#1 · Systems biology

Constraints and cross-feeding shape inferred metabolic fluxes and microbial niches

The dominant thread is inference of metabolic behavior from indirect or heterogeneous data under explicit constraints. Teraflux estimates transcriptome-specific fluxes free of thermodynamically infeasible cycles by maximizing expression-weighted Shannon entropy. A nonlinear growth balance analysis of coarse-grained microbial models quantifies growth costs of suboptimal protein allocation, including enzyme saturation. A consumer-resource model shows that cross-feeding network architecture reshapes microbial diversity under growth-inhibiting stress, and global metagenomes combined with metabolic models define marine heterotroph niches by function rather than taxonomy. A reaction-diffusion study of energy gradients addresses pre-cellular chemical organization and sits at the periphery of this thread. What is new is the combination of thermodynamic feasibility, network structure and function-based niche definition as routes to predicting metabolic state at cellular and community scales.