Density phase transition of spatially confined bacteria

Microbes often colonize spatial niches such as colonic crypts in a gut or glands on skin. Understanding colonization and competition processes within each spatial niche is fundamental to interpret metagenomic data. In this study, we culture fly-gut-derived Acetobacter indonesiensis cells in microfluidics, and find three distinct density states sharply depending on the chamber depth. The critical depth for the transition is shown to be determined by the ratio of the diffusion constant and growth rate of cells. With a reaction-diffusion model, we show that the density-dependent diffusion stabilizes the intermediate density phase. Our results not only propose a basic null model for microbial niche colonization but also suggest novel active matter physics of proliferating and diffusing particles.