pseudomonas kin competition
<p>Environmental pseudomonads<i> </i>colonize various niches including insect and plant environments. When invading these environments, bacteria are confronted with the resident microbiota. To cope with closely related strains they deploy narrow-spectrum weaponry such as tailocins, <i>i.e</i> phage tail-like particles. Little is known about the receptors for these tailocins especially among phylogenetically closely related species. Here, we studied the interaction between an R-tailocin from <i>Pseudomonas protegens </i>CHA0 and a targeted kin, <i>Pseudomonas protegens </i>Pf-5. Using genome-wide transposon insertion sequencing, we identified that lipopolysaccharides are involved in the sensitivity of Pf-5 towards the tailocin of CHA0. By generating Pf-5 lipopolysaccharide mutants and exposing them to extracted tailocin, we specified the two O-antigenic polysaccharides (O-PS) targeted by the tailocin. We affirmed the role of these O-PS through competition assays<i> in vitro </i>as well as in insects. Further, we demonstrate that O-PS are double-edge swords that are responsible for the sensitivity of <i>P. protegens</i> towards phage tail-like particles produced by their kin, but shield bacteria from the immune system of the insect. Our results shed light on the trade-off that bacteria are confronted with, where specific O-PS decorations can both be of benefit or disadvantage depending on the host environment and its bacterial inhabitants.</p>
Curated Phage Database (CPD) fasta file
<p>This is the fasta file including phage genomes used to generate the Curated Phage Database (CPD) utilized in our in review manuscript "The circulating phageome reflects bacterial infections". The corresponding phage characteristic data will be present in the manuscript as a supplemental file, and can be used to connect a Genbank ID to identified bacteriophage host and phage taxonomic information if known.</p> <p>Please note that this database is built from phage sequences in the NCBI nucleotide repository. Due to field bias towards sequencing human disease-related bacteria and their phage, this database is reflective of this bias and is most representative of bacteriophage associated with human pathogens and as such underrepresents environmental phages in comparison - a limitation to keep in mind when utilizing to interpret potential phage sequences.</p>
Phages enhance both phytopathogen density control and rhizosphere microbiome suppressiveness
<p>Bacteriophages, viruses that specifically target plant pathogenic bacteria, have emerged as a promising alternative to traditional agrochemicals. However, it remains unclear how phages should be applied to achieve efficient pathogen biocontrol, and to what extent their efficacy is shaped by indirect interactions with the resident microbiota. Here we tested if the phage biocontrol efficacy of <em>Ralstonia solanacearum</em> phytopathogenic bacterium can be improved by increasing the phage cocktail application frequency, and if the phage efficacy is affected by pathogen-suppressing bacteria already present in the rhizosphere. We find that increasing phage application frequency improves <em>R. solanacearum</em> density control, leading to a clear reduction in bacterial wilt disease in both greenhouse and field experiments with tomatoes. The high phage application frequency also increased the diversity of resident rhizosphere microbiota and enriched several bacterial taxa that were associated with the reduction in pathogen densities. Interestingly, these taxa often belonged to <em>Actinobacteria</em> known for antibiotics production and soil suppressiveness. To test if they could have had secondary effects on <em>R. solanacearum </em>biocontrol, we isolated Actinobacteria from <em>Nocardia</em> and <em>Streptomyces</em> genera and tested their suppressiveness to the pathogen <em>in vitro</em> and <em>in planta</em>. We found that these taxa could clearly inhibit <em>R. solanacearum</em> growth and constrain bacterial wilt disease, especially when combined with the phage cocktail. Together, our findings unravel an undiscovered benefit of phage therapy, where phages trigger a second line of defense by the pathogen-suppressing bacteria that already exist in resident microbial communities.</p>
Bacterial homologs of innate eukaryotic antiviral defenses provide phage protection.
