Not all microbes are pathogenic; in fact, pathogens make up a minority of microorganisms. Many simply coexist in the world with us, sometimes in a beneficial symbiosis. We’ve even utilized various species of microbes for thousands of years to make food and drinks, long before we realized such tiny creatures existed. In fact, if it wasn’t for microbes you wouldn’t be able to enjoy alcohol, coffee, or chocolate beverages. As these are diet staples for most of us (especially my fellow college students), here is an appreciation post for just a few of the drinks that require microbes for their creation.
Alcohol in General
Alcohol is a product of fermentation, a process of metabolic energy creation whose finer details I will spare you. It is a method by which many microbes gain the energy they need to function as living organisms without access to oxygen. Microbes take in an organic compound from the environment (most commonly sugars) and convert it to carbon dioxide and a fermentation product (such as ethanol). This process releases a smidgen of energy that the microbe snatches up to use for various cellular functions. Fermentation doesn’t yield very much energy, so the microbes have to undergo a ton of fermentation to get the energy they need. This means they produce an impressive amount of end products (pretty good for us when we’re using them to make alcohol!). Species of yeast are the most common microbes used to satisfy our alcoholic indulgences, although many beverages require a cocktail of bacteria and yeasts to create unique flavors and textures .
Champagne & Sparkling Wine
Champagne and sparkling wines have higher carbonation than still wines, traditionally as a result of a special method of fermentation and microbial growth. Méthode champenoise is the proper term for this process in champagne (wine-making is one of those fields where every aspect of the art has an exotic, unpronounceable name), during which a finished still wine is added to a bottle along with a liqueur de triage. This triage is a mixture of sugar and yeast, providing the perfect environment for further microbial fermentation: the yeast uses the sugar to produce more alcohol along with carbon dioxide for extra carbonation .
Once the triage has been added to the bottle of wine, it undergoes “riddling,” where the bottle is either placed in an A-frame neck down and rotated each day by hand, or placed in an automatic rotating machine for the lazy and/or mass production. Riddling takes 4-5 weeks, during which bottles occasionally explode from the buildup of pressure (this is why wines require cork seals, which can relieve some pressure). During these 4-5 weeks, many of the yeast cells burst and release their cellular innards into the wine. This provides a unique enriching of flavor (Mm, microbe guts), which many wine connoisseurs will claim is distinct from sparkling wines that are carbonated by mechanical infusion of carbon dioxide. Finally, at the end of the riddling process the living yeast cells are clumped at the neck of the bottle and each is dipped into 0°F brine to freeze the yeast for easy removal .
If you’re a wine connoisseur, you might recognize this special brand of wine that has been made in Portugal since the twelfth century. For those of us who are wine-ignoramuses (like me), it is a semi-sparkling wine with a low alcohol content (7% to be exact) that comes as a red, rosé, or white. The semi-sparkling texture is once again the work of microbes, although this time of the bacterial variety. In Vinho Verde, bacteria undergo malolactic acid fermentation: instead of using sugar, they use malic acid, which is a component of grapes. During this process, malic acid is converted to acetic acid and carbon dioxide. The term ‘malolactic acid fermentation’ is misleading as this is not traditional fermentation (which switches electrons around in an oxidation/reduction reaction), but rather it simply cuts the malic acid molecule to create the products. This lowers wine acidity, carbonates the wine, and enhances the flavor with tasty bacteria .
Malolactic fermentation is actually very common in wines, though it was poorly understood until the 1960’s. It was actually quite the source of embarrassment as it tended to occur outside of the control and understanding of the winery owners. Since the 1960’s, the bacterial species responsible have been identified and found to vary between wineries, resulting in unique wines due to the bacteria colonizing the fermentation or holding tanks. It promptly became a goal for wine makers to start malolactic fermentations with specific species of bacteria, and now many use bacteria alongside yeast .
If you ever win a lottery, you might want to try a bottle of this famous wine. It sells for over $150 a bottle, and comes highly praised by Emperor Napolean III and Thomas Jefferson; the author of our constitution ordered 250 bottles for himself and only one for George Washington. This wine actually requires the contribution of a fungus, Botrytis cinerea. Not only is it a fungus, but it’s a potentially lethal pathogen. Luckily it only infects plants, smothering them with an appetizing gray-colored mold. The fungus causes the plants to ooze nutrients, encouraging the growth of other fungi and insects. Grapes can catch this infection toward the end of growing season, coming down with ‘bunch rot’ which, bizarrely, someone decided looked like the perfect contribution to wine.
Surprisingly, they weren’t wrong. The fungus has gained the name ‘noble rot’ for its role in making this exquisitely flavored wine (though I do not, of course, speak from firsthand experience). When grapes become infected, the fungus consumes their water and malic acid content. This concentrates the grape juices, reduces the acidity, and makes the berries sweeter. The fungus also contributes to the wine’s golden hue and subtle flavor (Mm, fungi) as well as produces glycerin, which thickens the wine slightly and gives it a heavier body .
Sake, a Japanese rice wine, also requires the use of a fungus. Unlike the previous wine, sake’s fungal contributor is used to ferment the grains. Aspergillus oryzae, or Koji mold, is a filamentous fungus used to ferment soybeans for soy sauce as well as rice, grains, and potatoes to make alcohol, vinegar, and bean curd. The fungus was domesticated over 2000 years ago, contributing heavily to the Asian diet ever since .
