Weitz Group

Investigating how viruses transform human health and the fate of our planet

Investigating how viruses transform human health and the fate of our planet.      

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Daniel successfully defends his dissertation, earning his Ph.D. in Quantitative Biosciences.

June 10, 2022 by adavidson38

On June 9th, 2022, Daniel Muratore successfully defended his dissertation entitled “Emergence of Marine Biogeochemical Dynamics Across Scales Drive by Complex Microbial and Viral Communities,’’ earning his Ph.D. in quantitative biosciences.

Congratulations, Daniel!

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

Marine microbial populations are subject to the dual pressures of bottom-up nutrient limitation and top-down infection by abundant viruses. However, top-down and bottom-up controls do not act independently. Environmental conditions also have a large impact on the ecology and evolution of viral populations. This thesis explores the mutual feedbacks between the bottom-up and top-down drivers of marine microbial ecosystems.

The first part of this thesis studies two Lagrangian field campaigns conducted in oligotrophic gyres – one in the North Pacific and one in the Sargasso Sea. Emergent ecosystem-level diel cycles in nutrient uptake and assimilation show partitioning of key limiting resources. We also identify diel coordination of viral gene transcription across vast viral diversity.

The second part studies eco-evolutionary responses of marine virus infection strategies and variable environmental conditions. A comparative metagenomic study of genomic and proteomic nitrogen content across the Eastern Tropical North Pacific oxygen minimum zone identifies genome streamlining in bacteria, archaea, and viruses across nitrogen gradients. Then, we construct and analyze a game theoretic model of the evolution of strategies for viruses and their hosts in iron-limited environments, where viruses can use specialized host iron uptake mechanisms to facilitate infection. We identify conditions for the coexistence of hosts with and without this iron uptake capacity, and viruses that do or do not leverage it for infection.

Filed Under: Accomplishment Tagged With: Foundations of quantitative viral ecology, Microbial ecology & evolution

New paper published in Ecology Letters

January 31, 2022 by adavidson38 Leave a Comment

Look for our new paper out in Ecology Letters, titled “Leapfrog dynamics in phage-bacteria coevolution revealed by joint analysis of cross-infection phenotypes and whole genome sequencing.” This work is was done in collaboration with researchers from the University of California in San Diego as well as former group members Shengyun Peng and Chun Yin Leung.

Filed Under: Publication Tagged With: Foundations of quantitative viral ecology, Microbial ecology & evolution

Ashley successfully defends her dissertation, earning her Ph.D. in Physics.

November 22, 2021 by adavidson38 Leave a Comment

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.

Filed Under: Accomplishment Tagged With: Foundations of quantitative viral ecology, Microbial ecology & evolution

Graduate student feature: Marian Dominguez-Mirazo

October 29, 2021 by adavidson38 Leave a Comment

Quantitative Biosciences Ph.D. student Marian Dominguez-Mirazo successfully defended her thesis proposal on October 19th, 2021. We are delighted to feature Marian to commemorate her successful defense and progression to Ph.D. candidate.

Originally hailing from Iguala, Guerrero, Mexico, Marian joined the Weitz Group in 2018 after completing a bachelor’s degree in Genomics at the National University of Mexico (UNAM). We asked Marian some questions about her work, her time in the Weitz Group, her advice for the science-minded, and her plans for the future.

Describe your primary research project in 5 words or less.
“How do viruses shape populations?”

What initially interested you in viral ecology/quantitative/theoretical science?
There are very few things I like, but the ones I do like, I like A LOT. I really like viruses cause they are constantly defying our understanding of biology. I also like math a bunch, pretty much since I was a kid. So theoretical virology just made sense as a science path for me.

What three words would you use to describe your time in the Weitz Group?
Challenging, fun, insightful.

What is one thing you wish more people knew about being a scientist?
Science can only exist within society, therefore it is not isolated from social problems.

What are your plans for the future?
I would like to stay in science and travel the world while doing it.

 

Filed Under: Feature Tagged With: Foundations of quantitative viral ecology, Microbial ecology & evolution

Marian successfully defends her thesis proposal

October 20, 2021 by adavidson38 Leave a Comment

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.

Filed Under: Accomplishment Tagged With: Foundations of quantitative viral ecology, Microbial ecology & evolution

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The Weitz Group

Investigating how viruses transform human health and the fate of our planet

310 Ferst Dr
School of Biological Sciences
Georgia Institute of Technology
Atlanta, GA 30332, USA

Website developed by Audra Davidson for the Weitz Group, 2021. For more information on the group, contact Dr. Gabi Steinbach: gabi.steinbach (@) physics.gatech.edu

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