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290 results for “phages”
Complete dataset for the publication "Phage Paride can kill dormant, antibiotic-tolerant cells of Pseudomonas aeruginosa by direct lytic replication"
<p>This dataset enlists all individual datapoints shown in the publication "Phage Paride can kill dormant, antibiotic-tolerant cells of Pseudomonas aeruginosa by direct lytic replication" (https://doi.org/10.1038/s41467-023-44157-3). For detailed information regarding the individual contributions please check the "Author information" section in the publication. </p>
The Great Phage Escape: Activating and escaping lactococcal antiphage systems
<p>Structure files of several antiphages systems</p>
Bacterial cell surface characterization by phage display coupled to high-throughput sequencing
<p>This record contains the processed high-throughput sequencing data from the manuscript "Bacterial cell surface characterization by phage display coupled to high-throughput sequencing." Data was generated using the <a href="https://github.com/caseygrun/phage-seq">Snakemake workflows and Jupyter notebooks in this repository</a> and is intended to be analyzed further using the notebooks in that repository</p> <p>Each tarball within this record, when expanded, populates the <code>results</code> and <code>intermediate</code> directories of one of those workflows: <code>alpaca-library</code> ,<code>panning-small</code>, <code>panning-massive</code>, or <code>panning-extended</code>. Clone the <a href="https://github.com/caseygrun/phage-seq"><code>phage-seq</code> repository</a>, then download one or more of these tarballs to the corresponding directory of that directory. For example:</p> <blockquote> <pre><code>git clone https://github.com/caseygrun/phage-seq.git cd panning-extended wget https://zenodo.org/records/11246658/files/panning-extended-results.tar.gz tar vzxf panning-extended-results.tar.gz</code></pre> </blockquote> <p>More detailed instructions are included in the README for the <a href="https://github.com/caseygrun/phage-seq"><code>phage-seq</code> repository</a>.</p>
Differences in the genomic potential of soil bacterial and phage communities between urban greenspaces and natural arid soils.
<p>This repository holds the final data products from metagenomics processing of bacteria and viruses from the article : "Differences in the genomic potential of soil bacterial and phage communities between urban greenspaces and natural arid soils"</p> <p>Contents: </p> <ul> <li>LU_metadata.csv: information on the samples</li> <li>soil_chemistry.txt: physicochemical information on samples</li> <li>*_len.csv: tables containing the length information for annotated genes, divided by database. These are used to calculate RPKM abundances from count tables. </li> <li>BACTERIA</li> <li>ko_table, ko_unknown, ko2level, ko_description: count table of KEGG annotations, total counts for unnanotated genes, match of ko number to level and description</li> <li>all_bracken.csv: count table of taxonomic bacterial annotations using kraken2 and bracken</li> <li>mags_tax.csv: taxonomy assignments to MAGs (metagenome assembled genomes)</li> <li>mags_count_table.csv: abundante table of MAGs in counts</li> <li>ags_result, gc_mean, gc_variance: functional traits results, average genome size, and gc content</li> <li>lu_c_count, lu_n_count, card_d0, metals_count_table: abundance tables of genes annotated with Cazy (carbon), Ncydb (nitrogen), CARD (antibiotic resistance genes), and Bacmet (heavy metal resistance genes)</li> <li>VIRUS</li> <li>amg_summary.csv: results from AMG annotation with DRAM-V, filtered to keep genes of interest</li> <li>genomad_virus_summary.tsv: viral taxonomy annotations with geNomad</li> <li>virus_len.txt: length of inferred viruses (used for calculation of RPKM from count tables)</li> <li>all_host_prediction_to_genus.csv: virus host annotation with IPhop</li> <li>final_checkv.tsv: table of final viral inferences with quality estimates</li> <li>viral_species_count_table.txt: abundance table of infered viral contigs in counts</li> </ul>
Data Supporting The Paper 'Fine-tuned spatiotemporal dynamics of DNA replication during phage lambda infection'
<p>The dataset includes raw images, source code, raw vectors saved from MATLAB, and curated data used to generate figures and analyses in the paper <strong>'Fine-tuned spatiotemporal dynamics of DNA replication during phage lambda infection'</strong> by Z. Yu, et al.</p> <p>Additional information about the experiments will be available upon request. </p>
genomic sequencies of phages (prokaryotic vriuses) and their hosts