<p>Supplementary data regarding the 'Bacterial homologs of innate eukaryotic antiviral defenses provide phage protection' manuscript.</p><p> </p><p><strong>Abstract:</strong><br>Prokaryotes have evolved a multitude of defense systems to protect themselves from bacteriophage predation. Here, we discovered new phage defense systems related to innate antiviral genes from vertebrates and plants. Our search uncovered over 400 candidates from which eleven were selected and six novel phage defense systems validated. We identified a DNA replication helicase/nuclease 2 (Prometheus) which may act on transcription R-loops, an inositol-monophosphatase-like phage defense protein (Pan), and two ATPases from the NACHT family coupled to novel effectors NucS and SfsA (Nyx and Hypnos). In addition, a fused ubiquitin-like E1-E2-JAB protein combined with a putative MBL nuclease (6A-MBL) was found, and a novel member of the Thoeris family that contains four essential TIR domains with a putative effector SLOG domain (Thoeris type III). Collectively, these defense systems support the concept of deep evolutionary links and shared antiviral mechanisms between prokaryotes and eukaryotes.</p>
Files for 'Phage-bacteria dynamics during the first years of life revealed by trans-kingdom marker gene analysis'
<p>The archive contains most of the files that were used to generate the figures for "Phage-bacteria dynamics during the first years of life revealed by trans-kingdom marker gene analysis".</p> <p><span>data/TGVG_database_v1.1.VC_taxonomy_table.csv</span></p> <p><span>data/Marker-MAGu_virus_DB_v1.1_metadata.tsv</span></p> <p><span>data/MP142_CASE_CNTRL_T1D_LIST1.csv</span></p> <p><span>data/Mock_MSA1003_marker_magu_abundance_table1.tsv</span></p> <p><span>data/TGVG_database_v1.1.exemplars.iphop_genus_outputs1.csv</span></p> <p><span>data/TGVG_database_v1.1.exemplars.iphop_genus_outputs1.filt.csv</span></p> <p><span>data/some_teddy_MP142_metadata2.all_samples1.delivery.csv</span></p> <p><span>data/TGVG_database_v1.1.exemplars.iphop_genome_outputs1.csv</span></p> <p><span>data/Mock_MSA1003_mpa4_abundance_table.txt</span></p> <p><span>data/TGVG_database_v1.1.exemplars.bacphlip.tsv</span></p> <p><span>data/MP142_CASE_CNTRL_IA_LIST1.csv</span></p> <p><span>data/mp142_TGVG1.1_MPA4_combined_abundance_table_longform1.tsv</span></p> <p><span>data/mp142_TEDDY_marker_gene_detection_out1.reads_by_sample.tsv</span></p> <p><span>data/all_shuf_samples_samcov.tsv</span></p> <p><span>data/gtdb_ncbi_taxonomy_map_summary.tsv</span></p> <p><span>data/Mock_MSA1003_read_stats.tsv</span></p> <p><span>data/marker_gene_vir_bac_specificity_sensitivity_tests1.csv</span></p> <p><span>data/TGVG_database_v1.1.exemplars.iphop_genome_outputs1.filt.csv</span></p> <p><span>data/TGVG_database_v1.1.crassvirales_tbl.tsv</span></p> <p><span>data/TGVG_database_v1.1.checkv_completeness.tsv</span></p> <p> </p> <p>For code, see: <a href="https://github.com/mtisza1/teddy_vir_bac_marker_gene">https://github.com/mtisza1/teddy_vir_bac_marker_gene</a></p> <p> </p>
Flow Cytometry Data from "Bacterial cell surface characterization by phage display coupled to high-throughput sequencing"
<p>This record contains the flow cytometry data from the manuscript "Bacterial cell surface characterization by phage display coupled to high-throughput sequencing."</p> <p>Files are in <a href="https://docs.flowjo.com/flowjo/advanced-features/fj-acs/">Archive Cytometry Standard (ACS) format</a> . Each <code>.acs</code> file is a zip container which holds both the raw <code>.fcs</code> files and a FlowJo workspace (<code>.wsp</code>) file.</p> <p>Keywords in the workspace file identify which primary antibody (<code>primary</code>) was used and which cell genotype (<code>strain</code>) was used for each sample. The workspace also encodes the gating scheme and compensation matrix applied to each sample. Plots in the manuscript are exported from Layout views in the workspace.</p>
Structures of phages homing nucleases in complex with Zn and dsDNA
<p><span>Structures were predicted by AlphaFold3 on google servers at <a href="https://golgi.sandbox.google.com" target="_blank" rel="noopener">https://golgi.sandbox.google.com</a> by introducing the sequence of the HNH protein, a Zn<sup>++</sup> ion and a dsDNA of length between 26-32 base-pairs.</span></p> <p><span>The predicted models report interactions between two residues of HNHs and the </span><span>catalytic </span><span>Zn<sup>++</sup> ion</span><span> as well as with the dsDNA. The HNHs N-terminal domain fits in a large dsDNA groove, bringing the </span><span>Zn<sup>++</sup> ion in the vicinity of the dsDNA backbone upper lip of the small groove. Except for HNH3, HNH4, HNH9 and HNH10, the C-terminal domain fits in the following large groove. The HNH3 and 4 C-terminal domain fits on the other side of the dsDNA. HNH9 and 10 do not possess a globular C-terminal domain. Between the two globular domains, a linker helix fits into the small groove between the two large grooves. To note, this linker helix harbours at its N-terminus one of the Zn<sup>++</sup> ion binding residue.</span></p> <p> </p>
