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Background Intestinal bacteria of mammal can be influenced by many factors, environmental bacteria is an important factor. However, there are few studies on the interactions between environmental bacteria and intestinal bacteria in wild mammals. To explore the associations between the intestinal bacteriome and the related environmental bacteriome, the intestinal bacterial communities of  Eospalax cansus  at three different sites and the bacterial communities of the surrounding soil (outside and inside the cave) at each site were investigated by 16S rRNA sequencing. Results The composition and structure between zokor intestinal bacteria and related soil bacteria were distinct, and the soil of zokor habitat harbored significantly higher diversity than that of zokor intestinal bacteria. We have found that host factors may be more important than environmental factors in shaping intestinal bacteriome. In addition, it was found that the relative abundances of shared OTUs between zokors and related soil were significantly negatively related. These shared OTUs were present in the soil at relatively low abundance. However, these shared OTUs between zokors and soil were affiliated with diverse bacterial taxa, and they were related to the degradation of complex carbohydrates. Conclusions These results suggested that the zokor gut may mainly select for low-abundance but diverse soil bacteria, which may be a host- specific choice for zokor to meet the needs of its phytophagous dietary.

The associations between intestinal bacteria of Eospalax cansus and soil bacteria of its habitat