<p>This repository contains data relevant to the reserach <a href="https://github.com/yoheyokubo/MCL4PHI">Multi-Instance Contrastive Learning with Binomial K-Mers for Phage Host Interaction Prediction</a>. It is comprised of the preprocessed data (<em>data_preprocessed.zip</em>) to quickly reproduce our results and the raw genomic sequencies (<em>data_raw.zip</em>) of phages and hosts, originally from <a href="https://github.com/KennthShang/CHERRY">CHERRY's dataset</a>.</p>
Data from: Effects of prior exposure to antibiotics on bacterial adaptation to phages
Understanding adaptation to complex environments requires information about how exposure to one selection pressure affects adaptation to others. For bacteria, antibiotics and viral parasites (phages) are two of the most common selection pressures and are both relevant for treatment of bacterial infections: increasing antibiotic resistance is generating significant interest in using phages in addition or as an alternative to antibiotics. However, we lack knowledge of how exposure to antibiotics affects bacterial responses to phages. Specifically, it is unclear how the negative effects of antibiotics on bacterial population growth combine with any possible mutagenic effects or physiological responses to influence adaptation to other stressors such as phages, and how this net effect varies with antibiotic concentration. Here, we experimentally addressed the effect of pre-exposure to a wide range of antibiotic concentrations on bacterial responses to phages. Across 10 antibiotics, we found a strong association between their effects on bacterial population size and subsequent population growth in the presence of phages (which in these conditions indicates phage-resistance evolution). We detected some evidence of mutagenesis among populations treated with fluoroquinolones, quinolones and β-lactams at sub-lethal doses, but these effects were small and not consistent across phage treatments. These results show that, although stressors such as antibiotics can boost adaptation to other stressors at low concentrations, these effects are weak compared to the effect of reduced population growth at inhibitory concentrations, which in our experiments strongly reduced the likelihood of subsequent phage-resistance evolution.
Raw data for Characterization of the genetic switch from phage ɸ13 important for human colonization by Staphylococcus aureus
<p>Raw data for the manuscript with the title "Characterization of the genetic switch from phage ɸ13 important for human colonization by <em>Staphylococcus aureus". </em>All data produced in the study can be found in this Excel file.</p>
Human-gut phages harbor sporulation genes
<p>See README file for details.</p> <p><strong>Abstract: </strong>Spore-forming bacteria are prevalent in mammalian guts and have implications for host health and nutrition. The production of dormant spores is thought to play an important role in the colonization, persistence, and transmission of these bacteria. Spore formation also modifies interactions among microorganisms such as infection by phages. Recent studies suggest that phages may counter dormancy-mediated defense through the expression of phage-encoded sporulation genes during infection, which can alter the transitions between active and inactive states. By mining genomes and gut-derived metagenomes, we identified sporulation genes that are preferentially encoded by phages that infect spore-forming bacteria. These included genes involved in chromosome partitioning, DNA damage repair, and cell wall-associated functions. In addition, phages contained homologs of sporulation-specific transcription factors, notably <em>spo0A</em>, the master regulator of sporulation, which could allow phages to control the complex genetic network responsible for spore development. Our findings suggest that phages could influence the formation of bacterial spores with implications for the health of the human gut microbiome, as well as bacterial communities in other environments.</p> <p> </p>
Supplement: Functional strain redundancy and persistent phage infection in a Swiss hard cheese starter culture
