An interactive research device comprised of an orally ingested capsule with pockets rendering the capsule capable of sampling intestinal tracts (gut) substances and microbes before, during and after delivery of system perturbation substances and methods of use and associate system are described. Sensors are provided to simultaneously measure, monitor, record, and transmit data in real time obtained from within the exact vicinity of substance deployment and location of microbial assisted digestive processes. In vivo collected samples are also collected and preserved for in vitro analysis. Digestive processes and dysfunctions involving proteins that result in “gluten sensitivities” and dozens of gut-based diseases that develop in stages, and have been mysteries for over 2,000 years, can be analyzed. The capabilities were developed to permit research within the heretofore inaccessible and important regions of the small intestine where villi functions are compromised, and in the upper colon. Special focus includes determining roles microbes and their byproduct substances in cascade play in autoimmune system responses and diseases.
