Although Japanese empire depended heavily on the implementation of new relations with bacteria and other microbes based on the new sciences of microbiology and bacteriology, attention is scarcely paid to the bacteria, which are assumed (falsely) to remain inert or passive, part of an unchanging nature. The exclusive focus on human agency tends to restrict environmental inquiry in advance. There are sources for thinking otherwise. On the one hand, Imanishi Kinji’s efforts to think the art and culture and history of non-human organisms provides a conceptual framework. On the other hand, military scientists provide a record of complex negotiations between humans and non-humans to meet the demands of empire. These records show how microbiology, as practiced, created connections between clinical sciences and environmental sciences. Drawing on such sources, I propose to show how attention to bacteria in the context of Japanese empire may help us to understand contemporary forms of ‘bad environmentalism’ and slow violence in the context of climate change, where microbial life forms have unfortunately received less attention than they merit, given how central they are to larger life systems.