An orally ingestible capsule device with monitoring and control instruments is provided for practicing physicians to use in patient examining rooms. The Capsule is part of an in vivo gastrointestinal tract (GI Tract or Gut) healthcare system with capabilities of delivering medications to any point in the gut, administering them at any time, or autonomously based upon onboard measurements, and simultaneously measuring results, along with extra body function measurements. It is capable of delivering gut medications or autoimmune perturbation substances and simultaneously measure responses and sample gut substances/microbes at application points. Objectives, as part of patient diagnosis, include determining microbe roles in the patient's digestion process, along with toxic substances in contributing to illnesses or diseases, such as gluten sensitivities. Capsule embodiments include a belt with pockets for substance delivery or sampling, lab-on-a-chip devices, chip-based logic, sensor/transducer, control circuits, nanotech devices and data reduction and storage, for efficient, cost-effective diagnostics and treatment in minimal time.