The complex mixture of microbes in the gut (i.e. the gut microbiome) can have a major impact on host health, with effects ranging from altering nutrient absorption and creating chemical signals that modulate host physiology. A prominent example of microbiome-host interaction is chemical microbial modification of the host's bile acid pool. Certain microbes are capable of modulating the hydrophobicity of the bile acid pool through the activity of bile salt hydrolases. Bile salt hydrolases catalyze the hydrolysis of bile salts to free bile acids and amino acids. The result of BSH activity is a net change in the physicochemical properties of the bile acid pool, ultimately making it more hydrophobic, and therefore making fatty gut contents more prone to excretion. Increasing BSH activity is postulated to be an effective strategy for treating obesity and hypercholesterolemia. Currently, the bioassays for characterizing bile salt hydrolase activity are time-consuming or have poor sensitivity. We have invented a continuous fluorescence-based BSH assay that is easy to use and is compatible with gut microbiome samples. The chemistry of our assay is fundamentally different from other BSH assays. Because our assay provides a fluorescent readout in real time it is significantly easier to setup than other BSH assays, and has considerably higher sensitivity that assays that rely on detection of the amine product.