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153 results for “Bacteriophages”
Data from: Gain-of-function experiments in bacteriophage lambda uncover residues under diversifying selection in nature
Viral gain-of-function mutations frequently evolve during laboratory experiments. Whether the specific mutations that evolve in the lab also evolve in nature and whether they have the same impact on evolution in the real world is unknown. We studied a model virus, bacteriophage λ, that repeatedly evolves to exploit a new host receptor under typical laboratory conditions. Here we demonstrate that two residues of λ's J protein are required for the new function. In natural λ variants, these amino acid sites are highly diverse and evolve at high rates. Insertions and deletions at these locations are associated with phylogenetic patterns indicative of ecological diversification. Our results show that viral evolution in the laboratory mirrors that in nature and that laboratory experiments can be coupled with protein sequence analyses to identify the causes of viral evolution in the real world. Furthermore, our results provide evidence for widespread host-shift evolution in lambdoid viruses.
Data from: Parasite genetic distance and local adaptation in coevolving bacteria-bacteriophage populations
Antagonistic coevolution between hosts and parasites can lead to local adaptation (LA), such that parasite fitness is greatest in sympatric hosts (or vice versa). The magnitude of LA typically increases with geographic distance, which is assumed to be because genetic (and hence phenotypic) distance increases with geographic distance. Here we explicitly test the relationships between parasite genetic and phenotypic distance and LA using isolates of coevolved viral parasites (lytic bacteriophage ϕ2) and the host bacterium Pseudomonas fluorescens SBW25. We find positive relationships between parasite genotype and infectivity phenotype, but the strength of the relationship was greater when infectivity was defined by the identity of hosts that could be infected rather than the actual number of hosts infected (host range), and when measurements were compared within rather than among populations. Crucially, we find a monotonic relationship between LA and genetic distance across phage isolates from different populations, although in contrast to many geographic studies, parasite LA decreased with genetic distance. These results can be explained by the fact that bacteria can rapidly adapt to phage infectivity mutations, but that evolved resistance has a degree of specificity to the local phage population. Our results show that antagonistic coevolution alone can result in predictable links between genetic distance and host-parasite local adaptation.
Data from: Local biotic environment shapes the spatial scale of bacteriophage adaptation to bacteria
The ecological, epidemiological, and evolutionary consequences of host-parasite interactions are critically shaped by the spatial scale at which parasites adapt to hosts. The scale of interaction between hyperparasites and their parasites is likely to be influenced by the host of the parasite and potentially likely to differ among within-host environments. Here we examine the scale at which bacteriophages adapt to their host bacteria by studying natural isolates from the surface or interior of horse chestnut leaves. We find that phages are more infective to bacteria from the same tree relative to those from other trees but do not differ in infectivity to bacteria from different leaves within the same tree. The results suggest that phages target common bacterial species, including an important plant pathogen, within plant host tissues; this result has important implications for therapeutic phage epidemiology. Furthermore, we show that phages from the leaf interior are more infective to their local hosts than phages from the leaf surface are to theirs, suggesting either increased resistance of bacteria on the leaf surface or increased phage adaptation within the leaf. These results highlight that biotic environment can play a key role in shaping the spatial scale of parasite adaptation and influencing the outcome of coevolutionary interactions.
Experimental studies reveal bacteriophages can affect precipitation of mineral phases (raw data)
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Data from: Phenotypic stochasticity prevents lytic bacteriophage population from extinction during bacterial stationary phase
It is generally thought that the adsorption rate of a bacteriophage correlates positively with fitness, but this view neglects that most phages rely only on exponentially growing bacteria for productive infections. Thus, phages must cope with the environmental stochasticity that is their hosts' physiological states. If lysogeny is one alternative, it is unclear how strictly lytic phages can survive the host stationary phase. Three scenarios may explain their maintenance: (1) pseudolysogeny, (2) diversified or (3) conservative bet-hedging. In order to better understand how a strictly lytic phage survives the stationary phase of its host, and how phage adsorption rate impacts this survival, we challenged two strictly lytic phage λ, differing in their adsorption rates, with stationary phase Escherichia coli cells. Our results showed that, pseudolysogeny was not responsible for phage survival and that, contrary to our expectation, high adsorption rate was not more detrimental during stationary phase than low adsorption rate. Interestingly, this last observation was due to the presence of the "residual fraction" (phages exhibiting extremely low adsorption rates), protecting phage populations from extinction. Whether this cryptic phenotypic variation is an adaptation (diversified bet-hedging) or merely reflecting unavoidable defects during protein synthesis remains an open question.
The Use of Bacteriophage Phi X174 to Assess the Immune Competence of HIV-Infected Patients In Vivo
ClinicalTrials.gov study NCT00001540. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Bacteriophage Therapy of Difficult-to-treat Infections
ClinicalTrials.gov study NCT05498363. IPD Sharing: UNDECIDED. Countries: 0. Publications: 1.
PHAGE Study: Bacteriophages as Novel Prebiotics
ClinicalTrials.gov study NCT03269617. IPD Sharing: NO. Countries: 0. Publications: 2.
CYstic Fibrosis bacterioPHage Study at Yale (CYPHY)
ClinicalTrials.gov study NCT04684641. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Bacteriophage Clinical Trial for Periprosthetic Joint Infection of Multidrug Resistant Pseudomonas Aeruginosa
ClinicalTrials.gov study NCT06798168. IPD Sharing: Not stated. Countries: 1. Publications: 14.
Data from: Phenotypic stochasticity prevents lytic bacteriophage population from extinction during bacterial stationary phase
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Data from: Sublethal streptomycin concentrations and lytic bacteriophage together promote resistance evolution
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Data from: Evolutionary dynamics of separate and combined exposure of Pseudomonas fluorescens SBW25 to antibiotics and bacteriophage
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Data from: Frequency and fitness consequences of bacteriophage φ6 host range mutations
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Data from: Back to the future: evolving bacteriophages to increase their effectiveness against the pathogen Pseudomonas aeruginosa PAO1
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Data from: Local biotic environment shapes the spatial scale of bacteriophage adaptation to bacteria
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Data from: Gain-of-function experiments in bacteriophage lambda uncover residues under diversifying selection in nature
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Data from: Parasite genetic distance and local adaptation in coevolving bacteria-bacteriophage populations
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Data from: Migration enhances adaptation in bacteriophage populations evolving in ecological sinks
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Data from: A mathematical model of marine bacteriophage evolution
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