Biology subjects

Meyer, J. R.

Publications and source records attributed to Meyer, J. R..

At least 19 recordsLinked to original sources

bioRxiv2024

Experimental Phage Evolution Results in Expanded Host Ranges Against MDR and XDR Klebsiella pneumoniae Isolates

Resistance to antibiotics is approaching crisis levels for organisms such as the ESKAPEE pathogens (includes Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp., and Escherichia coli) that often are acquired in hospitals. These organisms sometimes have acquired plasmids that confer resistance to most if not all beta-lactam antibiotics such as those produced by Carbapenem Resistant Enterobacterales (CREs). We have been developing alternative means for dealing with antibiotic resistant microbes that cause infections in humans by developing viruses (bacteriophages) that attack and kill them. We have been working with one of the ESKAPEE pathogens, K. pneumoniae, that has one of the highest propensities for antimicrobial resistance, to develop phages that target and kill it. We identified a number of phages that have lytic capacity against only a few clinical isolates, and through experimental evolution over the course of 30 days, were able to vastly expand the host ranges of these phages to kill a broader range of clinical K. pneumoniae isolates including MDR (multi-drug resistant) and XDR (extensively-drug resistant) isolates. Most interestingly, they were capable of inhibiting growth of clinical isolates both on solid and in liquid medium over extended periods. That we were able to extend the host ranges of multiple naive MDR and XDR K. pneumoniae through experimental phage evolution suggests that such a technique may be applicable to other antibiotic-resistant organisms to help stem the tide of antibiotic resistance and offer further options for medical treatments. ImportanceBacterial pathogens are becoming greater threats given the rise in antibiotic resistance, where traditional therapies may no longer work to cure some infections. Chief amongst these multidrug resistant infections (MDR) and extensively drug-resistant infections (XDR) is Klebsiella pneumoniae, which is known to sometimes harbor genetic elements that render it incredibly difficult to treat with conventional antibiotics. Treatments like bacteriophages have not had much success against such pathogens because resistance to the phages used often develops rapidly. We adapted a co-evolutionary technique to develop K. pneumoniae phages to be highly active longitudinally against K. pneumoniae clinical isolates. In as few as 30 days, we were able to vastly expand the host ranges of K. pneumoniae phages against MDR and XDR clinical isolates and that maintain their infectivity over clinically relevant time periods. By adapting these established techniques to clinical MDR and XDR K. pneumoniae isolates, we believe we can establish similar techniques for expanding phage host ranges against most antibiotic-resistant bacteria. As such, phages can be viable alternatives to antibiotics when antibiotic resistance exists in hospitals and communities.

microbiology↗

bioRxiv2024

ARTIC RSV amplicon sequencing reveals global RSV genotype dynamics.

Respiratory syncytial virus (RSV) is a leading cause of lower respiratory tract infections (LTRIs) in young children and adults over 65, contributing significantly to global healthcare burdens. With the recent approval of multiple pharmacological interventions for RSV, there is an increased demand for efficient, high-throughput sequencing methods to monitor RSV genetic diversity and any potential impact these interventions may have. Here we introduce two novel amplicon-based sequencing schemes designed for RSV A and B, optimised for integration with widespread existing ARTIC sequencing workflows. We demonstrate that these primer schemes can produce high quality genomes from RSV samples across the globe, with eight laboratories in five countries generating complete genomes on both Nanopore and Illumina sequencing platforms. The ability to effectively multiplex these RSV A and B primer schemes, enables streamlined, high-throughput sequencing without prior subtyping. Furthermore, these results provide a snapshot of the circulating diversity of RSV. Phylogenetic analysis of the 882 samples sequenced for this study suggests only minimal geographic clustering of RSV sequences, underscoring the global nature of RSV spread. It also highlights the distinct lineage dynamics seen between RSV A and B. This study represents an advancement in RSV genomics, providing robust tools for global sequencing efforts aimed at tracking RSV evolution and assessing the efficacy of new therapeutic interventions both rapidly and at scale.

genomics↗

bioRxiv2024

Cryptic host phenotypic heterogeneity drives diversification of bacteriophage {lambda}

