Microorganisms can be considered a bio-colloid. That is, they have a characteristic outer surface that carries, or can carry, a charge. Precisely, differences in the surface can be exploited for separation by capillary electrophoresis (CE). In fact, methods based on CE seem to be very promising because they should produce rapid and high-efficiency separations. Although CE can be used to separate microbial (i.e., bacteria, virus, fungi, and whole cells) and subcellular particles (i.e., mitochondria and nuclei), this chapter is focused mainly on the determination of bacteria and virus for their interest. At difference to the separation off molecules, microorganisms are characterized as living. This makes their analysis more difficult because several aspects such as possible lysis, aggregation, evolution, growing etc. must be taken into count.
