Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1134382 | ENA |
REPOSITORIES: ENA
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Project description:Retrons are bacterial genetic elements that encode a reverse transcriptase and, in combination with toxic effector proteins, can serve as antiphage defense systems. However, the mechanisms of action of most retron effectors, and how phages evade retrons, are not well understood. Here, we show that some phages can evade retrons and other defense systems by producing specific tRNAs. We find that expression of retron-Eco7 effector proteins (PtuA and PtuB) leads to degradation of tRNA-Tyr and abortive infection. The genomes of T5 phages that evade retron-Eco7 include a tRNA-rich region, including a highly expressed tRNA-Tyr gene, which confers protection against retron-Eco7. Furthermore, we show that other phages (T1, T7) can use a similar strategy, expressing a tRNA-Lys, to counteract a tRNA anticodon defense system (PrrC170).
2024-09-12 | GSE229290 | GEO
Project description:Phage therapy is a therapeutic approach to treat multidrug resistant infections that employs lytic bacteriophages (phages) to eliminate bacteria. Despite the abundant evidence for its success as an antimicrobial in Eastern Europe, there is scarce data regarding its effects on the human host. Here, we aimed to understand how lytic phages interact with cells of the airway epithelium, the tissue site that is colonized by bacterial biofilms in numerous chronic respiratory disorders. Using a panel of Pseudomonas aeruginosa phages and human airway epithelial cells derived from a person with cystic fibrosis, we determined that interactions between phages and epithelial cells depend on specific phage properties as well as physiochemical features of the microenvironment. Although poor at internalizing phages, the airway epithelium responds to phage exposure by changing its transcriptional profile and secreting antiviral and proinflammatory cytokines that correlate with specific phage families. Overall, our findings indicate that mammalian responses to phages are heterogenous and could potentially alter the way that respiratory local defenses aid in bacterial clearance during phage therapy. Thus, besides phage receptor specificity in a particular bacterial isolate, the criteria to select lytic phages for therapy should be expanded to include mammalian cell responses.
2024-02-19 | GSE255619 | GEO
Project description:By performing single-cell RNA sequencing (scRNA-seq) analysis on the T cells which stimulated by phageome from normal or severe acute pancreatitis mice, we seek to understand which T cells contribute to the inflammation in pancreatitis. t-distributed stochastic neighbor embedding (tSNE) identified 5 distinct T cell cluster, including effector CD8, naïve CD8, CD4, proliferating CD8 and stem like CD8. Stimulation by different phages did not change the T cell heterogeneity. Comparison of genes revealed a significant enrichment in the cell proliferation after SAP derived phages treatment. Differential gene expression analysis confirmed that SAP derived phages treatment skewed the cell pattern toward more IL-7r expression, while control derived phages treatment induce the IL-22 expression.
2024-12-31 | GSE269903 | GEO
Project description:Virulent bacteriophages (or phages) are viruses that specifically infect and lyse a bacterial host. When multiple phages co-infect a bacterial host, the extent of lysis, dynamics of bacteria-phage and phage-phage interactions are expected to vary. The objective of this study is to identify the factors influencing the interaction of two virulent phages with different Pseudomonas aeruginosa growth states (planktonic, an infected epithelial cell line, and biofilm) by measuring the bacterial time-kill and individual phage replication kinetics. A single administration of phages effectively reduced P. aeruginosa viability in planktonic conditions and infected human lung cell cultures, but phage-resistant variants subsequently emerged. In static biofilms, the phage combination displayed initial inhibition of biofilm dispersal, but sustained control was achieved only by combining phages and meropenem antibiotic. In contrast, adherent biofilms showed tolerance to phage and/or meropenem, suggesting a spatiotemporal variation in the phage-bacterial interaction. The kinetics of adsorption of each phage to P. aeruginosa during single- or co-administration were comparable. However, the phage with the shorter lysis time depleted bacterial resources early and selected a specific nucleotide polymorphism that conferred a competitive disadvantage and cross-resistance to the second phage. The extent and strength of this phage-phage competition and genetic loci conferring phage resistance, are, however, P. aeruginosa genotype dependent. Nevertheless, adding phages sequentially resulted in their unimpeded replication with no significant increase in bacterial host lysis. These results highlight the interrelatedness of phage-phage competition, phage resistance and specific bacterial growth state (planktonic/biofilm) in shaping the interplay among P. aeruginosa and virulent phages.
2024-07-17 | GSE271537 | GEO
Project description:Gene content in Salmonella enterica sv Typhimurium TAQ100F2 (Ames strain, cured of Fels phages, and Fels2 reintroduced) after exposure to 2mM hydrogen peroxide Keywords: time-course
2004-05-10 | GSE817 | GEO
Project description:Gene content in Salmonella enterica sv Typhimurium TAQ100F2 (Ames strain, cured of Fels phages and Fels2 reintroduced) 3h after exposure to 2mM hydrogen peroxide Keywords: parallel sample
2004-05-10 | GSE818 | GEO
Project description:Gene content in Salmonella enterica sv Typhimurium TAQ100F1 (Ames strain, cured of Fels phages, and Fels1 reintroduced) 3h after exposure to 2mM hydrogen peroxide Keywords: parallel sample
2004-05-10 | GSE816 | GEO
Project description:Two tebuconazole adaptors, TJ1503 and TJ1669, were unstable. On YPD-agar plates, they gave rise to small (S) and large (L) colonies. We sequenced both types of colonies. TJ1503S and TJ1669S were the S colonies. TJ1503L and TJ1669L were the large colonies.
2023-09-06 | E-MTAB-13209 | biostudies-arrayexpress
Project description:Bacteriophage – host dynamics and interactions are important for microbial community composition and ecosystem function. Nonetheless, empirical evidence in engineered environment is scarce. Here, we examined phage and prokaryotic community composition of four anaerobic digestors in full-scale wastewater treatment plants (WWTPs) across China. Despite relatively stable process performance in biogas production, both phage and prokaryotic groups fluctuated monthly over a year of study period. Nonetheless, there were significant correlations in their α- and β-diversities between phage and prokaryotes. Phages explained 40.6% of total prokaryotic community composition, much higher than the explainable power by abiotic factors (14.5%). Consequently, phages were significantly (P<0.010) linked to parameters related to process performance including biogas production and volatile solid concentrations. Association network analyses showed that phage-prokaryote pairs were deeply rooted, and two network modules were exclusively comprised of phages, suggesting a possibility of co-infection. Those results collectively demonstrate phages as a major biotic factor in controlling bacterial composition. Therefore, phages may play a larger role in shaping prokaryotic dynamics and process performance of WWTPs than currently appreciated, enabling reliable prediction of microbial communities across time and space.
2016-12-29 | GSE92978 | GEO