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Today the research of microorganisms crosses boundaries between scientific fields and has infinite potential. One of the aims of our research is to predict and control bacterial activity by integrating theoretical and experimental approaches. The bacterial activity lies in a wide range of not only research fields but also spatio-temporal scales. The complex interactions beyond the hierarchies make it difficult to understand, predict, and control phenomena concerning bacteria, so that many issues still remain unsolved. We then perform multidisciplinary research consisting of a series of experiments, modeling, simulations, and theoretical analyses from trans-hierarchical viewpoints based on mathematical sciences, theoretical biophysics, genetic engineering, and so on. We investigate bacterial responses to environmental conditions in detail and analyze their interactions in order to clarify their role in macroscopic ecological systems. Moreover we try to reveal the governing mechanisms of the complex world of microorganisms with the aim of opening up new interdisciplinary applied microbiology that utilizes the sophisticated microbial systems. 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