Bacteriophages, the most abundant and genetically diverse life forms, seemingly defy fundamental ecological theory by exhibiting greater diversity than their numerous bacterial prey. This paradox raises questions about the mechanisms underlying parasite diversity. To investigate this, we took advantage of a surprising experimental result: when bacteriophage {lambda} is continually supplied a single host, {lambda} repeatedly evolves multiple genotypes within the same flask that vary in their receptor use. Measurements of negative frequency-dependent selection between receptor specialists revealed that diversifying selection drove their evolution and maintenance. However, the source of environmental heterogeneity necessary to generate this type of selection was unclear, as only a single isogenic host was provided and replenished every eight hours. Our experiments showed that selection for different specialist phages oscillated over the 8-hour incubation period, mirroring oscillations in gene expression of {lambda}s two receptors (Escherichia coli outer membrane proteins LamB and OmpF). These receptor expression changes were attributed to both cell-to-cell variation in receptor expression and rapid bacterial evolution, which we documented using phenotypic resistance assays and population genome sequencing. Our findings suggest that cryptic phenotypic variation in hosts, arising from non-genetic phenotypic heterogeneity and rapid evolution, may play a key role in driving viral diversity.

evolutionary biology↗

bioRxiv2024

Asesino: a nucleus-forming phage that lacks PhuZ

As nucleus-forming phages become better characterized, understanding their unifying similarities and unique differences will help us understand how they occupy varied niches and infect diverse hosts. All identified nucleus-forming phages fall within the proposed Chimalliviridae family and share a core genome of 68 unique genes including chimallin, the major nuclear shell protein. A well-studied but non-essential protein encoded by many nucleus-forming phages is PhuZ, a tubulin homolog which aids in capsid migration, nucleus rotation, and nucleus positioning. One clade that represents 24% of all currently known chimalliviruses lacks a PhuZ homolog. Here we show that Erwinia phage Asesino, one member of this PhuZ-less clade, shares a common overall replication mechanism with other characterized nucleus-forming phages despite lacking PhuZ. We show that Asesino replicates via a phage nucleus that encloses phage DNA and partitions proteins in the nuclear compartment and cytoplasm in a manner similar to previously characterized nucleus-forming phages. Consistent with a lack of PhuZ, however, we did not observe active positioning or rotation of the phage nucleus within infected cells. These data show that some nucleus-forming phages have evolved to replicate efficiently without PhuZ, providing an example of a unique variation in the nucleus-based replication pathway.

microbiology↗

bioRxiv2024

Bacteriophage {Phi}21s receptor-binding protein evolves new functions through destabilizing mutations that generate non-genetic phenotypic heterogeneity

How viruses evolve to expand their host range is a major question with implications for predicting the next pandemic. Gain-of-function experiments have revealed that host-range expansions can occur through relatively few mutations in viral receptor-binding proteins, and the search for molecular mechanisms that explain such expansions are underway. Previous research on expansions of receptor use in bacteriophage {lambda} has shown that mutations that destabilize {lambda}s receptor-binding protein cause the receptor-binding protein to fold into new conformations that can utilize novel receptors but have weakened thermostability. These observations led us to hypothesize that other viruses may take similar paths to expand their host range. Here, we find support for our hypothesis by studying another virus, bacteriophage 21 ({Phi}21), which evolves to use two new host receptors within two weeks of laboratory evolution. By measuring the thermodynamic stability of {Phi}21 and its descendants, we show that, as {Phi}21 evolves to use new receptors and expands its host range, it becomes less stable and produces viral particles that are genetically identical but vary in their thermostabilities. Next, we show that this non-genetic heterogeneity between particles is directly associated with receptor use innovation, as phage particles with more derived receptor use capabilities are more unstable and decay faster. Lastly, by manipulating the expression of protein chaperones during {Phi}21 infection, we demonstrate that heterogeneity in thermostability and receptor use breadth of phage particles is directly related to the folding of phage proteins into different conformers. Altogether, our results provide support for the hypothesis that viruses can evolve new receptor-use tropisms through mutations that destabilize the receptor-binding protein and produce multiple protein conformers.

evolutionary biology↗

bioRxiv2024

Design, optimization, and inference of multiphasic decay of infectious virus particles

