Gallery: These Funky Microbes Make Your Favorite Foods More Delicious
01penicillium-roqueforti
If you ask me, the best things to eat and drink almost always have a little something funky going on. Cucumbers are OK, but pickles are what I reach for when I want to make a kickass sandwich. Cabbage is boring, but kimchi rocks. When it comes to cheeses, a blue always trumps a jack. Edamame? Edama-meh. Give me miso soup and sake. What makes these foods better is the hard work of bacteria and fungi. These bugs transform the sugars and proteins in raw ingredients like fruits and grains into something else entirely, creating new flavors and more complexity. They're the reason an aged cheese tastes more interesting than milk and a well-made craft beer tastes better than a mouthful of barley. They put the umami in miso and make pickles more piquant. Humans have been intentionally inoculating food with microbes for millennia, says food writer [Harold McGee](http://curiouscook.typepad.com/site/about-harold-mcgee.html), whose classic book *On Food and Cooking* is a trove of information on microbe-enhanced cuisine (and everything else you need to know about the science of cooking). It probably started by accident. "My hunch is that foodstuffs would start to go off in various ways and they learned how to manage that and to appreciate some of the sensory changes that took place," McGee said. So what exactly are our invisible friends doing inside our food? Many of the macronutrients in the foods we eat -- the proteins, carbohydrates, and fats -- are too big to trigger our taste and odor receptors. As the microbes go about the business of breaking these molecules down into smaller pieces they can make use of themselves, they create amino acids, fatty acids, and sugars that we can taste and smell. They also synthesize new compounds for communication and other purposes, and some of these compounds contribute to taste or aroma as well, McGee says. "This process of breaking down and building up makes food much more complex in its sensory characteristics and more interesting." Culinary experimentation with microbes has gotten super trendy. Celebrity chef David Chang of [Momofuku](http://momofuku.com/) has opened a [fermentation lab](http://www.thebraiser.com/momofuku-fermentation-labs-video/) in New York that's engineering things like pistachio miso and [chickenbushi](http://latimesblogs.latimes.com/dailydish/2012/05/whats-rotting-at-david-changs-momofuku-lab.html) (chicken prepared in the style of Japanese [katsuobushi](http://en.wikipedia.org/wiki/Katsuobushi), which is made from fish that is boiled, smoked, and then fermented). At Copenhagen's [NOMA](http://noma.dk/), which has topped several lists of the world's best restaurants in recent years, chef René Redzepi is playing around with [fermenting everything](http://cookingdistrict.com/cd/general.nsf/blogbypop/942814FE2EC59A6485257AB4001CED43) from plums (mmm) to puréed grasshoppers (hmm). Chefs like Chang and Redzepi are interested in the idea of microbial *terroir,* the confluence of soil, climate, and other environmental factors that make food from a particular place unique. It's used more often to talk about wine, but regional differences in microbial communities could give a cheese from New York different characteristics than one from France, even if all the other ingredients are the same. Maybe. "We're starting to look at that in the lab right now," said [Rachel Dutton](https://sites.google.com/site/theduttonlab/), a microbiologist at Harvard who's consulted Chang and other chefs. "I don't think there's good evidence one way or the other." You don't have to be a fancy-pants chef or a Ph.D. biologist to get some microbes working for you in the kitchen. Anyone can get in the act, and there are plenty of how-to videos on YouTube. Thanks to [this one](http://www.youtube.com/watch?v=0sX_wDCbeuU), my fridge is stocked with fiery kimchi at all times. In this gallery several scientists -- including Dutton and mycologist [Benjamin Wolfe](http://www.benjaminewolfe.com/), who works in her lab -- helped us explore the biology of some