Feb 03 2014

Cultures, Microbial and Otherwise

It wouldn’t surprise anyone who reads this site that my list of favorite foods is exceedingly large, ranging from cheese to bread, beer to wine, sauerkraut to pickles. The common factor in all of these favorites? Fermentation. Though I could douse everything with soy sauce and can never turn down a hunk of clothbound aged cheddar, until recently, I hadn’t linked these fermented foods together, or understood that these cravings were nourishing a very important part of my body: the microbiome that resides in my gut, swirling with trillions of bacteria and other microbes. Over the last six months, I’ve devoured several books that delve into fermentation – notably, The Art of Fermentation and Cooked – and as is usually the case when I’m suddenly desperate for information on a new topic, I began finding articles and conversations surrounding fermentation and bacteria everywhere I looked.

Consider a few headlines from a recent slew of articles related to fermentation and microbes. They read like propaganda for a mystical cult science:

The more I read about fermentation, the more I felt myself bubbling (one might say, fermenting) over with palatable excitement about the wide range of fermented foods available to consume and create, curiosity about the cultures and communities from which these foods originate, and a growing awareness that fermented foods allow us to eat items that our bodies inherently crave and – unlike french fries – actually need to thrive.

Fermentation refers to an anaerobic metabolic process: the production of energy from nutrients without oxygen. Each ferment, whether the end result is pickles or dosas, relies on a substrate (plant, grain), a community of microorganisms (bacteria, yeasts), and the appropriate conditions (temperature, fermentation vessel, time, air) for the communities of microorganisms to consume sugars (and the proteins and fats broken down into simpler components by enzymes and bacteria) already present on the substrate or introduced to the food mixture. As the yeasts and bacteria consume sugars like maltose and glucose, they expel carbon dioxide, alcohol, and lactic acid, as well as unlock previously inaccessible nutrients in grains and seeds.

Though we most frequently think of fermentation in relation to edible substances like kombucha or beer, the same process also constantly occurs in nature and on non-edible substances: fermentation is simply a way to break down organic matter and recycle energy. The same basic process that transforms cabbage into sauerkraut also transforms compost heaps into rich soil, decomposing bodies into a collection of bones, and contaminated wastewater into potable water. Without fermentation, nothing would decompose and the world would be literally uninhabitable.

In an article endearingly titled “Some of my Best Friends are Germs”, Michael Pollan writes, “for every human cell that is intrinsic to our body, there are about 10 resident microbes”. This microbiome was first discovered in the mid 1600s, when Antonie van Leeuwenhoek “scraped the scum off his teeth, placed it under a microscope and discovered that it contained swimming creatures." We’ve spent the last four hundred years existing in an uncomfortable relationship with these bacteria, often battling and killing them with antibiotics, which while effective – and in many cases life-saving – are also blunt instruments that wipe out beneficial bacteria. We also employ their use for agricultural gain (see: Bt corn and the overuse of antibiotics in livestock), and promote sterility through copious use of products like Lysol and Purell. More recently, due to articles like Pollan’s and a growing scientific awareness of the complexity of these microbes, public knowledge and research is starting to shift our relationship with bacteria from combative to synergistic: how can we nurture them, so they can help us?

Generally, when writers or scientists reference the microbiome, they group several categories of microbes together:


Bacteria are single celled microorganisms and one of the first life forms to appear on earth. Lactic acid bacteria, including Leuconostoc mesenteroides (found on all plants) and many iterations of Lactobacillus, convert sugars (lactose) into lactic acid. These bacteria are classified based on what sugars they metabolize (glucose, maltose, sucrose, or lactose) and what byproducts they emit (ethanol, lactic acid, carbon dioxide). Lactic acid bacteria can be homofermentative or heterofermentative. Heterofermentative bacteria, like L. Mesenteroirdes, produce carbon dioxide, alcohol, and acetic acid, in addition to producing lactic acid. Homofermentative bacteria, including L. Plantarum, can tolerate high acidity and are more specialized. Of course, bacteria play a huge role in non-lactic acid ferments too: for example, B. Linens is a common bacteria found on washed rind (stinky!) cheeses.


