The present disclosure relates to methods of collecting and testing bacteria containing samples from within the gastrointestinal (GI) tract of a subject. The methods may include disposing an ingestible device in the GI tract, collecting a bacteria-containing sample from the GI tract, selectively lysing eukaryotic cells in the sample by combining the sample with a dried reagent, exposing bacteria in the sample to resazurin in the ingestible device to produce resorufin, emitting light from the ingestible device, the emitted light being filtered through an optical filter to control for scatter so that the light interacts with the resorufin to produce fluorescence, and measuring a total fluorescence from the resorufin; or a rate of change of fluorescence from the resorufin as a function of time within the GI tract of the subject; and correlating the measured parameter to a number of viable bacterial cells in the sample.