<p>Undefined starter cultures are bacterial communities used in cheese making. They are phenotypically stable and propagated under constant conditions in milk. This makes them interesting to understand the eco-evolutionary dynamics of microbial communities. While cheese starter cultures are known to be dominated by a few bacterial species, little is known about the composition, functional relevance, and temporal dynamics of strain-level diversity. Here, we applied shotgun metagenomics to analyze historical samples spanning 22 years and continuous propagation for 123 generations of an important Swiss cheese starter culture. We found that the bacterial community is highly stable and dominated by two species, Streptococcus thermophilus and Lactobacillus delbrueckii subsp. lactis. Each species is represented by a few coexisting strains. Genome sequencing, metabolomics analysis, and co-culturing experiments show that these strains are functionally redundant, but differ tremendously in their phage resistance potential. Moreover, we identified two highly abundant Streptococcus phages that seem to stably coexist in the community without any negative impact on bacterial growth or strain persistence, and despite the presence of a large diversity of matching CRISPR spacers. Our findings provide novel insights into strain-level diversity in domesticated microbial communities and highlight an important role of bacteria-phage interactions in cheese starter cultures. </p>
Phage genomes
<p>Dataset phage genomes for publication "Genomes of a novel group of phages using alternative genetic code found in human gut viromes"</p>
P68 Phage density obtained by Cryo-Electron Microscopy
<p>We clarify that this density map was created by Dominik Hrebik. However it is to be included in a larger manuscript, with other authors, currently under review at Nucleic Acids Research. The title, author list, and abstract of that manuscript follow:</p><h2>Are kuravirus capsid diameters quantized? The first all-atom genome tracing method for double-stranded DNA viruses </h2><p>Samuel Coulbourn Flores1, Michal Malý2, Dominik Hrebík3,<strong> </strong>Pavel Plevka3, Jiří Černý2</p><p>1Swedish University of Agricultural Sciences, Ulls Väg 26, Uppsala, and Stockholm University, Tomtebodavägen 23A, Solna, Sweden</p><p>2 Institute of Biotechnology of the Czech Academy of Sciences, Prumyslova 595, Vestec, 25250, Czech Republic</p><p>3Central European Institute of Technology, Kamenice 753/5, Brno, Czech Republic</p><h2>Abstract</h2><p>The revolution in Cryo-Electron Microscopy has resulted in unprecedented power to resolve large macromolecular complexes including viruses. Many methods exist to explain density corresponding to proteins and thus entire protein capsids have been solved at the all-atom level. However methods for nucleic acids lag behind, and no all-atom viral double-stranded DNA genomes have been published at all. We here present a method which exploits the spiral winding patterns of DNA in icosahedral capsids. The method quickly generates shells of DNA wound in user-specified, idealized spherical or cylindrical spirals. For transition regions, the method allows guided semiflexible fitting. For the <i>kuravirus </i>SU10, our method explains most of the density in a semiautomated fashion. The results suggest rules for DNA turns in the end caps under which two discrete parameters determine the capsid inner diameter. We suggest that other kuraviruses viruses may follow the same winding scheme, producing a discrete rather than continuous spectrum of capsid inner diameters. Our software may be used to explain the published density maps of other double-stranded DNA viruses and uncover their genome packaging principles.</p><p> </p>
Phage Therapy in Prosthetic Joint Infection Due to Staphylococcus Aureus Treated With DAIR.
ClinicalTrials.gov study NCT05369104. IPD Sharing: NO. Countries: 1. Publications: 0.
Bacteriophage Therapy for Difficult-to-treat Infections: the Implementation of a Multidisciplinary Phage Task Force
ClinicalTrials.gov study NCT06368388. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Existence in the Human Digestive Flora of Phages Able to Prevent the Acquisition of Multiresistant Enterobacteria
ClinicalTrials.gov study NCT03231267. IPD Sharing: UNDECIDED. Countries: 1. Publications: 2.
Evaluation of Phage Therapy for the Treatment of Escherichia Coli and Pseudomonas Aeruginosa Wound Infections in Burned Patients
ClinicalTrials.gov study NCT02116010. IPD Sharing: Not stated. Countries: 3. Publications: 1.
Phage 3Determination of Phage/Probiotic Synergistic Effects on Gastrointestinal Health
ClinicalTrials.gov study NCT05750433. IPD Sharing: NO. Countries: 1. Publications: 5.
Experimental Phage Therapy of Bacterial Infections
ClinicalTrials.gov study NCT00945087. IPD Sharing: Not stated. Countries: 1. Publications: 1.
The chronic wound virome: phage diversity and associations with wounds and healing outcomes
Open the record for dataset details and reuse information.
Data from: Effects of prior exposure to antibiotics on bacterial adaptation to phages
Open the record for dataset details and reuse information.
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