Human microbiota associated rats are frequently used as a model to study host microbe interactions. This study investigated the long-term stability of the bacterial community in such rats. Following the association of two strains of germ-free rats (12 male animals each) with fecal bacteria from a human donor the development of the microbiota was monitored for 12 months by PCR-denaturing gradient gel electrophoresis. During this time the Dice similarity coefficient (Cs) for the fecal microbial community of the rats associated with a human microbiota in comparison to the donor sample ranged between 73% +/- 8 and 74% +/- 3 for the Wistar and the Fischer 344 rats, respectively. After 12 months the similarity coefficients were 78% +/- 9 and 76% +/- 7, respectively, while the similarity coefficients for rat sample replicates ranged from 77% +/- 7 to 88% +/- 5; the similarity coefficient of the donor sample replicates was 78% +/- 9. DNA sequences of bands observed in the different denaturing gradient gel electrophoresis profiles exhibited the highest degree of identity to uncultured bacteria previously found in samples of human, mouse or pig intestinal origin. The results of this study suggest that the dominant human fecal microbiota can be maintained in the human microbiota associated rat model for at least one year.