of the microbes that make our food and drink more delicious. Isn't it time you got to know them a little better? Above: *Penicillium roqueforti* ------------------------------- Two species of *Penicillium* fungus are named after cheeses. *P. roqueforti*, above, gives blue cheeses like Roquefort (as well as Gorgonzola, Stilton, and Danish Blue) their pungent aroma and spiciness. Cheesemakers add *P. roqueforti* to the milk, so it's present throughout the cheese, says Dutton. But it needs a little oxygen to flourish, so cheesemakers punch holes in the cheese with metal spikes to let a bit of air in. The blue mold grows along these tracks, producing the beautiful blue veins that characterize these cheeses. *P. camemberti* produces the velvety white mold on the rind of Camembert cheese. It needs oxygen, which is why it grows on the surface, Dutton says. "It makes lots of mushroomy flavors and breaks down the cheese to a gooey texture." *Top image: Rachel Dutton. Bottom image: [Frédérique Voisin-Demery](http://www.flickr.com/photos/vialbost/4040202906/)/Flickr* 
02saccharamyces-cerevisiae
*Saccharomyces cerevisiae \------------------------* "I really do admire yeasts," food writer Harold McGee told me. "Among all the microbes they seem to be the ones that are best at synthesizing new aromas." One species in particular, *Saccharomyces cerevisiae*, has arguably done more to elevate our cuisine than any other microbe. It's used both in brewing and baking. "You've got the aromas in wine and beer and bread, which span a really wide range and are generally really delicious," McGee said. Even within this species, there are countless strains. Brewers have been exploiting this diversity for centuries. It's a big part of what distinguishes lagers from ales, and what sets British ales apart from Belgians. A tasting room that opened last year at [White Labs](http://www.whitelabs.com/), a San Diego company that grows yeast for amateur and professional brewers, gives visitors a chance to experience first hand the difference yeast makes in a beer. At any given time, there are about half a dozen styles of beer on tap, with each style represented by several versions brewed using the exact same recipe -- but different yeast. "I think people come away from it understanding more about the micro-organisms and how yeast impact the flavor," said White Labs co-founder Chris White. For example, they might brew the same pale ale recipe with California ale yeast, British-style Burton ale yeast, German Kölsch yeast, and a lager yeast. Of those four, the Burton ale yeast will produce the most esters, which give the ale more fruity aromas, White says. At the other end of the spectrum, the lager yeast will produce the fewest esters, and let more of the malt and hop character through. It's not common to brew an ale with lager yeast, which prefer cooler temperatures, but a classic example of this style is Anchor Brewing's [Steam Beer](http://www.anchorbrewing.com/beer/anchor_steam). White, who earned a PhD in biochemistry before becoming a yeast wrangler, is interested in the genetic differences among yeast strains that determine their optimal working conditions and what flavors they contribute to a brew. White Labs recently teamed up with [Illumina](http://www.illumina.com/), a San Diego company that makes gene sequencing equipment, to sequence the genomes of 96 strains of brewers yeast. "We're looking at the data now," he said. But it's going to take some time to make sense of it all: Each strain generates about 4 GB of genomic data, White says. *Top image: [ZEISS Microscopy](http://www.flickr.com/photos/75834543@N06/7361893014/in/photolist-cdxCiU-cdxCg7-cdxChq-cdxCqu-dEw83z-buWpsN-dSBRW7-dSBS4s-dSwmQe-dSBSe5-dSwipa-dSwh9e-dSBRLU-dSBSah-dSwhGn-dSBRso-dSBSWu-dSBRWA-dSBRWh-dSBS4E-dSwi4B-9iEPWE-9iEPQu/)/Flickr*. Bottom image: [Joker Venom](http://www.flickr.com/photos/joker_venom/8305721408/)/Flickr 
03Brettanomyces bruxellensis
