Droplet-based microfluidics utilizes micron-sized droplets surrounded by inert oil to create an isolated Micro-BioReactor (MBR). Compared to traditional microwell plates droplet-based microfluidics offers several advantages including more efficient mixing, lack of air-liquid interfaces, and the prevention of evaporation all of which can affect the growth of microbes. In microbial ecology MBRs have largely been used for single-cell genomics leaving the investigation of microbial communities largely unexplored. Bacteriophages (phage) are abundant and dynamic members of all microbial communities. As obligate intracellular parasites phage must create infectious virus particles within a hostile environment leading to the canonical virus-host “arms race”. This antagonistic coevolution between virus and host accelerates molecular evolution and drives innovation. Here we use a novel droplet-based millifludic device to investigate how phage drive the evolution of microbial communities. The Millidrop AnalyzerTM generates a 1,000 droplet train encased in plastic tubing using a 96-well plate template (Millidrop Company). Each droplet is surrounded by inert HFE-oil and separated from neighboring droplets through air plugs. The droplet train is kept in constant motion using air pressure that pushes the train back and forth between two coils. A fluorescent detector located between the coils measures up to three customizable fluorophores of each droplet every 30 minutes. Following incubation droplets of interest can be either isolated for further analysis, or diluted to generate a new droplet train thus creating a continuous “evolution machine”.