About
We combine experimentation, data analysis, and mathematical modeling to unravel the eco-physiology of microbes — from individual cells to the gut microbiome and its impact on the human host.
Research topics
- Computer Science
- Biology
- Computational biology
- Engineering
- Chemistry
- Economics
- Biophysics
- Environmental resource management
- Cell biology
- Biotechnology
- Biochemical engineering
- Biological system
- Genetics
Selected publications
An optimal regulation of fluxes dictates microbial growth in and out of steady state
eLife · 2023 · 53 citations
Senior authorCorresponding- Cell biology
- Biology
- Biochemical engineering
establishes this regulatory mechanism's biological veracity and demonstrates that a remarkably wide range of growth phenomena in and out of steady state can be predicted with quantitative accuracy. This predictive power, achieved with only a few biological parameters, cements the preeminent importance of optimal flux regulation across conditions and establishes low-dimensional allocation models as an ideal physiological framework to interrogate the dynamics of growth, competition, and adaptation in complex and ever-changing environments.
Suboptimal resource allocation in changing environments constrains response and growth in bacteria
Molecular Systems Biology · 2021 · 77 citations
Senior authorCorresponding- Computer Science
- Biology
- Computational biology
To respond to fluctuating conditions, microbes typically need to synthesize novel proteins. As this synthesis relies on sufficient biosynthetic precursors, microbes must devise effective response strategies to manage depleting precursors. To better understand these strategies, we investigate the active response of Escherichia coli to changes in nutrient conditions, connecting transient gene expression to growth phenotypes. By synthetically modifying gene expression during changing conditions, we show how the competition by genes for the limited protein synthesis capacity constrains cellular response. Despite this constraint cells substantially express genes that are not required, trapping them in states where precursor levels are low and the genes needed to replenish the precursors are outcompeted. Contrary to common modeling assumptions, our findings highlight that cells do not optimize growth under changing environments but rather exhibit hardwired response strategies that may have evolved to promote fitness in their native environment. The constraint and the suboptimality of the cellular response uncovered provide a conceptual framework relevant for many research applications, from the prediction of evolution to the improvement of gene circuits in biotechnology.
Frequent coauthors
- 34 shared
Erwin Frey
- 22 shared
Anna Melbinger
Center for NanoScience
- 18 shared
Terence Hwa
- 9 shared
Tomoya Honda
Lawrence Berkeley National Laboratory
- 9 shared
Tobias Reichenbach
Friedrich-Alexander-Universität Erlangen-Nürnberg
- 9 shared
Anatolij Gelimson
University of Oxford
- 9 shared
Markus Arnoldini
ETH Zurich
- 8 shared
Leonardo Mancini
University of Cambridge
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