Daki warm treatment (daki-ire) is performed during the process of seed mash preparation in the brewing of Japanese sake in order to promote the saccharification of rice by koji enzyme and to enhance the growth of Saccharomyces cerevisiae. Although it is important to control the growth of lactic acid bacteria in the preparation of kimoto-style seed mash (traditional sake-brewing method), it has not been known whether the transient increase in the temperature and/or appropriate temperature zone produced by daki-ire influences the growth of bacteria. A temperature increase generally helps bacterial growth, but we have found no published investigation of the influence of temperature changes in daki-ire on bacterial growth during the kimoto-style seed mash preparation process. In this first comprehensive evaluation of the effects of the temperature change by daki-ire on bacterial communities, we investigated the bacterial community in three batches that were brewed by the same brewery using identical ingredients. The results demonstrated that the bacterial community or its transition during lactic acid fermentation was diverse despite the use of the same brewing conditions. We observed that (i) some lactic acid bacteria were carried over to the subsequent batches, and (ii) the increase in the initial amount of lactic acid bacteria plays an important role in the formation of the bacterial community. Our analysis of the bacterial growth activity before and after daki-ire indicated that the transient increase in temperature and/or local appropriate temperature by daki-ire, in and of itself, has relatively little direct impact on bacterial growth.