Multiscale mechanistic modeling of microbial communities: linking molecular interactions to ecological behavior

Microbial communities are complex, multiscale systems in which molecular interactions shape emergent ecological behaviors. From host–phage dynamics to cooperative networks in soil, gut, or engineered consortia, microbes reprogram and exchange metabolites in ways that influence both ecosystem stability and host physiology. Constraint based and kinetic modeling approaches have long been used to study microbial metabolism, yet integrating these into predictive frameworks that capture interspecies cooperation, competition, and adaptation remains a major challenge. Recent developments in genome scale metabolic modeling, dynamic flux balance analysis, and hybrid learning frameworks now make it possible to connect enzymatic level mechanisms with emergent community level processes, offering new opportunities to decode the principles of microbial ecology and design synthetic consortia for biotechnology, health, and environmental applications.This Research Topic aims to bring together systems biologists, modelers, and microbial ecologists to advance mechanistic understanding of microbial community dynamics across spatial and temporal scales. The goal is to bridge metabolic level models of individual microbes with predictive simulations of community interaction, stability, and resource allocation. By combining mechanistic approaches with machine learning and data driven inference, this collection seeks to promote robust modeling workflows that can explain natural microbial behaviors, guide synthetic ecology design, and predict functional outcomes in complex microbiomes.To gather further insights into multiscale mechanisms that govern microbial systems, we welcome articles addressing, but not limited to, the following themes:• Host–phage and pathogen reprogramming using constraint based models of metabolic hijacking and host–pathogen interactions• Division of labor, cooperation, and mutualism modeled through resource sharing and thermodynamic constraints• Hybrid modeling workflows integrating data driven approaches with mechanistic frameworks (e.g., dynamic flux balance analysis, ODE based models)• Modeling of temporal and spatial dynamics in microbial degradation, growth, and community stability• Synthetic ecology and rational design of microbial consortia for industrial or environmental applicationsWe welcome Original Research, Methods, Review, Mini Review, and Perspective articles. Topic editors: Song Feng, Atif Khurshid Wani, Mohammad Shahid Source: https://www.frontiersin.org/research-topics/84207/multiscale-mechanistic-modeling-of-microbial-communities-linking-molecular-interactions-to-ecological-behavior