Despite considerable attention, the mechanisms by which the microbiota affect brain function and host behaviour via the gut-brain axis remain undefined. Identifying microbe-specific pathways that influence neuronal function and bi-directional communication between the gut microbiota and the host central nervous system is challenging due to the extreme microbial diversity in the gut of conventionally-reared mice. Herein, we describe the use of the altered Schaedler flora (ASF) mouse model as an alternative to conventionally-reared and germ-free animals. Colonized with only 8 bacterial species, use of ASF mice greatly simplifies the examination of microbiota-host interactions. We assessed the extent to which behaviour differed between mice with a limited consortium of bacteria compared with a complex, conventional microbiota. The elevated plus maze and open-field assays were utilized to assess murine behaviour. Histological analysis of ileum and colon was performed to evaluate intestinal morphology, and 16 s rRNA gene taxonomic profiling was performed to determine host-stress induced changes in fecal microbial communities. Behavioural and serum corticosterone differences were observed between ASF and conventionally-reared mice, while no differences were found between the intestinal morphology of these two groups. The stress of the behavioural tests induced significant changes in the ASF fecal microbial community but not in that of the conventionally-reared mice. In contrast to the conventionally-reared mice, the results indicated that the ASF mice displayed a marked anxiogenic-like behaviour. These data indicate that ASF mice represent a unique model to elucidate mechanisms governing microbiota-gut-brain communication affecting behaviour.