When we tell people we’re microbiologists, they typically ask two questions: 1. “What disease do you study?” and 2. “Have you found a cure?”
These days, our studies at the Harvard FAS Center for Systems Biology are focused on cheese. And no, we haven’t found a cure for it yet.
We’re in the business of finding out why cheese tastes like it does—and of finding out what’s happening, on a microbiological level, when milk turns into the wonder that is cheese. Most folks have a negative perception of microbes, and we want to demonstrate the many positive aspects of bacteria and fungi. People around the world have long harnessed the powers of tiny organisms to break down food in really interesting ways, ways that make said food more delicious and nutritious and prevent it from becoming disgusting and spoiled. Cheese is just one example.
Things like cheese are fermented foods. Fermentation is the product of microbial activity, and it contributes a ton to the flavor, aroma, and texture of the finished product. Other examples of fermented success stories include wine, beer, bread, and kimchi—and, of course, miso.
Making miso is a traditional process, one that’s been practiced for thousands of years. Essentially, you steam rice, inoculate it with fungus, add steamed soybeans, and let the mixture ferment in wooden barrels for a variable period of time. The microbes that are most active and influential in the process are ones that we know quite a bit about.
All miso starts with koji. Koji is rice that has been colonized by a fungus called Aspergillus oryzae. Most of the time, the fungus lives on rice quite politely, but when you cook that rice and leave it sitting at a certain temperature and humidity, the fungus comes to life and does its work. Koji, essentially, is moldy rice, and it makes up a significant percentage of miso.[1. This means that at some point in history, someone saw a lump of fuzzy rotten rice and took a bite. And you know what they found? That it tastes good! It’s incredibly sweet, with an almost jammy kind of flavor.]
Koji provides a great solution to a “problem” with rice. Rice is a great source of starch, but it doesn’t come naturally equipped with the enzymes needed to break down that starch into sugars. Barley presents a similar obstacle, and people have learned to malt it to create the enzymes that break down its starch. That’s what one does for things like baking, brewing, and distilling.
The brilliance of the people who discovered koji is that they found that you can use microbes to do that work for you. (Part of the art of making miso is in selecting what kind of koji you’re going to use to do this; different strains have different properties. Sake producers select particular kojis to alter the flavors of their sakes, and miso producers do the same.) The Aspergillus is like an enzyme factory: it produces so many enzymes that they literally ooze out of the hyphae. (Those are the filaments that cover the fungus.)
One of those enzymes is called amylase. Amylase can break down long chains of starch, chopping them into little pieces that are sweet-tasting. These add sweetness to the finished product, but they’re also helpful for feeding other organisms at different stages in the miso-making process.
The other enzyme that koji produces in large quantities is called a protease. (That name refers to any enzyme that can break down proteins in a certain way.) This isn’t necessarily useful in the first stage, when the rice is being broken down, but it really kicks in and helps produce the flavors in the second stage of miso fermentation, when the soybeans go in.
The soybeans bring some important naturally occurring microbes of their own. One is a yeast called Zygosaccharomyces; the other is a bacterium called Tetragenococcus. These are both salt-tolerant, so they thrive in the salty soybean mixture. Tetragenococcus is a type of lactic-acid bacteria—it’s the “live active cultures” in yogurt and the cloudy stuff in a jar of pickles, and ubiquitous in other fermented foods. Tetragenococcus is a really wonderful bacterium, and it produces a lot of the acids that contribute to the flavor of miso.
Zygosaccharomyces, on the other hand, is not the most glamorous microbe known to man—it produces small colonies, and it’s plain-looking. But it smells sweet like sake. The proteases produced by Zygosaccharomyces, in cooperation with the proteases from the koji, break down the proteins in the soybeans—there’s a ton of protein is soybeans—into peptides and amino acids. This process is what gives miso its robust, almost meaty umami quality. It produces glutamic acid, which yields the flavor of umami, and accounts for the rich and savory aspect of miso.
That’s the basic science of miso-making.