Digital Cell Division Counting Reveals Microbiotal Dynamics in the Mammalian Gut

The gut microbiota is a vibrant ecosystem of critical importance to animal health. To study microbiotal dynamics, we engineered bacteria that count cell divisions using genetically encoded, digitally segregating fluorescent particles. We tested our system by counting for up to 14 generations in continuous culture across an order of magnitude in growth rate. We then engineered E. coli from the mouse gut, introduced them into mice, and determined that cells double every 3 hours during the first 12 hours of passage through the animal. Taken together, we have generated the first living digital counter that can function in animals and thus can be used to further study the physiology of microbes in diverse environments.