Little is known about the role of the gastrointestinal microbiota in susceptibility to infection with enteric pathogens and response to live oral vaccines. This study examined the effect of immunization with an oral live-attenuated Shigella dysenteriae 1 vaccine and challenge with wild-type S. dysenteriae 1 on the gastrointestinal microbiota of cynomolgus macaques using 16S rRNA analysis. Multi-dimensional cluster analysis identified distinct bacterial community types within healthy macaques. The microbiota found in association with Mauritian macaques is distinct from and characterized by significantly higher diversity than the microbiota found in macaques from other geographic origins. Mauritian macaques also contain genetically distinct microsatellites in loci spanning the major histocompatibility complex (MHC) region, providing a possible link between the MHC repertoire and the intestinal microbiota. The intestinal microbiota in distinct macaque populations responds differently to immunization and subsequent challenge with wild-type Shigella, and is altered in fecal samples collected post-immunization and post-challenge in macaques from Indonesia, Indochina and the Philippines, but not from Mauritius. Specifically, Shigella exposure results in the appearance of a community type that is dominated by Enterococcus, a genus typically present at low abundance. While both Mauritian and non-Mauritian macaques exhibit anti-Shigella antibody responses upon immunization and challenge, clinical symptoms of shigellosis post-challenge are only observed in non-Mauritian macaques. These studies highlight the importance of further investigation into the possible protective role of the microbiota against enteric pathogens and the importance of host genetic backgrounds in conducting vaccine studies.