An ingestible capsule device collects fluid aspirates from locations within the body, locations such as the small intestine, and retains the fluid aspirates free from contamination as the capsule device is expelled from the body. The device allows for microbial and metabolomics analysis for a variety of gastrointestinal, allergic, endocrinologic, and oncologic diseases. In some examples, the capsule device is a multi-stroke device that includes a capsule shell and two reservoirs located within the shell. Check valves work in conjunction with a vacuum pressure pumping mechanism to control fluid movement from one reservoir to another, where one of the reservoirs may be expandable and permeable to some fluids. In other examples, the capsule device employs a peristaltic pump fluid control with the capsule device, and a single semi-permeable bladder stores collected fluid aspirate.
