From the first hours of life until the last, the human body is colonized by microbes that consume and produce a wide array of metabolites, predominantly within the gastrointestinal tract. These microbial metabolites are intimately linked to inflammation and immune signaling. Molecules such as short-chain fatty acids (SCFAs) and indoles have been shown to attenuate host inflammatory responses,...
Systematically mapping species interactions in microbial communities remains a central challenge. Community-level elementary flux modes (cEFMs) provide a complete description of community metabolism, but are intractable at genome-scale, necessitating optimization-based approaches. However, the latter introduce thermodynamically infeasible cycles (TICs) across organisms, leading to spurious...
Understanding microbial communities is crucial for advancing fields like ecology, biotechnology, and human health. Recently, constraint-based metabolic models of individual organisms have been combined in various ways to study microbial consortia. In this work, we present a comprehensive geometric approach to characterize all feasible microbial interactions. First, we project community models...
Microbial communities play key roles in biotechnology, environmental systems, and human health. Understanding and predicting the dynamics of interacting microbial populations is essential for both advancing fundamental knowledge and enabling the rational design and optimization of these systems. Mechanistic models provide a powerful framework for this purpose, enabling hypothesis testing and...
Microbial communities play a central role in ecosystems, biotechnology, and human health. Understanding how these communities grow, interact, and respond to environmental change requires a strong theoretical foundation that can bridge the gap between genome-scale experimental data and community-level behavior. This minisymposium aims to bring together researchers working on the theory of...
