Abstract
Do mechanical properties of natural microenvironments impose selective pressures on bacterial communities? Past work using homogeneous liquid or flat plate cultures implicates either biochemical cues or genetic alterations to explain how bacteria interact with their surroundings. However, most natural habitats are disordered 3D systems with spatiotemporally varying material properties, such as tissues, soil, and mucus. A long-standing question is whether and how fundamental biological processes such as growth are altered by the physical properties of such complex microenvironments. To address this, we design mechanically tunable, optically transparent, biomimetic 3D granular matrices that capture the viscoelastic properties and micro-confinement of mucosal samples. By growing several different bacterial strains isolated and characterized from the gut mucus of red flour beetles within 3D microenvironments, we ask how altered mechanical regimes influence growth success. Combining confocal microscopy, agent-based simulations, and biochemical alterations to cellular morphology, we find that high-aspect ratio bacteria outperform low-aspect ratio bacteria under elevated physical confinement. Directionally-biased growth patterns and inefficient 3D packing of rod-shaped bacteria allow them to form elongated colonies which enjoy superior nutrient access - as opposed to spherical cells, which organise into rounded, compactly-packed clusters. Remarkably, this phenomenon is agnostic to organismal biology. We further validate these findings using competitive co-cultures, which show a species-independent enrichment bias towards rod-shaped bacteria within high confinement matrices. Finally, two spatially distinct zones of high-performing rods and low-performing spheres emerge within a universal phase space described by the single cell aspect ratio and the growth success under elevated confinement. Our work unequivocally establishes that the cellular shape selectively imposes growth advantages under 3D physical confinement.
