The custom of making homemade miso every year and drinking miso soup every day is thought to be useful for maintaining good health by regulating the disorganized indigenous bacterial ecosystem of modern people. We made our own "homemade miso" and compared the bacterial species contained in miso and commercial miso by genome analysis. We found that lactobacilli, which are mainly contained in commercial miso, were not observed in the homemade miso, and that Staphylococcus aureus, an indigenous skin bacterium, was found in the homemade miso. We plan to increase the number of samples in the future for further verification.