The microbial flora of the nose, throat, and feces of male beagle dogs housed in a "locked environment" (i.e. confined to germfree-style isolators and supplied with sterile food, air, and water) or an open environment were assessed between 26 and 30 months into the study. Forty-five genera and 170 different species or types of microorganisms were cultured from the nose, throat, and feces of the beagles. Clostridia, eubacteria, corynebacteria, bacteroides, lactobacilli, and anaerobic, gram-positive cocci accounted for most of the microbial diversity in the flora. Some of the facultative anaerobes, especially streptococci and lactobacilli (in feces), occurred in numbers that were comparable to the most numerous anaerobic species. Confinement to the locked environment resulted in an increased diversity of microorganisms in the flora, but the total microbial counts did not increase to any great extent. Even with the increased diversity of bacteria in the flora of confined dogs, some bacteria seemed to favor certain areas of the gastrointestinal tract over others. The increased diversity of bacteria observed in these confined dogs may pose some infectious disease problems for other mammals (including humans) that may be confined to a locked, ultra-clean environment for a prolonged period of time.