Biology subjects

Nguyen, T. V. P.

Publications and source records attributed to Nguyen, T. V. P..

3 recordsLinked to original sources

bioRxiv2023

Using population dynamics to count bacteriophages and their lysogens

Traditional assays for counting bacteriophages and their lysogens are labor-intensive and highly perturbative to the host cells. Here, we present a high-throughput infection method where all steps--cell growth, viral encounters, and post-infection recovery--take place in a microplate reader, and the growth dynamics of the infected culture are measured continuously using the optical density (OD). We find that the post-infection dynamics are reproducible and interpretable. In particular, the OD at which the culture lyses scales linearly with the logarithm of the initial phage concentration, providing a way of measuring phage numbers in unknown samples over nine decades and down to single-phage sensitivity. Interpreting the measured dynamics using a mathematical model for the coupled kinetics of phages and bacteria further allows us to infer the rates of viral encounters and cell lysis. Adding a single step of antibiotic selection provides the ability to measure the rate of host lysogenization. To demonstrate the application of our assay, we characterized the effect of bacterial growth rate on the propensity of lambda phage to lysogenize E. coli. When infected by a single phage, the probability of lysogenization is found to decrease approximately exponentially with the host growth rate. In growing, but not in stationary, cells, the propensity to lysogenize increases ~50-fold when multiple phages co-infect the cell. These findings illuminate how host physiology feeds into the lysis/lysogeny decision circuit, and demonstrate the utility of high-throughput infection to interrogating phage-host interactions.

microbiology↗

bioRxiv2023

Co-infecting phages impede each other's entry into the cell

Bacteriophage lambda tunes its propensity to lysogenize based on the number of viral genome copies inside the infected cell. Viral self-counting is believed to serve as a way of inferring the abundance of available hosts in the environment. This interpretation is premised on an accurate mapping between the extracellular phage-to-bacteria ratio and the intracellular multiplicity of infection (MOI). However, here we show this premise to be untrue. By simultaneously labeling phage capsids and genomes, we find that, while the number of phages landing on each cell reliably samples the population ratio, the number of phages entering the cell does not. Single-cell infections, followed in a microfluidic device and interpreted using a stochastic model, reveal that the probability and rate of individual phage entries decrease with MOI. This decrease reflects an MOI-dependent perturbation to host physiology caused by phage landing, evidenced by compromised membrane integrity and loss of membrane potential. The dependence of phage entry dynamics on the surrounding medium is found to result in a strong impact of environmental conditions on the infection outcome, while the protracted entry of co-infecting phages increases the cell-to-cell variability in infection outcome at a given MOI. Our findings demonstrate the previously unappreciated role played by entry dynamics in determining the outcome of bacteriophage infection.

microbiology↗

bioRxiv2021

Bacteriophage self-counting in the presence of viral replication

When host cells are in low abundance, temperate bacteriophages opt for dormant (lysogenic) infection. Phage lambda implements this strategy by increasing the frequency of lysogeny at higher multiplicity of infection (MOI). However, it remains unclear how the phage reliably counts infecting viral genomes even as their intracellular number increases due to replication. By combining theoretical modeling with single-cell measurements of viral copy number and gene expression, we find that, instead of hindering lambdas decision, replication facilitates it. In a nonreplicating mutant, viral gene expression simply scales with MOI rather than diverging into lytic (virulent) and lysogenic trajectories. A similar pattern is followed during early infection by wildtype phage. However, later in the infection, the modulation of viral replication by the decision genes amplifies the initially modest gene expression differences into divergent trajectories. Replication thus ensures the optimal decision--lysis upon single-phage infection, lysogeny at higher MOI.

systems biology↗