*Brettanomyces bruxellensis* ---------------------------- European brewers have been making sour beers for centuries by allowing whatever microbes happen to blow in through the brewery windows to have a go at their fermenting grains. These beers range from the slightly sour and funky [Berliner Weisse](http://en.wikipedia.org/wiki/Berliner_Weisse), to undeniably tart [Flanders red ales](http://en.wikipedia.org/wiki/Flanders_red_ale), to downright puckery Belgian [Gueuzes](http://en.wikipedia.org/wiki/Gueuze). Lately the trend seems to be taking off in the U.S. "It's a cool place for brewers to experiment," said White Labs founder Chris White. "These are very artsy sensory driven beers." There are many styles of sour beers, but what they all share in common is the addition of microbes other than the standard brewer's yeast, *Saccharomyces cerevisiae.* Most of the sourness comes from lactic acid produced by the addition of bacteria such as *Lactobacillus* and *Pediococcus.* But the other characteristic flavors of sour beers come mainly from *Brettanomyces* yeast. This genus includes several species, including *B. bruxellensis* (above), that gobble up sugars *S. cerevisiae* won't touch and produce flavors that sound absolutely awful individually but somehow end up working together to produce some delicious beers that rival wine in their complexity. *Brettanomyces* yeast produce a lot of phenol compounds, for example. These are often described as clove-y, smoky, or medicinal. "Like chewing on a Band-Aid," White said. "*Brett* also makes a whole bunch of smaller compounds that we describe as barnyard or horse blanket." Mmm, horse blanket. But seriously, you are just going to have to take my word for it that these flavors are not necessarily bad in small doses. Or better yet, don't -- go get a sour beer and decide for yourself. *Top image: [Maxdesbacchus](http://commons.wikimedia.org/wiki/File:Aspect_de_brettanomyces_bruxellensis_sur_g%C3%A9lose_YPD.JPG)/Wiki Commons. Bottom image: [Stacy Clinton](http://www.flickr.com/photos/stacyjclinton/4872960174/in/photolist-8qBchJ-8qy7dH-8qy6s2-8qBdq7-9Jg9xs-eXN6Fd-9zb7aY-aNkN1c-aNkLpB-9p88EZ-9QUejb-9hv4Mw-9zxMjb-9EFPsE-fxtq58-c3aY8h-a3Udmh-9oZVvV-a2YaEi-9U4Ggn-bLiotp-bsmz1B-9kYMzV-8LgCLz-9Cix6U-dXgkoE-aqw1pH-8j3x9G-bobHGE-aqwdaK-booQnY-8ZkMFm-bZZ9AA-8j3x9Q-e9his1-ecWQ9r-9D3Kj7-e9bHxX-aFQzic-9QTWBL-fdSgJd-e33yg5-beqdSc-7UWwB6-eAxz3Q-8CDXum-a3Udm7-dGPwC1-ehTSEU-a2YaEr-dXgfAb/)/Flickr* 
04Noble-rot
*Botrytis cinerea* ------------------ Also known as noble rot, this mold grows on grapes and essentially turns them into raisins, dehydrating them and increasing the sugar concentration. "It looks like rotten grapes, but it makes these beautiful wines that are super expensive but just amazing," said Wolfe. French Sauternes wines are the classic example of an intensely fruity and aromatic "botrytized" wine. Craft brewers have been experimenting with moldy grapes too: [Dogfish Head's Noble Rot](http://www.dogfish.com/brews-spirits/the-brews/occasional-rarities/noble-rot.htm) is one interesting example I tried recently. They bill it as combining the best aspects of both wine and beer, which sounds pretty pretentious. But it kind of does. And I kind of liked it. *Image: Benjamin Wolfe*
• SCIMAT05leuconostoc-mesenteroides
*Leuconostoc mesenteroides \-------------------------* You could build an entire picnic around foods fermented with lactic acid bacteria. And it would be an awesome picnic. There would be pickles, olives, cheeses, salami, sourdough bread, chocolate, and coffee. Lactic acid bacteria encompass hundreds of species, including *Leuconostoc mesenteroides* above. In all these different foods, they do the same thing: They consume sugars and produce lactic acid. "It's an end product of their metabolism," said Maria Marco, a microbiologist at UC Davis. "It's basically a waste product." But don't let that put you off. Not only does lactic acid put the tang in pickles and kimchi (below), it also makes life miserable for other bacteria that could make you sick. Lactic acid bacteria are among the few microbes that can thrive in salty, low-oxygen environments, and once they get a foothold and start churning out acid, most other bugs don't stand a chance. Sushi, in one of its earliest incarnations, was made