Virus population dynamics are driven by counter-balancing forces of production and loss. Whereas viral production arises from complex interactions with susceptible hosts, the loss of infectious virus particles is often approximated as a first-order kinetic process. As such, experimental protocols to measure infectious virus loss are not typically designed to identify non-exponential decay processes. Here, we propose methods to evaluate if an experimental design is adequate to identify multiphasic virus particle decay and to optimize the sampling times of decay experiments, accounting for uncertainties in viral kinetics. First, we evaluate synthetic scenarios of biphasic decays, with varying decay rates and initial proportions of subpopulations. We show that robust inference of multiphasic decay is more likely when the faster decaying subpopulation predominates insofar as early samples are taken to resolve the faster decay rate. Moreover, design optimization involving non-equal spacing between observations increases the precision of estimation while reducing the number of samples. We then apply these methods to infer multiple decay rates associated with the decay of bacteriophage ( phage) {Phi}D9, an evolved isolate derived from phage {Phi}21. A pilot experiment confirmed that {Phi}D9 decay is multiphasic, but was unable to resolve the rate or proportion of the fast decaying subpopulation(s). We then applied a Fisher information matrix-based design optimization method to propose nonequally spaced sampling times. Using this strategy, we were able to robustly estimate multiple decay rates and the size of the respective subpopulations. Notably, we conclude that the vast majority (94%) of the phage {Phi}D9 population decays at a rate 16-fold higher than the slow decaying population. Altogether, these results provide both a rationale and a practical approach to quantitatively estimate heterogeneity in viral decay.

microbiology↗

bioRxiv2024

Inferring strain-level mutational drivers of phage-bacteria interaction phenotypes

The enormous diversity of bacteriophages and their bacterial hosts presents a significant challenge to predict which phages infect a focal set of bacteria. Infection is largely determined by complementary - and largely uncharacterized - genetics of adsorption, injection, cell take-over and lysis. Here we present a machine learning approach to predict phage-bacteria interactions trained on genome sequences of and phenotypic interactions amongst 51 Escherichia coli strains and 45 phage{lambda} strains that coevolved in laboratory conditions for 37 days. Leveraging multiple inference strategies and without a priori knowledge of driver mutations, this framework predicts both who infects whom and the quantitative levels of infections across a suite of 2,295 potential interactions. We found that the most effective approach inferred interaction phenotypes from independent contributions from phage and bacteria mutations, accurately predicting 86% of interactions while reducing the relative error in the estimated strength of the infection phenotype by 40%. Feature selection revealed key phage{lambda} and E. coli mutations that have a significant influence on the outcome of phage-bacteria interactions, corroborating sites previously known to affect phage{lambda} infections, as well as identifying mutations in genes of unknown function not previously shown to influence bacterial resistance. The methods success in recapitulating strain-level infection outcomes arising during coevolutionary dynamics may also help inform generalized approaches for imputing genetic drivers of interaction phenotypes in complex communities of phage and bacteria.

bioinformatics↗

bioRxiv2023

Upper bound on the mutational burden imposed by a CRISPR-Cas9 gene-drive element

CRISPR-Cas9 gene drives (CCGDs) are powerful tools for genetic control of wild populations, with applications from disease eradication to species conservation. However, Cas9 alone and in a complex with gRNA can cause double-stranded DNA breaks at off-target sites, which could increase the mutational load and lead to unintended loss-of-heterozygosity (LOH) events. These undesired effects raise potential concerns about the long-term evolutionary safety of CCGDs, but the magnitude of these effects is unknown. To measure how the presence of a CCGD or a Cas9 alone in the genome affects the rates of LOH events and de novo mutations, we carried out a mutation accumulation experiment in yeast Saccharomyces cerevisiae. We found no detectable effects on the genome-wide rates of mutations or LOH events. Our power calculations suggest that CCGD or Cas9 affect these rates by less than 30%, which is much less than natural variation for these traits in yeast. A more detailed examination shows that CCGD or Cas9 may alter the lengths and genomic distributions of LOH events, but the statistical support for these effects is weak. Thus, our results demonstrate that CCGDs impose at most a weak additional mutational burden in the yeast model. Although mutagenic effects of gene drives need to be further evaluated in other systems, our results add credence to the proposition that the evolutionary risks posed by well designed gene drives are likely acceptable.

evolutionary biology↗

bioRxiv2023

A mobile intron facilitates interference competition between co-infecting viruses

Mobile introns containing homing endonucleases are widespread in nature and have long been assumed to be selfish elements that provide no benefit to the host organism. These genetic elements are common in viruses, but whether they confer a selective advantage is unclear. Here we studied a mobile intron in bacteriophage {Phi}PA3 and found its homing endonuclease gp210 contributes to viral competition by interfering with the virogenesis of co-infecting phage {Phi}KZ. We show that gp210 targets a specific sequence in its competitor {Phi}KZ, preventing the assembly of progeny viruses. This work reports the first demonstration of how a mobile intron can be deployed to engage in interference competition and provide a reproductive advantage. Given the ubiquity of introns, this selective advantage likely has widespread evolutionary implications in nature.

