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To understand the essential feature of gut microbiome and better preserve Père David’s deer, stool samples from captive and wild deer were used to identify healthy core microbiome in the gut of this species and investigate how dietary factor influence the gut microbiome. 16S rRNA high-throughput sequencing and comparative analysis were adopted in the present study. The results showed that the core gut microbiome in healthy deer was consisted of the Firmicutes and Bacteroidetes. The core microbiome was stable that might not change drastically with dietary factor. The difference in diet between captive and wild deer might influence on the success of reintroduction into the wild, but the influence might be very little. These results could be informative for future applications of population management in Père David’s deer conservation.<b> </b>