On November 18th, 2021, Ashley Coenen successfully defended her dissertation entitled “Inferring ecological interactions from dynamics in phage-bacteria communities,’’ earning her Ph.D. in physics.

To learn more about Ashley’s dissertation, read the abstract below.

Characterizing how viruses interact with microbial hosts is critical to understanding microbial community structure and function. However, existing methods for quantifying bacteria-phage interactions are not widely applicable to natural communities. First, many bacteria are not culturable, preventing direct experimental testing. Second, “-omics” based methods, while high in accuracy and specificity, have been shown to be extremely low in power. Third, inference methods based on time-series or co-occurrence data, while promising, have for the most part not been rigorously tested. This thesis work focuses on this final category of quantification strategies: inference methods.

In this thesis, we further our understanding of both the potential and limitations of several inference methods, focusing primarily on time-series data with high time resolution. We emphasize the quantification of efficacy by using time-series data from multi-strain bacteria-phage communities with known infection networks. We employ both in silico simulated bacteria-phage communities as well as an in vitro community experiment. We review existing correlation-based inference methods, extend theory and characterize tradeoffs for model-based inference which uses convex optimization, characterize pairwise interactions in a 5×5 virus-microbe community experiment using Markov chain Monte Carlo, and present analytic tools for microbiome time-series analysis when a dynamical model is unknown. Together, these chapters bridge gaps in existing literature in inference of ecological interactions from time-series data.

On October 19th, 2021, Marian Dominguez-Mirazo successfully defended her thesis proposal entitled “Cell fate modulation from infection to population dynamics’’ and was officially admitted for her Ph.D. candidacy.

To learn more about Marian’s thesis work, read the abstract below.

Viruses are obligate parasites that require their host’s synthesis machinery to replicate. Viruses are the most abundant biological entity on our planet yet account for less than 0.05% of the total biomass. Viruses of microbes can be found virtually everywhere, from the deep sea to the human gut. They can have impacts at the ecosystem level.

Yet viruses can do more than kill their microbial hosts. Some viruses, such as temperate bacteriophage, are capable of carrying out two types of infection: lytic or lysogenic. In a lysogenic pathway, there is viral integration into the host’s genome. Following viral integration, the virus is transmitted vertically until environmental stressors, or spontaneous induction, trigger lysis. In some cases, viral genetic material can be degraded producing a defective prophage incapable of lysing. As long as their genome remains integrated, viral survival and success depend directly on the host’s prosperity. The virus-host relationship is not limited to antagonism. Instead, the relationship is complicated and can range from antagonism to mutualism by means of superinfection exclusion or incorporation of beneficial genes by prophages.

The lytic pathway can beneficially or deleteriously shape host populations as we observe during viral invasion of biofilms. Biofilms are a complex form of bacterial organization where bacteria stick to each other and/or to a surface surrounded by an extracellular matrix of DNA, lipids, and proteins. The biofilm’s matrix and architecture can confer protection to bacteria from environmental hazards like antibiotics, microbial predators, or viruses. Viral invasion of biofilms can result in deleterious outcomes for the host like biofilm elimination, or beneficial ones like enhanced biofilm protection.

The microbial population dynamics resulting from viral invasion depend largely on viral traits. The latent period is the time from viral adsorption to viral progeny release. Latent period variability in a population can arise from cell-to-cell variability and have a profound impact on virus-microbe dynamics.

Using modeling and data analysis, we aim to study cell fate modulation through viral infection and its impact on microbial populations. We intend to explore the virus-microbe relationship at different stages of the infection cycle through 1) study of the presence and role of defective prophage in plant-associated bacteria, 2) reexamination of the viral latent period in virus-microbe systems focusing on the nature and impact of latent period variability in microbial populations, and 3) evaluation of the effect of phage invasion on biofilm-forming bacterial communities.