Abstract: A process for isolating microorganisms from samples, particularly Shigella spp. from food samples, and a system, apparatus and composition therefor are provided. Magnetic particles are used to capture microorganisms and a system having separate magnetically-based apparatuses for collecting, concentrating and retrieving is used to isolate the magnetic particles having bound microorganisms. The apparatus for concentrating magnetic particles utilizes a small magnet assisted by vibration to concentrate collected particles at a localized region on the bottom of a container. The process, system and apparatus of the present invention are simple and inexpensive providing improved magnetic particle recovery adaptable to large scales.