Publications by authors named "Joshua S Weitz"

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 among 51 strains and 45 phage λ strains that coevolved in laboratory conditions for 37 days.

View Article and Find Full Text PDF

Bacteriophages (phages) are increasingly considered for both treatment and early detection of bacterial pathogens given their specificity and rapid infection kinetics. Here, we exploit an engineered phage expressing nanoluciferase to detect signals associated with lysis spanning single cells to populations. Using several strains we found that the latent period, burst size, fraction of infected cells, and efficiency of plating inferred from fluorescent light intensity signals were consistent with inferences from conventional population assays.

View Article and Find Full Text PDF

Bacteriophage (or 'phage' - viruses that infect and kill bacteria) are increasingly considered as a therapeutic alternative to treat antibiotic-resistant bacterial infections. However, bacteria can evolve resistance to phage, presenting a significant challenge to the near- and long-term success of phage therapeutics. Application of mixtures of multiple phage (i.

View Article and Find Full Text PDF

Unlabelled: Infections caused by multidrug resistant (MDR) pathogenic bacteria are a global health threat. Bacteriophages ("phage") are increasingly used as alternative or last-resort therapeutics to treat patients infected by MDR bacteria. However, the therapeutic outcomes of phage therapy may be limited by the emergence of phage resistance during treatment and/or by physical constraints that impede phage-bacteria interactions .

View Article and Find Full Text PDF

Viral impacts on microbial populations depend on interaction phenotypes-including viral traits spanning the adsorption rate, latent period, and burst size. The latent period is a key viral trait in lytic infections. Defined as the time from viral adsorption to viral progeny release, the latent period of bacteriophage is conventionally inferred via one-step growth curves in which the accumulation of free virus is measured over time in a population of infected cells.

View Article and Find Full Text PDF

Communicating information about health risks empowers individuals to make informed decisions. To identify effective communication strategies, we manipulated the specificity, self-relevance, and emotional framing of messages designed to motivate information seeking about COVID-19 exposure risk. In Study 1 (N=221,829), we conducted a large-scale social media field study.

View Article and Find Full Text PDF

The evolution of multicellular life spurred evolutionary radiations, fundamentally changing many of Earth's ecosystems. Yet little is known about how early steps in the evolution of multicellularity affect eco-evolutionary dynamics. Through long-term experimental evolution, we observed niche partitioning and the adaptive divergence of two specialized lineages from a single multicellular ancestor.

View Article and Find Full Text PDF

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.

View Article and Find Full Text PDF

Photosynthesis fuels primary production at the base of marine food webs. Yet, in many surface ocean ecosystems, diel-driven primary production is tightly coupled to daily loss. This tight coupling raises the question: which top-down drivers predominate in maintaining persistently stable picocyanobacterial populations over longer time scales? Motivated by high-frequency surface water measurements taken in the North Pacific Subtropical Gyre (NPSG), we developed multitrophic models to investigate bottom-up and top-down mechanisms underlying the balanced control of Prochlorococcus populations.

View Article and Find Full Text PDF

Infections caused by multi-drug resistant (MDR) pathogenic bacteria are a global health threat. Phage therapy, which uses phage to kill bacterial pathogens, is increasingly used to treat patients infected by MDR bacteria. However, the therapeutic outcome of phage therapy may be limited by the emergence of phage resistance during treatment and/or by physical constraints that impede phage-bacteria interactions .

View Article and Find Full Text PDF

The rise of antimicrobial resistance has led to renewed interest in evaluating phage therapy. In murine models highly effective treatment of acute pneumonia caused by relies on the synergistic antibacterial activity of bacteriophages with neutrophils. Here, we show that depletion of alveolar macrophages (AM) shortens the survival of mice without boosting the .

View Article and Find Full Text PDF

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 strains and 45 phage strains that coevolved in laboratory conditions for 37 days.

View Article and Find Full Text PDF

Interactions between species catalyze 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 spatial isolation or long evolutionary timescales. We show that multiscale network structure can evolve rapidly under simple ecological conditions without spatial structure.

View Article and Find Full Text PDF

During the COVID-19 pandemic, individuals depended on risk information to make decisions about everyday behaviors and public policy. Here, we assessed whether an interactive website influenced individuals' risk tolerance to support public health goals. We collected data from 11,169 unique users who engaged with the online COVID-19 Event Risk Tool (https://covid19risk.