microbiology↗

bioRxiv2023

Competition-driven eco-evolutionary feedback reshapes bacteriophage lambda's fitness landscape and enables speciation

A major challenge in evolutionary biology is explaining how populations navigate rugged fitness landscapes without getting trapped on local optima. One idea illustrated by adaptive dynamics theory is that as populations adapt, their newly enhanced capacities to exploit resources alter fitness payoffs and restructure the landscape in ways that promote speciation by opening new adaptive pathways. While there have been indirect tests of this theory, none have measured how fitness landscapes deform during adaptation, or test whether these shifts promote diversification. Here, we achieve this by studying bacteriophage , a virus that readily speciates into co-existing receptor specialists under controlled laboratory conditions. We used a high-throughput gene editing-phenotyping technology to measure s fitness landscape in the presence of different evolved- competitors and found that the fitness effects of individual mutations, and their epistatic interactions, depend on the competitor. Using these empirical data, we simulated s evolution on an un-changing landscape and one that recapitulates how the landscape deforms during evolution. heterogeneity only evolved in the shifting landscape regime. This study provides a test of adaptive dynamics, and, more broadly, shows how fitness landscapes dynamically change during adaptation, potentiating phenomena like speciation by opening new adaptive pathways.

evolutionary biology↗

bioRxiv2023

Rapid bacteria-phage coevolution drives the emergence of multi-scale networks

Interactions between species have catalyzed the evolution of multiscale ecological networks-including both nested and modular elements that regulate the function of diverse communities. One common assumption is that such complex pattern formation requires long evolutionary timescales, spatial isolation, or other exogenous processes. Here we show that multiscale network structure can evolve rapidly under simple ecological conditions without spatial structure. In just 21 days of laboratory coevolution, Escherichia coli and bacteriophage {Phi}21 coevolve and diversify to form elaborate cross-infection networks. By measuring [~]10,000 phage-bacteria infections and testing the genetic basis of interactions, we identify the mechanisms that create each component of the multiscale pattern. Initially, nested patterns form through an arms race where hosts successively lose the original receptor (LamB) and phages evolve to use a second (OmpC) and then a third (OmpF) receptor. Next, modules form when the cost of losing the third receptor, OmpF, increases and bacteria evolve resistance mutations that modify the OmpF receptors extramembrane loops. In turn, phages evolve adaptations that facilitate specialized interactions with different OmpF variants. Nestedness reemerges within modules as bacteria evolve increased resistance and phages enhance infectivity against module-specific receptor variants. Our results demonstrate how multiscale networks evolve in parasite-host systems, illustrating Darwins idea that simple adaptive processes can generate entangled banks of ecological interactions.

evolutionary biology↗

bioRxiv2023

Fecal virome transplantation is sufficient to alter fecal microbiota and drive lean and obese body phenotypes in mice

BackgroundThe gastrointestinal microbiome plays a significant role in numerous host processes and has an especially large impact on modulating the host metabolism. Prior studies have shown that when mice receive fecal transplants from obese donors that were fed high-fat diets (HFD) (even when recipient mice are fed normal diets after transplantation), they develop obese phenotypes. These studies demonstrate the prominent role that the gut microbiota play in determining lean and obese phenotypes. While much of the credit has been given to gut bacteria, studies have not measured the impact of gut viruses on these phenotypes. To address this shortcoming, we gavaged mice with viromes isolated from donors fed HFD or normal chow. By characterizing the mices gut bacterial biota and weight-gain phenotypes over time, we demonstrate that viruses can shape the gut bacterial community and affect weight gain or loss. ResultsWe gavaged mice longitudinally over 4 weeks while measuring their body weights and collecting fecal samples for 16S rRNA amplicon sequencing. We evaluated mice that were fed normal chow or high-fat diets, and gavaged each group with either chow-derived fecal viromes, HFD-derived fecal viromes, or phosphate buffered saline controls. We found a significant effect of gavage type, where mice fed chow but gavaged with HFD-derived viromes gained significantly more weight than their counterparts receiving chow-derived viromes. The converse was also true: mice fed HFD but gavaged with chow-derived viromes gained significantly less weight than their counterparts receiving HFD-derived viromes. These results were replicated in two separate experiments and the phenotypic changes were accompanied by significant and identifiable differences in the fecal bacterial biota. Notably, there were differences in Lachnospirales and Clostridia in mice fed chow but gavaged with HFD-derived fecal viromes, and in Peptostreptococcales, Oscillospirales, and Lachnospirales in mice fed HFD but gavaged with chow-derived fecal viromes. Due to methodological limitations, we were unable to identify specific bacterial species or strains that were responsible for respective phenotypic changes. ConclusionsThis study confirms that virome-mediated perturbations can alter the fecal microbiome in an in vivo model and indicates that such perturbations are sufficient to drive lean and obese phenotypes in mice.

