Jamming and dynamic arrest in sheltered microbial communities*

Microbes often colonize spatially-constrained habitats, such as pores in the skin or crypts in the colon. The resulting micro-communities are often stable and contribute to the genetic diversity and function of our microbiomes. It is, however, unclear how spatial constraints influence microbial community assembly. By monitoring and modeling microbial populations under controlled microfluidic confinement, we find a rich spectrum of dynamical patterns that are controlled by the competition between density-dependent outflow and population growth. Our results show that density-dependent passive diffusion can drive a reproducing population to a jamming threshold. The resultig loss of mixing and intra-species competition controls the resilience and evolution of these sheltered communities.