Ontology highlight
ABSTRACT:
PROVIDER: PRJNA592009 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10580534_1.fastq.gz | Fastqsanger.gz | |||
| SRR10580534_2.fastq.gz | Fastqsanger.gz | |||
| SRR10580535_1.fastq.gz | Fastqsanger.gz | |||
| SRR10580535_2.fastq.gz | Fastqsanger.gz | |||
| SRR10580536_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 112 |
Similar Datasets
Project description:Phages that infect synthetic soil community members
| PRJEB55820 | ENA
Project description:The present work describes LC-ESI-MS/MS analyses of tryptic digestion peptides from phages that infect Staphylococcus aureus-causing mastitis, and isolated from dairy products. A total of 1935 non-redundant peptides belonging to 1282 proteins were identified and analyzed. Among them, 80 staphylococcal peptides from phages were confirmed. These peptides belong to proteins such as phage repressors, structural phage proteins, uncharacterized phage proteins and complement inhibitors. Moreover, of the phage origin peptides found, eighteen of them were specific to S. aureus strains. These diagnostic peptides could be useful for the identification and characterization of S. aureus strains that cause mastitis. Furthermore, a study of bacteriophage phylogeny and the relationship among the identified phage peptides and the bacteria they infect was also performed. The results show the specific peptides which are present in closely related phages, and the existing links between bacteriophage phylogeny and the respective Staphylococcus spp. infected.
2021-03-25 | PXD023530 | Pride
Project description:Virus cocktail containing phages that infect Pseudomonas aeruginosa and others
| PRJNA1008675 | ENA
Project description:In this study we isolated phages that infect non-growing bacteria
| PRJEB67828 | ENA
Project description:By entering a reversible state of reduced metabolic activity, dormant microorganisms are able to contend with suboptimal conditions that would otherwise reduce their fitness. In addition, certain types of dormancy like sporulation, can serve as a refuge from parasitic infections. Phages are unable to attach to spores, but their genomes can be entrapped in the resting structures and are able to resume infection upon host germination. Thus, dormancy has the potential to affect both the reproductive and survival components of phage fitness. Here, we characterized the distribution and diversity of sigma factors in nearly 3,500 phage genomes. Homologs of bacterial sigma factors that are responsible for directing transcription during sporulation were preferentially recovered in phages that infect spore-forming hosts. While non-essential for lytic infection, when expressed in Bacillus subtilis, we demonstrate that phage-encoded sigma factors activated sporulation gene networks and reduced spore yield. Our findings suggest that the acquisition of host-like transcriptional regulators may allow phages to manipulate the expression of complex traits, like the transitions involved in bacterial dormancy.
2021-11-05 | GSE187004 | GEO
Project description:Phages are viruses that infect prokaryotes and can shape microbial communitiesby lysis, thus offering applications in various fields. However, challengesexist in sampling, isolation and accurate prediction of the host specificity ofphages as well as in the identification of newly replicated virions in response toenvironmental challenges. A new workflow using biorthogonal non-canonicalamino acid tagging (BONCAT) and click chemistry (CC) allowed combinedanalysis of phages and their hosts, the identification of newly replicated virions,and the specific tagging of phages with biotin for affinity chromatography.Replication of phage λ in Escherichia coli was selected as a model for workflowdevelopment. Specific labeling of phage λ proteins with the non-canonicalamino acid 4-azido-L-homoalanine (AHA) during phage development in E. coliwas confirmed by LC–MS/MS. Subsequent tagging of AHA with fluorescentdyes via CC allowed the visualization of phages adsorbed to the cell surfaceby fluorescence microscopy. Flow cytometry enabled the automated detectionof these fluorescent phage-host complexes. Alternatively, AHA-labeled phageswere tagged with biotin for purification by affinity chromatography. Despitebiotinylation the tagged phages could be purified and were infectious afterpurification. Applying this approach to environmental samples would enablehost screening without cultivation. A flexible and powerful workflow for thedetection and enrichment of phages and their hosts in pure cultures has beenestablished. The developed method lays the groundwork for future workflowsthat could enable the isolation of phage-host complexes from diverse complexmicrobial communities using fluorescence-activated cell sorting or biotinpurification. The ability to expand and customize the workflow through thegrowing range of compounds for CC offers the potential to develop a versatiletoolbox in phage research. This work provides a starting point for these furtherstudies by providing a comprehensive standard operating procedure.
2024-08-29 | PXD044316 | Pride
Project description:Cyanobacteria are highly abundant in the oceans where they are constantly exposed to lytic viruses. Some viruses are restricted to a narrow host range while others infect a broad range of hosts. It is currently unknown whether broad-host range phages employ the same infection program, or regulate their program in a host-specific manner to accommodate for the different genetic makeup and defense systems of each host. Here we used a combination of microarray and RNA-seq analyses to investigate the interaction of three phylogentically distinct Synechococcus strains, WH7803, WH8102, and WH8109, with the broad-host range T4-like myovirus, Syn9, during infection. Strikingly, we found that the phage led a nearly identical expression program in the three hosts despite considerable differences in host gene content. On the other hand, host responses to infection involved mainly host-specific genes, suggesting variable attempts at defense against infection. A large number of responsive host genes were located in hypervariable genomic islands, substantiating genomic islands as a major axis of phage-bacteria interactions in cyanobacteria. Furthermore, transcriptome analyses and experimental determination of the complete phage promoter map revealed three temporally regulated modules and not two as previously thought for cyanophages. In contrast to T4, an extensive, previously unknown regulatory motif drives expression of early genes and host-like promoters drive middle-gene expression. These promoters are highly conserved among cyanophages and host-like middle promoters extend to other T4-like phages, indicating that the well-known mode of regulation in T4 is not the rule among the broad family of T4-like phages. We investigated the infection process and transcriptional program of the P-TIM40 cyanophage during infection of a Prochlorococcus NATL2A host. The results are discussed in conjunction with results obtained from the infection process for the Syn9 cyanophage in three different Synechococcus hosts: WH7803 (Dufresne et al. 2008), WH8102 (Palenik et al. 2003) and WH8109 (sequenced as part of this study).
2015-08-30 | E-GEOD-63690 | biostudies-arrayexpress