Description
Microbial interactions unfold within environments structured by physical transport and chemical gradients, yet most mechanistic studies rely on well-mixed systems that obscure how metabolism and ecology influence one another. To examine how spatial heterogeneity reshapes microbial interactions in the gut, we investigated how oxygen gradients affect a canonical polysaccharide-mediated interaction between Bacteroides thetaiotaomicron, a strict anaerobe and primary degrader of dietary starch, and Escherichia coli, a facultative anaerobe incapable of complex polysaccharide hydrolysis.
By combining microfluidic experiments, Rna-seq, genetic perturbations, isotope tracing, and reaction–transport modeling, we show that the ecological outcome of this trophic interaction depends strongly on environmental context. In well-mixed cultures, E. coli exploits metabolites released during polysaccharide degradation by B. thetaiotaomicron. Under spatially structured conditions that generate crypt-like oxygen gradients, however, this interaction is fundamentally transformed. The two species segregate into complementary spatial niches: polysaccharide degradation by B. thetaiotaomicron supports E. coli growth in oxygenated regions, while E. coli respiration locally depletes oxygen, thereby expanding the anoxic habitat available to the anaerobe.
Together, these results show how coupled metabolic and environmental feedbacks convert a simple cross-feeding interaction into a facilitative and dynamic niche-construction process, illustrating how spatial structure reshapes microbial interactions.