Curated data for phage-bacteria hosts for BioML Hackathon
<p>This is the accompanying raw data for this github: https://github.com/havu73/hackathonBio</p> <p>A brief summary of the datasets:</p> <p>For every dataset we have genome sequences for hosts and phages and all positive pairs between phages and hosts (majority of the possible pairs are negative, so we do not save them explicitly). </p> <ul> <li><strong>E.coli: </strong>325 bacterial hosts and 96 phages<strong> </strong>(source study link: https://doi.org/10.1101/2023.11.22.567924)</li> <li><strong>Vibrio: </strong>259 bacterial hosts and 239 phages (source study link: https://doi.org/10.1038/s41467-021-27583-z)</li> <li><strong>Klebsiella:</strong> 149 bacterial hosts and 115 phages (source study link: https://doi.org/10.1038/s41467-024-48675-6)</li> <li><strong>phageDB: </strong>74 bacterial hosts and 4766 phages<strong> </strong>(source link: https://phagesdb.org/)</li> <li><strong>phageScope: </strong>180 bacterial hosts and 4434 phages (source link: https://phagescope.deepomics.org/database)</li> </ul>
Diversity in CRISPR-based immunity protects susceptible genotypes by restricting phage spread and evolution
Diversity in host resistance often associates with reduced pathogen spread. This may result from ecological and evolutionary processes, likely with feedback between them. Theory and experiments on bacteria-phage interactions have shown that genetic diversity of the bacterial adaptive immune system can limit phage evolution to overcome resistance. Using the CRISPR-Cas bacterial immune system and lytic phage, we engineered a host-pathogen system where each bacterial host genotype could be infected by only one phage genotype. With this model system, we explored how CRISPR diversity impacts the spread of phage when they can overcome a resistance allele, how immune diversity affects the evolution of the phage to increase its host range, and if there was feedback between these processes. We show that increasing CRISPR diversity benefits susceptible bacteria via a dilution effect, which limits the spread of the phage. We suggest that this ecological effect impacts the evolution of novel phage genotypes, which then feeds back into phage population dynamics.
Bacteria-phage coevolution with a seed bank
<p>Dormancy is an adaptation to living in fluctuating environments. It allows individuals to enter a reversible state of reduced metabolic activity when challenged by unfavorable conditions. Dormancy can also influence species interactions by providing organisms with a refuge from predators and parasites. Here we test the hypothesis that, by generating a seed bank of protected individuals, dormancy can modify the patterns and processes of antagonistic coevolution. We conducted a factorially designed experiment where we passaged a bacterial host (<em>Bacillus subtilis</em>) and its phage (SPO1) in the presence versus absence of a seed bank consisting of dormant endospores. Owing in part to the inability of phages to attach to spores, seed banks stabilized population dynamics and resulted in minimum host densities that were 30-fold higher compared to bacteria that were unable to engage in dormancy. By supplying a refuge to phage-sensitive strains, we show that seed banks retained phenotypic diversity that was otherwise lost to selection. Dormancy also stored genetic diversity. After characterizing allelic variation with pooled population sequencing, we found that seed banks retained twice as many host genes with mutations, whether phages were present or not. Based on mutational trajectories over the course of the experiment, we demonstrate that seed banks can dampen bacteria-phage coevolution. Not only does dormancy create structure and memory that buffers populations against environmental fluctuations, it also modifies species interactions in ways that can feed back onto the eco-evolutionary dynamics of microbial communities. </p>
Dataset: Live cell dynamics of production, explosive release and killing activity of phage tail-like weapons for Pseudomonas kin exclusion
<p>This dataset is related to "Live cell dynamics of production, explosive release and killing activity of phage tail-like weapons for Pseudomonas kin exclusion" and contains the raw data obtained.</p>
Phage-antibiotic synergy: cell filamentation is a key driver of successful phage predation
