Motility turns sour: glucose fermentation by dense suspensions of Escherichia coli results in metabolic shutdown and prevents swimming

We study the motility of dense suspensions of Escherichia coli supplied with abundant sugar in anaerobic conditions. We find that the bacteria become non-motile unexpectedly quickly, and that this motility decay is jointly associated with the secretion of organic acids and the acidification of the medium. At the same time, the intracellular pH of the bacteria decreases and they stop metabolising the available sugar. Through experiments and numerical simulations, we show that these physiological changes are quantitatively driven by the progressive accumulation of protonated organic acids in the medium, which are uncharged and can cross the cytoplasmic membrane of the bacteria. Those findings are relevant to bacterial physiology in environments that contain high concentrations of bacteria, such as the human gut.