The role of gut microbiome in the host health is a growing interest and they play various roles for the maintenance of homeostasis. It has been shown that the composition of the microbiome is associated with many factors such as age, race, gender, geographical distribution, and genetic features. Yet, the gut microbiome-host interaction fully remains unknown. Compared to the human, there were limited studies were carried out on the gut microbiome studies on the companion animals. In this study, we analyzed canine gut microbiome with National Center for Biotechnology Information (NCBI) with SRA database. From the SRA database, total 982 SRA data with 1.22 TB from 8 countries were included. According to distance-based redundancy analysis (dbRDA), the Peptoclostridium and Fusobacterium were mostly correlated with disease of Epileptic and Giardia intestinalis, respectively. From the network analysis with spearman rank-based correlation coefficient (ρ), we identified interactions within genera lists as candidate biomarkers. The results showed that the composition of the canine gut microbiome differed with disease specific microbes, suggesting that these species lists are considered as biomarker candidate for epileptic and giardia intestinalis.