microbiology↗

bioRxiv2022

Comparison of bacterial suppression by phage cocktails, dual-receptor generalists, and coevolutionarily trained phages

The evolution and spread of antibiotic resistant bacteria have renewed interest in phage therapy, the use of bacterial viruses (phages) to combat bacterial infections. The delivery of phages in cocktails where constituent phages target different modalities (e.g., receptors) may improve treatment outcomes by making it more difficult for bacteria to evolve resistance. However, the multipartite nature of cocktails may lead to unintended evolutionary and ecological outcomes. Here, we compare a 2-phage cocktail with a largely unconsidered group of phages: generalists that can infect through multiple, independent receptors. We find that both generalists and cocktails that target the same receptors suppress bacteria similarly for ~2 d. Yet a "trained" generalist phage, which previously adapted to its host via 28 d of coevolution, demonstrated superior suppression. To understand why the trained generalist was more effective, we measured the resistance of bacteria against each of our phages. We find that, when bacteria were assailed by 2 phages in the cocktail, they evolved mutations in manXYZ, a host inner-membrane transporter that {lambda} uses to move its DNA across the periplasmic space and into the cell for infection. This provided crossresistance against the cocktail and untrained generalist. However, these mutations were ineffective at blocking the trained generalist because, through coevolutionary training, it evolved to bypass manXYZ resistance. The trained generalists past experiences in training make it exceedingly difficult for bacteria to evolve resistance, further demonstrating the utility of coevolutionary phage training for improving the therapeutic properties of phages.

evolutionary biology↗

bioRxiv2021

Host-parasite coevolution promotes innovation through deformations in fitness landscapes

During the struggle for survival, populations occasionally evolve new functions that give them access to untapped ecological opportunities. Theory suggests that coevolution between species can promote the evolution of such innovations by deforming fitness landscapes in ways that open new adaptive pathways. We directly tested this idea by using high throughput gene editing-phenotyping technology (MAGE-Seq) to measure the fitness landscape of a virus, bacteriophage {lambda}, as it coevolved with its host, the bacterium Escherichia coli. Through computer simulations of {lambda}s evolution on the empirical fitness landscape, we showed that {lambda} was more likely to evolve to use a new receptor if it experienced a shift in its fitness landscape caused by coevolution. This result was further validated by additional laboratory experiments. This study provides direct evidence for the role of coevolution in driving evolutionary novelty and provides a quantitative framework for predicting evolution in coevolving ecological communities.

evolutionary biology↗

bioRxiv2020

Coevolutionary phage training leads to greater bacterial suppression and delays the evolution of phage resistance

The evolution of antibiotic resistant bacteria threatens to become the leading cause of worldwide mortality. This crisis has renewed interest in the practice of phage therapy. Yet, bacterias capacity to evolve resistance is likely to debilitate this therapy as well. To combat the evolution of phage resistance and improve treatment outcomes, many have suggested leveraging phages ability to counter resistance by evolving phages on target hosts before using them in therapy (phage training). We found that during in vitro experiments, a phage trained for 28 days suppressed bacteria [~]1000-fold for 3-8 times longer than its untrained ancestor. This extension was due to a delay in the evolution of resistance. Several factors contributed to this prolonged suppression. Mutations that confer resistance to trained phages are [~]100x less common and, while the target bacterium can evolve complete resistance to the untrained phage in a single step, multiple mutations are required to evolve complete resistance to trained phages. Mutations that confer resistance to trained phages are more costly than mutations for untrained phage resistance. And when resistance does evolve, trained phages are better able to suppress these forms of resistance. One way the trained phage improved was through recombination with a gene in a defunct prophage in the host genome, which doubled phage fitness. This direct transfer of information encoded by the host but originating from a relict phage provides a previously unconsidered mode of training phage. Overall, we provide a case study for successful phage training and uncover mechanisms underlying its efficacy. Significance StatementThe evolution of antibiotic resistant bacteria threatens to claim over 10 million lives annually by 2050. This crisis has renewed interest in phage therapy, the use of bacterial viruses to treat infections. A major barrier to successful phage therapy is that bacteria readily evolve phage resistance. One idea proposed to combat resistance is "training" phages by using their natural capacity to evolve to counter resistance. Here, we show that training phages by coevolving them with their host for one month enhanced their capacity for suppressing bacterial growth and delayed the emergence of resistance. Enhanced suppression was caused by several mechanisms, suggesting that the coevolutionary training protocol produces a robust therapeutic that employs complementary modes of action.