Yeasts, a type of fungus, are single celled organisms capable of anaerobic fermentation and aerobic fermentation (more accurately known as oxidative respiration). In oxidative respiration, yeasts grow quickly, but don’t produce alcohol; in anaerobic fermentation these yeasts produce alcohol and carbon dioxide. The alcohol yeasts excrete will eventually kill them: yeast strains can tolerate an alcohol concentration of 10–15% before dying. Brewers and winemakers incorporate different strains of yeasts into their creations, depending on the desired alcohol content.

The most common, and most studied, yeast is Sacchorymores Cerevisiae, a yeast that plays a prominent role in the fermentation of wine, beer, distilled alcohol, and bread. If you bake bread with commercial yeast, this is the yeast strain you’re sprinkling on top of your flour and water mixture.


Fungi are eucaryotes (meaning that they have true nuclei in cells) and obtain their nutrition via decomposition. Molds are a type of fungus that grows in the form of multicellular filaments called hyphæ. Molds need oxygen, moisture, and heat to grow and thrive, but all three in moderation.

Common molds used in fermentation include molds in the Asperigullus family, such as Aspergillus oryzae and Aspergillus soyae, and the Rhizopus species. These fungi break down starches (much like enzymes) and produce sugar for the proliferating bacteria. For example, to make soy sauce, soybeans and flour are inoculated with the Asperigullus oryzae or soyae mold, which influences the growth of bacteria. The bacteria then ferment the resulting paste to create soy sauce.

A common fungus found in cheeses like Camembert and Brie is called Geotrichum Candidum, which has enzymes that break down fats and proteins and release ammonia. The resulting ammonia neutralizes the pH of the rind, which creates a desirable environment for new strains of bacteria, yeasts, and fungus to take hold.

If you want to learn more about molds and yeasts, here’s a handy chart that breaks down their differences and uses.

In many cases, the necessary bacteria to initiate fermentation are already present on the food, and fermentation happens spontaneously – a process known as wild fermentation. The nature of the substrate (the food about to be fermented) determines what kind of fermentation will spontaneously occur. Yeasts are abundant on grapes, cueing an alcoholic fermentation, while there’s an abundance of lactic acid on all plants (and lactose in milk), which cues a lactic acid fermentation. All fermented foods originally started as “wild ferments”, but over time, cultures learned how to replicate and manipulate conditions to direct and influence fermentation. Instead of waiting for the right conditions to appear (a method that doesn’t work if you’re trying to consistently replicate a certain kind of ferment, especially for scaled-up production), many fermenters introduce “cultures”, an isolated organism or community that will initiate fermentation. These cultures can take the form of a starter (a mature ferment added to a new substrate) or an actual physical entity known as a SCOBY (Symbiotic Community Of Bacteria and Yeast). SCOBYs, used to ferment kombucha and kefir, coordinate their reproduction and have evolved into distinct, physical forms – they produce a shared skin which then rests in the substrate during fermentation.

With all ferments, there’s a microbial dance occurring in the bubbly jar of pickles, oozing container of sourdough starter, or thickening yogurt. Take sourdough bread: there’s not a single creature responsible for the air, texture, expansion, and flavor. Instead, the resulting bread is the product of a symbiotic relationship between a yeast (C. Milleri) and a bacteria (L. Sanfranciscensis), and the yeasts and bacteria that result as the environment changes. As the yeasts die, their proteins break down into amino acids which the lactobacilli use to grow. There are around 20 different types of yeast and 50 different types of bacteria in a sourdough culture, all entering into similar relationships with each other.

The mind blowing thing about these sourdough cultures? The yeasts and bacteria are virtually the same whether your sourdough starter resides in Portland, Oregon or Sochi, Russia. Even though lactic acid bacteria and yeasts exist everywhere, the same 70-ish strains are found in sourdough cultures the world over. To have such similar microbial populations in vastly different environments is certainly an argument for nurture over nature – and further explains the interlinking relationship we have with bacteria. When we create a certain environment for specific microbes to thrive, the microbes create valuable products for us to eat. As long as we nurture the fermentation environments in specific ways – temperature, vessel, feeding schedule, oxygen access, humidity, acidity – we’ll get to enjoy the microbes’ desirable, crave-able byproducts.