View Article and Find Full Text PDF

The horizontal transfer of genes is fundamental for the eco-evolutionary dynamics of microbial communities, such as oceanic plankton, soil, and the human microbiome. In the case of an acquired beneficial gene, classic population genetics would predict a genome-wide selective sweep, whereby the genome spreads clonally within the community and together with the beneficial gene, removing genome diversity. Instead, several sources of metagenomic data show the existence of "gene-specific sweeps", whereby a beneficial gene spreads across a bacterial community, maintaining genome diversity.

View Article and Find Full Text PDF

Dormancy is an adaptation to living in fluctuating environments. It allows individuals to enter a reversible state of reduced metabolic activity when challenged by unfavorable conditions. Dormancy can also influence species interactions by providing organisms with a refuge from predators and parasites.

View Article and Find Full Text PDF

Estimating the differences in the incubation-period, serial-interval, and generation-interval distributions of SARS-CoV-2 variants is critical to understanding their transmission. However, the impact of epidemic dynamics is often neglected in estimating the timing of infection-for example, when an epidemic is growing exponentially, a cohort of infected individuals who developed symptoms at the same time are more likely to have been infected recently. Here, we reanalyze incubation-period and serial-interval data describing transmissions of the Delta and Omicron variants from the Netherlands at the end of December 2021.

View Article and Find Full Text PDF
Article Synopsis
  • European countries are implementing strategies like testing, isolation, and booster vaccinations to combat the winter surge of COVID-19, but face challenges due to pandemic fatigue and low compliance.
  • A multicountry survey involving 4,594 participants showed high willingness to comply with testing and isolation requirements, with variation in intentions to receive booster vaccinations across France, Belgium, and Italy.
  • The use of epidemic modeling suggests that effective testing and isolation can significantly reduce transmission rates, while simpler isolation mandates and high booster uptake can enhance overall public compliance and reduce costs.
View Article and Find Full Text PDF

Asymptomatic infections have hampered the ability to characterize and prevent the transmission of SARS-CoV-2 throughout the pandemic. Although asymptomatic infections reduce severity at the individual level, they can make population-level outcomes worse if asymptomatic individuals-unaware they are infected-transmit more than symptomatic individuals. Using an epidemic model, we show that intermediate levels of asymptomatic infection lead to the highest levels of epidemic fatalities when the decrease in symptomatic transmission, due either to individual behavior or mitigation efforts, is strong.

View Article and Find Full Text PDF

We propose and analyze a family of epidemiological models that extend the classic Susceptible-Infectious-Recovered/Removed (SIR)-like framework to account for dynamic heterogeneity in infection risk. The family of models takes the form of a system of reaction-diffusion equations given populations structured by heterogeneous susceptibility to infection. These models describe the evolution of population-level macroscopic quantities S, I, R as in the classical case coupled with a microscopic variable f, giving the distribution of individual behavior in terms of exposure to contagion in the population of susceptibles.

View Article and Find Full Text PDF

The COVAX program aims to provide global equitable access to life-saving vaccines. Despite calls for increased sharing, vaccine protectionism has limited progress towards vaccine sharing goals. For example, as of April 2022 only ~20% of the population in Africa had received at least one COVID-19 vaccine dose.

View Article and Find Full Text PDF

Nutrient availability can significantly influence microbial genomic and proteomic streamlining, for example, by selecting for lower nitrogen to carbon ratios. Oligotrophic open ocean microbes have streamlined genomic nitrogen requirements relative to those of their counterparts in nutrient-rich coastal waters. However, steep gradients in nutrient availability occur at meter-level, and even micron-level, spatial scales.

View Article and Find Full Text PDF

For decades, biomedically centered studies of bacteria have focused on mechanistic drivers of disease in their mammalian hosts. Likewise, molecular studies of bacteriophage have centered on understanding mechanisms by which bacteriophage exploit the intracellular environment of their bacterial hosts. These binary interactions - bacteriophage infect bacteria and bacteria infect eukaryotic hosts - have remained largely separate lines of inquiry.

View Article and Find Full Text PDF

The evolution of multicellular life spurred evolutionary radiations, fundamentally changing many of Earth’s ecosystems. Yet little is known about how early steps in the evolution of multicellularity transform eco-evolutionary dynamics, e.g.

View Article and Find Full Text PDF

Asymptomatic and symptomatic SARS-CoV-2 infections can have different characteristic time scales of transmission. These time-scale differences can shape outbreak dynamics as well as bias population-level estimates of epidemic strength, speed, and controllability. For example, prior work focusing on the initial exponential growth phase of an outbreak found that larger time scales for asymptomatic vs.

View Article and Find Full Text PDF