evolutionary biology↗

bioRxiv2020

Leapfrog dynamics in phage-bacteria coevolution revealed by joint analysis of cross-infection phenotypes and whole genome sequencing

Viruses and their hosts can undergo coevolutionary arms races where hosts evolve increased resistance and viruses evolve counter-resistance. Given these arms race dynamics (ARD), viruses and hosts are each predicted to evolve along a single trajectory as more recently evolved genotypes replace their predecessors. Here, by coupling phenotypic and genomic analyses of coevolving populations of bacteriophage {lambda} and Escherichia coli, we find conflicting evidence for ARD. Virus-host infection phenotypes fit the ARD model, yet whole genome analyses did not. Rather than coevolution unfolding along a single trajectory, cryptic genetic variation emerges during initial virus-host coevolution. This variation is maintained across generations and eventually supplants dominant lineages. These observations constitute what we term leapfrog coevolutionary dynamics, revealing weaknesses in the predictive power of standard coevolutionary models. The findings shed light on the mechanisms that structure coevolving ecological networks and reveal the limits of using phenotypic assays alone in characterizing coevolutionary dynamics.

evolutionary biology↗

bioRxiv2019

Canonical host-pathogen tradeoffs subverted by mutations with dual benefits

Tradeoffs between life history traits impact diverse biological phenomena, including the maintenance of biodiversity. We sought to study two canonical tradeoffs in a model host-parasite system consisting of bacteriophage lambda and Escherichia coli: i) parasite resistance for growth and ii) phage infectivity for host-range. We report that these previously hypothesised tradeoffs are, in fact, tradeups. While the observation of tradeups was surprising, they should be expected because if traits X and Y tradeoff, so too traits Y and Z, then X and Z will tradeup. By considering five different E. coli trait correlations we uncovered several tradeups and tradeoffs. Using mathematical models, we establish that tradeups need not inhibit biodiversity, as previously thought, and can help maintain it through high-dimensional trait interactions. We provide a mechanistic explanation for how tradeups emerge and give reasons for why tradeups can even evolve in well-adapted genomes.\n\nAll data will be posted at https://github.com/rebear217 and mirrored at http://people.exeter.ac.uk/reb217/rebHomePage/data.html on acceptance.

evolutionary biology↗

bioRxiv2019

Viral host-range evolvability changes in response to fluctuating selection

The concept of evolvability (the capacity of populations to evolve) has deep historical roots in evolutionary biology. Interest in the subject has been renewed recently by innovations in microbiology that permit direct tests of the causes of evolvability, and with the acknowledgement that evolvability of pathogens has important implications for human health. Here, we investigate how fluctuating selection on the virus, Bacteriophage {lambda}, affects its evolvability. We imposed dynamic selection by altering the expression of two host outer membrane receptors. This, in turn, selected phage to alternately infect the host via a single, or multiple, receptors. Our selection regime resulted in two orthogonal evolutionary behaviors, namely enhanced or reduced evolvability. Strains with enhanced evolvability readily evolved between receptors, losing and gaining the ability to bind multiple receptors more quickly than the ancestral {lambda}. This suggests the receptor-binding protein retained a genetic memory of past states and that evolutionary history can be used to predict future adaptation. Strains with reduced evolvability were refractory to re-specialization and remained generalists on both receptors. Consistent with this behavior, unevolvable strains had reduced rates of molecular evolution in the receptor-binding protein compared to their evolvable counterparts. We found a single mutation in the receptor-binding protein was sufficient to render these strains resistant to evolution and did so by counteracting a receptor-binding trade-off associated with generalism. In this way, cost-free generalization allowed for reduced evolution and evolvability while maximizing success in both environments. Our results suggest the response to fluctuating selection is contingent and can lead to distinct differences in evolvability. These findings contribute to a growing understanding of the causes and consequences of evolvability and have important implications for infectious disease management.

evolutionary biology↗