In his book, The Art of Fermentation, Sandor Katz writes that our precursors (pre-Neolithic Era) were exposed to alcohol in fruit, and this exposure elicited physiological adaptations and preferences. This alcohol, and the development of fermented traditions with grains, led to an intricate, co-dependent web between yeasts, plants, and animals that still exists today. In Cooked, Michael Pollan shares that there are some theories that posit that civilization moved from hunter-gatherer to farmer/grower because of the thirst for alcohol and the need to settle down to create and experiment with alcohol production. The grains used for alcohol were also eventually used to make bread (and before that, in an unleavened porridge), and set us on the domestic – and co-dependent – path in which we firmly reside today.

Along with our inherent desire for alcohol, fermentation traditions developed out of necessity: before refrigeration, cultures across the world were forced to develop a range of techniques to slow enzymatic and bacterial degradation of meat, fish, fruits, and vegetables. Even after the dawn of refrigeration and 24 hour grocery stores, these techniques are still prominent in today’s fermented food, and include drying, salting, smoking, curing, and pickling. Each method exists to create selective environments that inhibit the growth of pathogenic bacteria and allow for more desirable forms of microbial growth. Fermenting organisms’ metabolic by-products (alcohol, lactic acid, carbon dioxide) inhibit certain microbial and enzymatic processes, which in turn create a selective, acidic environment that limits what can grow, including bacteria that you probably want no part of, such as Clostridium botulinum.

As a concurrent benefit, while our cultural ancestors fermented for shelf stability and alcohol, they were also giving themselves an important health boost that extended the longevity of their culture’s existence. All grains, seeds, legumes, and nuts contain phytic acid, a compound designed to bind minerals in the seed, as it’s in the plant’s best interest to protect these minerals for a future seedling’s nutrition. Fermentation awakens the phytase enzyme, which frees these minerals for our absorption. Sandor Katz writes that “the same qualities that make grains so stable also make them difficult to digest. The process of fermentation unlocks previously unavailable nutrients like Vitamin B and lysine that these seeds and grains lock up in anti-nutrient barriers.” In addition, fermentation aids in metabolizing organic compounds and increases the availability of certain vitamins and amino acids.

And, perhaps mostly importantly, fermentation benefits our intestinal microbiota and stimulates the production of antibodies. Microbes’ survival depends on our survival (we’re their host after all), so they do all sorts of things to keep us alive and well. For example, gut bacteria break down indigestible carbs that in turn nourish the gut wall; other bacteria adhere to the inner surface of the epithelium so they can crowd out pathogenic strains like E. Coli and salmonella. Gut microbes also train our immune system to respond appropriately, manufacture essential vitamins, and work with the central nervous system to moderate appetite and fat storage.

Some bacteria are known as “probiotics” – which is really just a label for any microbe that benefits the organism (us) who digests them. These probiotics (which can take the form of live cultures – living bacteria available when the food hasn’t been pasteurized) don’t land in our gut and reside there permanently; instead, they stimulate antibodies and interact with the current intestinal microbiota and cells. In The Art of Fermentation, Katz cautions that the specific bacteria strains are less important than incorporating a diverse variety of bacteria into our diets – which belies the health benefits of always seeking out a yogurt with one known bacteria.

If shelf stability, gut health, and toxin-freedom aren’t enough, you can usually sway a person to drink or eat a fermented food simply from its flavor and taste. Think about that first chew into a piece of sourdough bread, how much satisfaction you get from an afternoon yogurt snack, or how nothing...nothing...tastes better on a humid summer day than a cold ginger beer (preferably a Rachel’s Ginger Beer, in my book).

