In the second season the story continues exactly where it left off previously. Professor Itsuki's Fermentation Cellar and laboratory is ready for operation and with Sawaki Tadayasu's unique gift to see and communicate with microbes to help, Itsuki's motley group of students begin to process different fermented products like soy sauce and sake.
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(Source: Anime News Network)

Enter Tadayasu, a freshman college student who can see and talk to cute, chibi bacteria and other microscopic organisms. It's not all fun and games like it sounds, though, because it gets him into all sorts of trouble. Join Tadayasu as he enters his first year at the Agriculture University, what crazy events await him?

Tadayasu Sawaki has a gift: he can see all kinds of microbes, from the ones that ferment sake to everyday bathroom mold. Not only that, but they're not scientifically accurate but instead cute chibi creatures. When he enters an agricultural university and a professor finds out about his gift, he begins to meet new people that help him discover more about his abilities and himself.

Music video for ClariS' single "Wake Up." The song was used as the opening theme for Moyashimon Returns.

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