A system and methods of characterizing a population of a virus, bacteriophage, or other microbes in a microbiome that includes the steps of separating a sample of microbiota into more than one fraction by continuous capillary zone electrophoresis based on the physiochemical properties of the microbes in the microbiota using a constant voltage applied to the sample during the continuous zone electrophoresis. At least one separated fraction includes an intact virus, bacteriophage, or other microbe that may be visualized and/or directly sequenced to characterize the population of the virus, bacteriophage, or other microbe in the microbiome.