Acetate inhibits bacterial growth by shrinking the metabolite pool size

Acetate, propionate, and butyrate are short-chain fatty acids (SCFA) that accumulate to high concentrations in the mammalian gut and other environments dominated by fermentation. These SCFAs acidify the growth environment and inhibit the growth of many different types of bacteria. However, despite the ubiquity of this problem, bacterial strategy resisting SCFA stress is unclear. Here we present a quantitative physiological study of E. coli under acetate stress, complemented by proteomic and metabolomic analysis. The results reveal growth inhibition arises from two orthogonal factors: reduced internal pH and massive accumulation of acetate in the cytoplasm. The acetate accumulation in particular reduces growth by acting as a “useless metabolite” which excludes other metabolites. Further, we establish that cells balance the problem presented by these two stresses by optimizing their internal pH to minimize acetate accumulation. As adaptation to both factors requires changes to protein properties at the genome scale, gut microbes are forced to choose between growing fast at neutral pH or tolerating SCFAs at low pH, phenotypes evolved by the two major phyla Bacteroidetes and Firmicutes, respectively, in the gut.