Physical confinement selectively favours bacterial growth based on cell shape

How are bacterial communities altered by changes in their microenvironment? Evidence from homogeneous liquid or flat plate cultures implicates biochemical cues -- such as variation in nutrient composition 1,2, response to chemoattractants and toxins 3,4, and inter-species signalling 5,6 -- as the primary modes of bacterial interaction with their microenvironment. However, these systems fail to capture the effect of physical confinement on bacteria in their natural habitats. Bacterial niches like the pores of soil, mucus, and infected tissues are disordered microenvironments with material properties defined by their internal pore sizes and shear moduli7-11. Here, using three-dimensional matrices that match the viscoelastic properties of gut mucus, we test how altering the physical properties of their microenvironment influences bacterial growth under confinement. We find that low aspect-ratio bacteria form compact, spherical colonies under confinement while high aspect-ratio bacteria push their progenies further outwards to create elongated colonies with a higher surface area, enabling increased access to nutrients. As a result, the population level growth of high aspect-ratio bacteria is more robust to increased physical confinement compared to that of low aspect-ratio bacteria. Thus, our results capture experimental evidence showing that physical constraints can play a selective role in bacterial growth based on cell shape.