  Culturing cells confined in microscale geometries has been reported in many
studies this last decade, in particular following the development of
microfluidic-based applications and lab-on-a-chip devices. Such studies usually
examine growth of Escherichia coli. In this article, we show that E. coli may
be a poor model and that spatial confinement can severely prevent the growth of
many micro-organisms. By studying different bacteria and confinement
geometries, we determine that the growth inhibition observed for some bacteria
results from fast dioxygen depletion, inherent to spatial confinement, and not
to any depletion of nutriments. This article unravels the physical origin of
confinement problems in cell culture, highlighting the importance of oxygen
depletion, and paves the way for the effective culture of bacteria in confined
geometries by demonstrating enhanced cell growth in confined geometries in the
proximity of air bubbles.
