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Background  Sika deer ( Cervus nippon ) have different dietary preferences to other ruminants and are tolerant to tannin-rich plants. Because the rumen bacteria in domestic Sika deer have not been comprehensively studied, it is important to investigate its rumen bacterial population in order to understand its gut health and to improve the productivity of domestic Sika deer.    Results  The rumen bacterial diversity in domestic Sika deer ( Cervus nippon ) fed oak leaves- (OL group) and corn stalks-based diets (CS group) were elucidated using 16S rRNA gene libraries and denaturing gradient gel electrophoresis (DGGE). Overall, 239 sequences were examined from the two groups, 139 clones from the OL group were assigned to 57 operational taxonomic units (OTUs) and 100 sequences from the CS group were divided into 50 OTUs.  Prevotella -like sequences belonging to the phylum Bacteroidetes were the dominant bacteria in both groups (97.2% OL and 77% CS), and sequences related to  Prevotella brevis  were present in both groups. However,  Prevotella shahii -like,  Prevotella veroralis -like,  Prevotella albensis -like, and  Prevotella salivae -like sequences were abundant in the OL group compared to those in the CS group, while  Succinivibrio dextrinosolvens -like and  Prevotella ruminicola -like sequences were prevalent in the CS group. PCR-DGGE showed that bacterial communities clustered with respect to diets and the genus  Prevotella  was the dominant bacteria in the rumen of domestic Sika deer. However, the distribution of genus  Prevotella  from two groups was apparent. In addition, other fibrolytic bacteria, such as  Clostridium populeti  and  Eubacterium cellulosolvens  were found in the rumen of domestic Sika deer.    Conclusions  The rumen of domestic Sika deer harbored unique bacteria which may represent novel species. The bacterial composition appeared to be affected by diet, and sequences related to  Prevotella  spp. may represent new species that may be related to the degradation of fiber biomass or tannins. Moreover, the mechanism and biological functions of  Prevotella  spp. in the rumen ecosystem, and synergistic interactions with other microorganisms should be noticed.

Molecular diversity of rumen bacterial communities from tannin-rich and fiber-rich forage fed domestic Sika deer (Cervus nippon) in China