Moyashimon: Tales of Agriculture (2007) IMDb
A freshman at an agricultural university unintentionally reveals his ability to see microbes with the naked eye, and communicate with them. They don’t appear to him they way they do under a microscope, but rather as talking, slightly anthropomorphic little critters. His family has been running a yeast shop since the Muromachi period (~1336 to 1573), and his confrontation with modern science is pretty colourful.
College comedy. Ideologically interesting, with several speeches on the role of agriculture and the foregrounding of microbial life as a substance of musubi, akin to old Shintō ideas.