During the brewing of sake, rice undergoes multiple parallel fermentation, which is an obtuse way to say multiple microbial fermentation processes are used. After the grains have their exterior proteins and oils removed, they are washed, steeped, and then steamed. A. oryzae is then added to the steamed rice for 5-7 days. It grows on and inside of rice, secreting enzymes that produce a unique fragrance and flavor, as well as converting the starch into fermentable sugar. Yeast is then added to the moldy mixture to ferment for another week. This is then turned into a ‘mash’ which ferments for another few weeks before the resulting alcohol is filtered and bottled [4,7]. Sounds really appetizing, doesn’t it?
Cocoa & Coffee
To branch away from alcohol, microbes are also vital for the classic hot cocoa (actually, chocolate in any form) as well as coffee. Both use microbes somewhat similarly, but chocolate has higher microbe flavor contribution so I will focus on the creation of that decadent masterpiece.
The vast majority of cocoa is farmed in developing countries (70% from Africa!) where the production practices are very rustic, with the source of the microbes being the hands of workers, knives used to cut cocoa pods open, and the baskets they’re stored in. Cocoa pods are picked, and the pulp and beans placed in bins where the microbes flourish and work their fermenting magic. For seven days a plethora of organisms work to convert the bitter tasting beans into the chocolate flavor we love. Scientists have identified most of the vital species. Yeast degrades the pulp, producing aromatic compounds contributing to the flavor and providing molecules for bacteria to utilize. Lactic-acid bacteria start to proliferate as the yeast cells die, lowering the pH of the cocoa by producing lactic acid, acetic acid, ethanol, and mannitol. Acetic-acid bacteria then use ethanol and acetic acid to produce carbon dioxide and water in a reaction that acts as the primary foundation of the chocolate flavor. Aerobic spore-forming bacteria of the Bacillus genus also alter acidity and produce products influencing the flavor [1,6].
In summary, yeast starts off the chemical reactions needed for the flavor of chocolate. Bacteria then produce various acids that help kill the cocoa beans and shape the flavor, aroma, and coloring of the cocoa. The climate and when the beans are picked also influence the flavor, which is finalized during the drying and roasting process following fermentation.
Kombucha is an interesting drink (and when I say ‘interesting,’ I’m being delicate. Pictures of it tend to make people run screaming in the opposite direction). It is a fermented sugar tea, which utilizes a unique assortment of bacteria and yeast to form what has been misleadingly called a tea fungus. It came into existence in China in 220 BCE, an instant hit that won it the title Divine Tea. Several hundred years later in 414 CE, a man called Doctor Kombu brought it to Japan from Korea in an attempt to cure the Emperor of digestive troubles. The name apparently stuck, although I’m not sure if the Emperor appreciated the gift. It morphed into ‘Tea Kvass’ when it made its way through Russia, and was introduced to Europe in the 1900’s, ending the blissful ignorance of the western world . Apparently it tastes like sparkling apple cider. Go try it and let me know.
Black tea and white sugar are most commonly used to create Kombucha. The tea is brewed and sugar is added. Once the sugar tea has cooled down, it is placed in a jar and acidified by the addition of vinegar or previously brewed Kombucha. Then, the tea fungus (which is not a fungus!) is laid on top and the jar is covered with a cloth. This ferments for 1-8 weeks before the tea fungus with its new growth is removed and the tea filtered for consumption. If you do not have a tea fungus on hand, a culture of bacteria and yeast is added which will start the growth of your own tea fungus [2,5].
The tea fungus actually consists of several yeast species along with acetic acid bacteria species, and no fungi whatsoever (it is frequently called a mushroom, which it is decidedly not). The yeast and bacteria grow in a web of cellulose produced by the bacteria Acetobacter xylinum, giving it the fungi-like appearance. The microbes undergo fermentation in the tea, releasing enzymes that shift the flavor to a fruity, lightly sour tea that becomes more vinegar-like the longer it ferments [2,5].
Perhaps one of the persuasive forces that lure people into drinking this tea is the widespread rumor of its health benefits: it provides resistance against cancer, prevents cardiovascular diseases, aids digestion, stimulates the immune system, and reduces inflammation. Scientists have failed to find any proof of these benefits. Generally there are no adverse effects to drinking this concoction; a few people end up with upset stomachs, some have allergic reactions, and occasionally a case report of a toxic reaction crops up. Researchers are hesitant to rule out possible benefits, however; very little research has actually been conducted on Kombucha, and many other healthy foods (yogurt, wine, cheese) contain live bacteria. As such, the general consensus seems to be lukewarm, with one paper simply providing the mild cautionary advice: drink plenty of water along with it (to help facilitate the elimination of toxins) [2,5].
 Ardhana, MM, & Fleet, GH. (2003). The microbial ecology of cocoa bean fermentations in Indonesia. International journal of food microbiology, 86(1-2), 87-99.
 Food Research and Development Center. “Tea, Kombucha, and health: a review.” Food Research International. 1999. 33(2000):409-421.
 Ingraham, John L. March of the Microbes: Sighting the Unseen. Cambridge, MA: Belknap of Harvard UP, 2010. Print.
 Machida, M. et al. “Genomics of Aspergillus oryzae: learning from the history of Koji mold and exploration of its future.” DNA Research. 2008. 15:173-183.
 Mayse, P. et al. “The yeast spectrum of the ‘tea fungus Kombucha.’” Mycoses. 1995. 38:289-295.
 Schwan, RF, & Wheals, AE. (2004). The microbiology of cocoa fermentation and its role in chocolate quality. Critical reviews in food science & nutrition, 44(4), 205-21.
 Uno, T. et al. “Ferulic Acid Production in the Brewing of Rice Wine (Sake).” J Inst Brew. 2009. 115(2):116–121