with rice fermented with lactic acid bacteria. In modern sushi, a dollop of rice vinegar acidifies the rice, but in the old days bacteria did the job. McGee says he sought out this delicacy, *funazushi*, on a trip to Japan last year. "It's a very rare thing now," he said. "I had to ask people and hunt around for a few days." When he finally got it, he sat in the lobby of his hotel and prepared to try it. The aroma was pretty strong. "The hostess came and asked us to move," McGee said. But he says he liked it, or at least found it interesting. "I guess I would say it was a cross between fishy and cheesy," he said. "We think of modern day sushi as so pristine and fresh. This was a very different experience." One of Marco's research interests is the role of lactic acid bacteria and other microbes in olive fermentation. Olives freshly picked from the tree are bitter and hard, so producers soak them in vats of brine for months to make them more edible. Marco has identified certain yeasts that break down pectins in the olives to make them softer. Lactic acid bacteria, meanwhile, help reduce bitterness and improve flavor, turning the unappetizing raw fruit into something worthy of your next martini. In chocolate and coffee production, raw fruit is left to ferment in the sun. Lactic acid bacteria again do their thing. "They consume the sugars and degrade the tissue to release flavors from the chocolate pod or coffee cherry," Marco said. Along with yeasts, molds, and other bacteria present in the fermenting fruit they help develop complexity that comes through when the beans are roasted. If you've been to San Francisco, you've probably been pressured into eating sourdough bread. That too is the product of a lactic acid bacterium -- *Lactobacillus* *sanfranciscensis*. But despite its name and the popular myth that San Francisco sourdough bread is superior to sourdough bread from elsewhere, *L. sanfranciscensis* is not endemic to the city by the bay. "It's everywhere," Marco said. "It was only discovered here." *Top image: SCIMAT/Getty Images. Bottom image: [Jason Jacobs](http://www.flickr.com/photos/hisc1ay/5322113990/)/Flickr* 
06Geotrichum-candidum
*Geotrichum candidum \-------------------* If you go to a cheese shop and seek out the French section, you're likely to see some with ripply rinds that look a bit like brains or coral. That's the work of *Geotrichum candidum*. "It's kind of a confused yeast," said Wolfe. "Most yeast we don't really see because they're single cells like bacteria, but this one grows stuff that look like mold hyphae." Those are the multicellular filaments you've probably seen growing on those leftovers you left in the fridge too long. This odd behavior has an evolutionary explanation, Wolfe says. "Geotrichum is an ancestral yeast," he said. "Yeast are derived from mold so this is like a yeast in transition." *Geotrichum* grows everywhere: on plants, in the soil, even inside our bodies. And it makes for stinky cheese. "It gives up all these funky cabbagey flavors," Wolfe said. "It also tends to smell like farts when you grow it in the lab." *Top image: Benjamin Wolfe. Bottom image: [Another Pint Please](http://www.flickr.com/photos/anotherpintplease/9221992763/)/Flickr* 
07Staphylococcus-xylosus
*Staphylococcus* ---------------- You might recognize the name *Staphylococcus* from the black sheep of this bacterial genus, the ones that cause abscesses, food poisoning, and other nasty infections. But not all *Staphyloccocus* bacteria are bad actors. Some species contribute buttery flavors to certain cheeses. The colorful splotches in the image above are colonies of four *Staphylococcus* species growing on the rind of a blue cheese. The bright orange one, *S. xylosus,* contributes flavor and pigmentation to cheddars and other cheeses*.* "It almost smells like Cheetos when you grow it in the lab," Wolfe said. *S. xylosus* and other *Staphylococcus* species, notably *S.carnosus,* also contribute to the meaty funkiness of salamis and other cured meats. *Top image: Benjamin Wolfe. Bottom image: [Jesper Hauge](http://www.flickr.com/photos/jesper_hauge/3043460885/)/Flickr* 
