Abstract: Methods and apparatus for improved microbial sampling of foods and sample treatment are provided herein. Such methods may include sampling production lots of produce or other food items such as meat using an aggregating sampler to create one or more samples. Methods and devices that improve concentration of the fluid sample obtained from the aggregate sample include filtering of fluid sample through a filter and/or filter aid materials and lysing target material trapped within the filter and/or filter aid materials to release molecules from targeted microorganisms, which are recovered in a concentrated fluid sample for testing. Sample treatment systems and methods can be automated with various buffer reservoirs and removable cartridges that facilitate controlled flow of fluid sample therethrough to produce a purified, concentrated fluid sample, typically within two hours or less. Such systems can further be configured with removable cartridges and use with sample filter cups and collection cups.