Since Antonie van Leeuwenhoek originally discovered the presence of microbes, and Louis Pasteur shed more light on bacteria and the effects of pasteurization, we’ve approached bacteria in several ways. We either declare war on bacteria, overprescribing antibiotics for humans and Lysol-ing everything in sight, or we attempt to use bacteria for our own gain, which includes using antibiotics subtherapeutically to promote weight gain of farm animals, injections into GMO crops, and current plans to add soil bacteria into depleted starved monocrop soil. Of course, pathogenic bacteria exist – one only has to look at recent food safety reports to see that certain bacteria, when given the right conditions, can run rampant on our food supply and endanger its eaters. (I’m sure you’re as familiar with the usual suspects as I am: E. coli, salmonella, and listeria.) And antibiotics have transformed surgery and cured infections that were once a sure death sentence. Yes, there are certain conditions that encourage destructive bacteria to take hold in our food supply and in our guts, but when we destroy bacteria indiscriminately, we create conditions that allow only the strongest, most pathogenic to take hold, and eliminate the complicated system of checks and balances among the microbes.

It’s in our cultural lexicon to have a knee-jerk reaction to bacteria as scary or dangerous, and to associate the word with a black mold growing on shower tile instead of with a relaxing evening spent drinking a bottle of wine or with the pickles you eat for lunch. But good versus bad isn’t the right way to look at bacteria (or let’s face it, most things): even though a bacteria like E. coli can wreak havoc, bacteria, yeasts, and molds shouldn’t be classified as scary...or always helpful. There’s a hugely complicated relationship among microbes, and among our bodies and microbiome, that scientists are only beginning to understand. Pollan has written that until recently, scientists focused on the handful of bacteria that could grow in a petri dish, yet most bacteria residing in our gut refuse to grow in typical laboratory conditions. A recent study examined bacteria in the stool of nearly 300 Danish volunteers, and at the study’s completion, scientists reported that 90% of the bacterial genes uncovered were previously unknown.

The most telling example I’ve read about bacteria’s flexibility and refusal to be classified in rigid categories involves the stomach bacteria Helicobacter pylori. This bacteria is linked with ulcers and stomach cancer, and thus modern medicine has waged war against its kind. But h. pylori is also involved in regulatory functions related to stomach acid and appetite controlling hormones. When h. pylori is eliminated, ulcers may be less likely to occur, but stomach acid and obesity could increase. We gain and we lose.

Bacteria are versatile and only beginning to be understood. Consider that every square centimeter of our lungs is home to 2,000 microbes. Or new studies like the one that found that asthmatics have a different collection of microbes than healthy people, or another finding that obese people have a different set of species in their guts than people of normal weight. We have a long way to go before we’ll grasp the complexity of the microbiome, but encouragingly, scientists are beginning to make fascinating links, both in food production and human health.

All food, fermented or otherwise, exists in a broad context. Centralized, mass-produced food diminishes not only its flavor, but also the food’s surrounding culture, tradition, and community. Fermented foods, like a tangy house cheese from a café in rural France, or an extra potent kimchee in a Korean village, weren’t created to be replicated, copied or duplicated for worldwide consumption. These fermented foods developed their memorable flavors because of the environmental factors that surrounded their fermentation: the climate, terrain, specific microorganisms, animals, and humans facilitating the process. Fermentation depends on flexibility, observation, and intuition, and the community and culture around that fermentation.

With those tenants in mind – flexibility, observation, and intuition – I’ve begun to incorporate fermentation in my own life, creating two sourdough starters (both alive and bubbling after 14 days), as well as more consistently soaking grains, beans, and oats before cooking them. Most importantly, my growing knowledge related to fermentation serves to further extend my awareness of how intricate – and complex – food and food cultures are, ultimately illustrating that I’m merely a player in this often mysterious world.

To further my understanding of fermentation and to explore individual ferments more deeply, this year I plan to interview respected fermenters – cheesemakers, kombucha brewers, hot sauce mavens, and picklers – to gain a deeper knowledge of their community and culture (both microbial and human), what led them down their fermentation journey, and their community’s response to their products. Stay tuned.