Nine male beagle dogs, housed in either a conventional or locked environment for 2.5 years, were killed, and the bacterial flora present in various regions of each gastrointestinal tract was assessed by culture techniques, light microscopy, and scanning electron microscopy. All dogs possessed a complex microflora in their colons; in almost every dog anaerobes predominated. The highest number of bacteria cultured was 10(10)/g (dry weight) of tissue and contents; highest counts obtained with a Petroff-Hauser counting chamber were 10(10)/ml (wet weight). Although there was a consistency in the detectable genera, there were also noticeable differences in the flora of dogs housed under different environmental conditions. These differences included qualitative and quantitative changes in the flora as well as alterations in the distribution and localization of microorganisms along the gastrointestinal tract and in the crypts of Lieberkuhn. No bacterial layers were detected on the surfaces of stomach or proximal bowel in any of the dogs. Dogs housed in a conventional, open, environment had bacteria that occurred in layers on their ceca and colons and in their crypts of Lieberkuhn; however, dogs housed under "locked" environmental conditions did not possess them or had them less frequently. Dogs removed from the locked environment and kept (30 days) in conventional housing conditions were the only ones with detectable segmented filamentous microbes in their ilea. This study shows that the microbial flora does not simplify when dogs are housed in a locked environment. Indeed, it may increase in complexity and cause alterations in the bacterial flora that is associated closely with gastrointestinal epithelial cells and crypts of Lieberkuhn.