<div class="t-landing__text-wall "> <p><span>Phages are promising tools to fight antibiotic-resistant bacteria, and as for now, phage therapy is essentially performed in combination with antibiotics. Interestingly, combined treatments including phages and a wide range of antibiotics lead to an increased bacterial killing, a phenomenon called phage-antibiotic synergy (PAS), suggesting that antibiotic-induced changes in bacterial physiology alter the dynamics of phage propagation. Using single-phage and single-cell techniques, each step of the lytic cycle of phage HK620 was studied in <em>E. coli</em> cultures treated with either ciprofloxacin or cephalexin, two filamentation-inducing antibiotics. In the presence of sublethal doses of antibiotics, multiple stress tolerance and DNA repair pathways are triggered following activation of the SOS response. One of the most notable effects is the inhibition of bacterial division. As a result, a significant fraction of cells forms filaments that stop dividing but have higher rates of mutagenesis. Antibiotic-induced filaments become easy targets for phages due to their enlarged surface areas, as demonstrated by fluorescence microscopy and flow cytometry techniques. Adsorption, infection and lysis occur more often in filamentous cells compared to regular-sized bacteria. In addition, the reduction in bacterial numbers caused by impaired cell division may account for the faster elimination of bacteria during PAS. We developed a mathematical model to capture the interaction between sublethal doses of antibiotics and exposition to phages. This model shows that the induction of filamentation by sublethal doses of antibiotics can amplify the replication of phages and therefore yield PAS. We also use this model to study the consequences of PAS on the emergence of antibiotic resistance. A significant percentage of hyper-mutagenic filamentous bacteria are effectively killed by phages due to their increased susceptibility to infection. As a result, the addition of even a very low number of bacteriophages produced a strong reduction of the mutagenesis rate of the entire bacterial population. We confirm this prediction experimentally using reporters for bacterial DNA repair. Our work highlights the multiple benefits associated with the combination of sublethal doses of antibiotics with bacteriophages.</span></p> </div>
Supplementary Movies – Pattern formation by bacteria-phage interactions
<p>Supplementary movies of the manuscript "Pattern formation by bacteria-phage interactions".</p>
Molecular reshaping of phage-displayed Interleukin-2 at beta chain receptor interface to obtain potent super-agonists with improved developability profiles-primary dataset
<div class="c-message_kit__blocks c-message_kit__blocks--rich_text"> <div class="c-message__message_blocks c-message__message_blocks--rich_text"> <div class="p-block_kit_renderer"> <div class="p-block_kit_renderer__block_wrapper p-block_kit_renderer__block_wrapper--first"> </div> </div> </div> </div> <p>Interleukin-2 (IL-2) had been been engineered up to now by yeast display and in silico rational design. In this article we reshaped IL-2 interface with the IL-2 receptor beta subunit to increase binding affinity between both interacting partners, using phage display. Multiple IL-2 mutated variants were selected from large phage-displayed libraries, showing shared molecular patterns. An accumulation of negative charges in the segment 81-87 of IL-2 primary sequence was observed, as well as the strong preponderance of the replacement I92L. The first feature contributed to an optimized electrostatic complementarity between IL-2 and IL-2 receptor beta chain, resulting in higher affinity and faster association kinetics than the ones of previously reported H9 superkine retrieved from yeast display libraries. The presence of a Leu residue at position 92 was the key molecular determinant for a favourable biophysical profile characterized by high stability and production in mammalian-cell based recombinant systems, and decreased aggregation propensity. The new beta super-binders behaved as potent super agonists, both in vitro and in vivo. The latter scenario showed their better preformance when compared to both non-mutated IL-2 and H9. The current dataset contains source data for graphics showing frequency mutations and charge distribution among unselected variants contained in phage-displayed libraries and selected clones enriched after selection on immobilized beta chain. Data showing the direct comparison between different IL-2 mutated variants produced as Fc-fusion proteins are also presented. The comparison includes the results of beta chain binding assays (ELISA), proliferation and phosphorylation assays in vitro, in vivo expansion of lymphocyte populations and anti-tumor activity in animal models. Taken together, the above described data support the unique features of the new beta super-binders and their potential as immunostimulatory and anti-cancer agents.</p>
Data from: Phage combination therapies for bacterial wilt disease in tomato
Open the record for dataset details and reuse information.
Pivotal role of O-antigenic polysaccharide display in the sensitivity against phage tail-like particles in environmental Pseudomonas kin competition
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.