(2s) How Physicochemical Forces Shape Microbial Recombination in the Host Environment

Doctoral work:

I obtained my PhD in Chemistry in the Division of Chemistry and Chemical Engineering at the California Institute of Technology, where I was an NSF Graduate Research Fellow and a Caltech Caldwell CEMI Graduate Fellow. Under the mentorship of Rustem Ismagilov, I focused on elucidating how polymers in the human diet influence gut structure and function through physicochemical interactions. The human gut abounds in secreted polymers (e.g., mucus, proteins) and ingested polymers (e.g., dietary fibers, food additives, therapeutics). These polymers affect the composition of the gut microbiome and diseases such as inflammatory bowel disease, yet the underlying physics by which these polymers alter gut physiology is not well understood. Through a combination of in vivo and ex vivo mouse experiments and numerical calculations, I was able to develop a coarse-grained, statistical mechanics approach for understanding how dietary polymers impact gut physiology, which enabled quantitative predictions based solely on measurables such as polymer size and concentration. My work yielded a unique insight beyond the scope of traditional microbiology and molecular biology: polymer-driven osmotic forces can compress colonic mucus and influence the aggregation of particles in the gut (1-3). Both mucus compression and aggregation have important implications regarding altered protection against pathogens and drug uptake. This merger of polymer physics and animal work revealed that, by modulating the physical chemistry of polymers, these osmotic forces can be tuned by the host, microbiota, and diet.

Postdoctoral Work:

Because of my PhD work on the gut, I developed an interest in building quantitative frameworks for understanding microbial evolution. Therefore, my postdoctoral work with Edo Kussell at the Center for Genomics and Systems Biology at New York University has focused on microbial population genetics and bioinformatics. As a Simons Postdoctoral Fellow of the LSRF at NYU, I am studying the myriad ways by which homologous recombination impacts microbial evolution. While microbial evolution was once thought to be solely the consequence of mutation, it has become increasingly apparent that recombination plays a key role in reshaping the microbial genome. It can dramatically alter the evolutionary trajectories of microbial populations, as it is involved in the proliferation of antibiotic resistance, antigen variation, and adaptation to the host niche. Despite its importance, quantifying homologous recombination rates in bacteria and viruses has remained challenging due to its obfuscation of clonal relationships, which stymies classical phylogenetic methods. With the Kussell Lab, I have been working on extending and applying their recently developed method for inferring homologous recombination rates in bacteria, which relies on the measurement of statistical correlation functions in large-scale sequencing data, to a range of problems in microbial evolution. Specifically, we have quantified the variation in homologous recombination across core and accessory genes (essential genes present in all strains of a given microbial species and niche-adaptive genes present in a subset of strains) (4). We analyzed >100,000 genomes from 12 bacterial species and found that, despite being the most conserved part of the genome, core genes often have higher homologous recombination rates than accessory genes. Quantifying this intra-genomic variation will allow us to better understand how selective pressures interact with recombination to shape different classes of genes. In a separate project, I adapted the theory and computational approach of our method to measure recombination rates in RNA viruses and, particularly, SARS-like coronaviruses (5). This method allows for the rapid analysis of hundreds of thousands of whole genome sequences. Using this technique, we have uncovered new insights into the clonal relationships of SARS-like coronavirus sequences and the recombination dynamics of SARS-like coronavirus gene pools. This new tool will allow us to better understand and predict both SARS-like coronavirus and RNA virus evolution.

Research Vision:

As a principal investigator, I will merge my expertise from both my PhD and postdoctoral work to understand how physicochemical forces in the gut (and other important mucosal interfaces) influence microbial recombination both from a computational and experimental perspective. My primary aims will be:

1. To understand the link between selective pressures induced by physicochemical forces (e.g., polymer-induced osmotic forces, biochemically-mediated agglutination) and homologous recombination using large-scale metagenomics data. By applying the recombination pipeline I helped develop during my postdoctoral work, we can understand how different environmental states induced by diet, drugs, and disease influence homologous recombination in the gut microbiome and pathogens.
2. Building on Aim 1, I will leverage the expertise I developed during my PhD to perform in vivo and ex vivo animal experiments (likely also in collaboration with other experimentalists) in which we will understand the causal relationship between different physicochemical forces and homologous recombination. To do this, we will perform targeted experiments in which we isolate specific factors (e.g., diet, drugs, immunodeficient mice) to determine how they influence recombination rates in the gut microbiome and pathogens.
3. If Aims 1 and 2 are successful, we will build on this to determine how changes in recombination rates induced by physicochemical forces impacts the function of bacterial core genes (e.g., metabolism) and niche-adaptive genes (e.g., drug resistance). We will use animal experiments to assess both how this influences gut microbiome evolution and, subsequently, how this impacts host health.

Additionally, as described in my postdoctoral work, I have developed a recombination pipeline for the analysis of RNA viruses. We will in parallel apply this approach to understand the evolution of viruses in vivo and how this is influenced by different selective pressures. For this project, I plan on working closely with experimental collaborators with expertise in virology.

Teaching Interests:

I served as a Supplemental Instruction Leader for the General Chemistry course at Brandeis University for six semesters. My responsibilities included leading weekly review sessions, proctoring quizzes, and answering questions students had about course materials. During my undergraduate and PhD work, I took courses in thermodynamics, statistical mechanics, and transport phenomena. I am thus equipped to teach these core courses at the undergraduate and graduate levels. Based on my research interests, I am interested in designing a course focused on the interplay between soft matter physics and microbial evolution, in which students learn to navigate the biophysics literature, and gain a better understanding of the intersection of biological soft matter and microbial evolution. This would involve the review of case studies from the literature, and ultimately students would propose new solutions within this space. I am also interested in teaching a specialized course on data analysis in bioengineering for advanced undergraduates and graduate students. This course would give students the basic tools they need in terms of programming, statistics, and modeling to make insights into complex biological systems.

Selected Publications:

1. Preska Steinberg, A. et al. High-molecular-weight polymers from dietary fiber drive aggregation of particulates in the murine small intestine. eLife 8, e40387 (2019).

2. Datta, S. S., Preska Steinberg, A. & Ismagilov, R. F. Polymers in the gut compress the colonic mucus hydrogel. Proc. Natl. Acad. Sci. U. S. A. 113, 7041-7046 (2016).

3. Preska Steinberg, A., Wang, Z. G. & Ismagilov, R. F. Food polyelectrolytes compress the colonic mucus hydrogel by a Donnan mechanism. Biomacromolecules 20, 2675-2683 (2019).

4. Preska Steinberg, A., Lin, M. & Kussell, E. Core genes can have higher recombination rates than accessory genes within global microbial populations. bioRxiv 2021.09.13.460184.

5. Preska Steinberg, A., Silander, O.K., Kussell, E. Correlated substitutions reveal SARS-like coronaviruses recombine frequently with a diverse set of structured gene pools. In review at Proc. Natl. Acad. Sci. U. S. A.