Now this is a nice proposition, because Japanese food culture is after all a culture of micro organisms: take koji, a mold called officially Aspergillus Oryzae. This is used in the manufacture of sake, soy sauce, miso and mirin and Japanese cuisine has been rightly called a "Koji Cuisine."
The protagonist of the story, Sawaki Tadayasu, is the son of a tane-koji-ya, a producer of such koji spores. [Note: in the Wikipedia, this is mistakenly translated as "yeast starters" which is something quite different!] Since his youth, he can see koji and other micro-organisms much larger than they appear under a microscope and even communicate with them, a weird faculty...
Sawaki has become freshman at an agricultural university in Tokyo. He attends the opening ceremony together with his childhood friend and fellow-freshman Yuki Kei, whose parents run a sake brewery (making them customers for koji spores of Sawaki's parents).
They become students of Itsuki Keizo, an aged professor with a mania for fermented foods who is an acquaintance of Sawaki's family and already knows about his amazing ability. At their first meeting, he shocks both freshmen by setting his teeth in Kiviak, a weird dish from Greenland made from the raw flesh of an auk which has been buried under a stone inside a sealskin (!) until reaching an advanced stage of decomposition. (Yuk!) Talking about fermented foods...
The most impressive member of the study group of the professor is postgraduate student Hasegawa Haruka, a young women who for personal reasons always wears sexy bondage-style clothing under her lab coat. She is rather violent and likes to swing her little whip around. In the beginning, she has some difficulty believing Sawaki's microbe-spotting faculties are real.
Other characters include Oikawa Hazuki, a woman with an obsession against bacteria (she always carries a spray) and two fellow students Misato and Kawahama, who try to make easy money out of Sawaki's abilities.
But the real protagonists are of course the micro-organisms, who appear with faces and in animated form. The most important is the above-mentioned Aspergillus Oryzea or koji mold; others are Baccillus Natto used to make the fermented beans so popular among foreigners, Lactobacillus Bulgaricus used to make yoghurt, Trichophyton Rubrum which causes Miss Hasegawa to suffer athlete's foot, the common green mold Penicillium Chrysogenum and the bad boy of the story, Lactobacillus Fructivorans or Hiochi-kin which causes sake to go bad.
The manga has been running in Kodansha's Evening magazine since August 2004. In 2007, eleven installments of an anime television series were aired by Fuji TV. I have enjoyed it very much, as well as the anime version (based closely on the manga) - it is a great lesson about all the micro-organisms that surround us daily here in Japan!
The Japanese Wikipedia has a very detailed article. See also the English Wikipedia.