08Brevibacterium-linens
*Brevibacterium linens \---------------------* The orange dots in the high magnification image above are colonies of *Brevibacterium linens* cultured from the rind of a Stilton cheese. The other dots are other bacteria, yeasts, and molds that together form a microbial community in the rind. *B. linens* gives pungent cheeses like Munster and Limburger their stinky aroma. "It's closely related to bacteria that grow on the skin and produce foot odor and body odor," Dutton said. "That's why those cheeses kind of smell like stinky feet." *Top image: Benjamin Wolfe. Bottom image: [bl0ndeeo2](http://www.flickr.com/photos/bl0ndeeo2/3273865056/)/Flickr* 
09Acetobacter-Zygosaccharomyces
*Acetobacter* and *Zygosaccharomyces* ------------------------------------- The first time I tried kombucha, I thought it was disgusting. The second time I tried it, I wondered why I hadn't learned my lesson the first time. Kombucha may be the one exception to my rule that funkier is better. But lots of people love the stuff, gauging from the line that forms at the kombucha bar at my local Whole Foods. For the uninitiated, kombucha is a slightly effervescent sour drink made from sweet tea. It's cultured with a goopy mat of microrganisms that non-scientists generally refer to as a "mother" and scientists prefer to call a SCOBY: a symbiotic community of bacteria and yeast. It may have originally reminded the Japanese of seaweed: kombu is the word for kelp. Kombucha usually contains several yeast and bacteria species. The high magnification image above shows two typical residents: yeast from the genus *Zygosaccharomyces*, and bacteria from the genus *Acetobacter*. The yeast consume the sugar and produce alcohol and carbon dioxide, which provides the bubbles. The bacteria go to work on the alcohol, breaking it down and producing acetic acid, which gives the drink its vinegary flavor. The bacteria also churn out the cellulose that gives the mother its mat-like structure. *Top image: Benjamin Wolfe. Bottom image: [Hella Delicious](http://www.flickr.com/photos/0x/3350395927/in/photostream/)/Flickr* 
10aspergillus-oryzae
*Aspergillus oryzae \------------------* The beautiful mold growing on rice in the photo above is *Aspergillus oryzae*. "It's probably one of the oldest domesticated microbes," Dutton said. It's crucial in the production of sake and miso. A culture of rice or grains and *A. oryzae* is called a koji. The fungus converts starches in the rice or grains into sugars that can be used by other microbes, says Wolfe. "You grow the mold on rice, or it can be barley or even chickpeas if you wanted, and it releases enzymes called amylases that break down the starch into sugars." In sake production, the sugars created by *A. oryzae* become food for *Saccharomyces cerevisiae,* the same yeast used to brew beer and wine. To make miso, the koji is traditionally made from rice and/or soybeans cultured with *A. oryzae,* and the product of that fermentation is fed to a different type of yeast, *Zygosaccharomyces rouxii* (see next page). *Top image: Benjamin Wolfe. Bottom image: [Allan Chatto](http://www.flickr.com/photos/besighyawn/6471137563/)/Flickr* 
11Zygosaccharomyces-rouxii
*Zygosaccharomyces rouxii \------------------------* The savory funkiness of miso soup (below) or miso-glazed anything is due to the work of *Zygosaccharomyces rouxii.* In the first step of miso production (see previous page), some combination of rice, soybeans, and other grains is fermented with *Aspergillus oryzae* mold to release sugars. *Z. rouxii* feeds on these sugars and produces a range of byproducts in the process that contribute interesting flavors. "It's breaking down the protein into amino acids which gives you the umami flavor," Dutton said. The yeast also produce aromatic compounds that contribute to the characteristic flavor of miso, she adds. *Z. rouxii* and related species also contribute to the rich flavor of soy sauce and balsamic vinegar. *Top image: Benjamin Wolfe. Bottom image: [Samuraijohnny](http://www.flickr.com/photos/samuraislice/3332512298/)/Flickr* 
