What is Fermentation? An Essential Guide

What is Fermentation? An Essential Guide



Guest Blogger, Summer Bock


As a fermentationist who trains people on functional ferments, the creator of my own course on fermentation —  The Fermentationist™ Certification Program — and Happy Gut Life’s guest content contributor for the month of September, it’s no surprise that I get asked “What is fermentation?” all the time.

It’s also probably no surprise that I could write an encyclopedia just to answer this one, seemingly simple , question.

If you’re surprised that fermentation could be that complex, you’re not alone. The Wikipedia summary of the science and history of fermentation is watered-down at best. Most educational resources on fermentation fail to grasp the magic we all experience the first time you chop up vegetables, stuff them into a jar, let them bubble at room temperature on your countertop, and then consumed the final product — filled with living organisms, enzymes, organic acids, bioactive metabolites, and activated vitamins.

And so, this week — the first of a 3-part series on fermentation — I’m going to teach you all about fermentation, what it really is, what it means to me, and what it can mean to you and your health.

A Background on Fermentation

Our ancestors depended on fermented foods to survive. Sauerkraut used to be an essential source of vitamin C, and Captain James Cook received the Great Copley Medal for his observation that sauerkraut was an effective preventative food for scurvy by providing vitamin C to sailors who previously died from the “plague of the sea.”

(It’s actually the second oldest food preservation method and there’s evidence of fermentation from over 10,000 years ago.) Dairy kefir dates back many centuries to the shepherds of the Caucasus mountains. They discovered that fresh milk carried in leather pouches would occasionally ferment into an effervescent beverage that was preserved much longer than fresh milk.

Fermentation was originally developed as a way to preserve food using beneficial bacteria.

Clearly, fermentation has a long, rich role in human history. And these days, fermentation is still a huge deal. Decades after we no longer needed it for food preservation purposes — or for preventing the severe vitamin C deficiency in sailors — fermentation is still all around us. Clearly, something must be special about fermentation for this technique to be protected and passed down by generations, cherished by families, and praised by health experts across the globe for its health benefits.

Personally, I wasn’t always this passionate about fermented foods and the little microbes that inhabit them. You see, I used to be very sick.

“I struggled with rashes, fatigue, anxiety, bloating, IBS, food intolerances, and panic attacks.”

I was a barely-functioning hot mess. I spent my childhood popping antibiotics a few times every year for strep throat and when I was 20 years old, it got to the point where I could only eat about 30 foods without a reaction. (This is back before you could Google gut health and find Dr. Pedre’s website.) One of the many doctors along my path recommended probiotics, which I hadn’t heard of before.

Then, I started taking the probiotics and everything changed.

My food was fully digested, my bloated belly calmed down, and I started going to the bathroom 2 to 3 times per day like clockwork.  As a trained herbalist, I asked myself, “what is the whole food version of probiotics?” —  I knew they weren’t popping white capsules of powder made in a lab. 

Around the same time, I lived with a Korean family in San Francisco that always had two, 5-gallon buckets of kimchi — a traditional Korean food made of fermented cabbage and radish — in their fridge. All of a sudden, I had my answer.

Fermented Foods

Fermented foods were the whole food version of probiotic supplements.

The only problem was that at the time, fermented foods were not available in many grocery stores. If I wanted the health benefits of fermented foods, I had to learn to make them myself. And that’s when I began to understand what fermentation really is.

What is Fermentation?

More than its role in food preservation history,

fermentation is really about the ability to create your own living medicine.

Normally, you eat food and it breaks down into nutrients that your body either absorbs or passes through your system and out of your body. But with fermentation, there are an extra few steps in between. The invisible microbes in fermented foods and the many beneficial bacteria already living in your gut — called probiotics(from the Greek “pro” meaning “for” and “biotic” meaning “life” — also break down the fiber in the food that you eat. And when the bacteria break down these fibers, they release byproducts that the body needs to function optimally.

As you can see, having plenty of beneficial bacteria in the gut is a great way to support optimal health and digestion — and fermentation is how you safeguard your gut ecosystem.

As I researched fermented foods, I quickly learned that the basic formula to create fermentation is simple:

Food + cultures (microbes) + time = fermentation


Fermentation Crock
For example, to make sauerkraut you chop cabbage (which has naturally occurring bacteria on the leaves), add salt, and tamp it down into a crock to create an anaerobic environment, which allows the naturally occuring bacteria to start fermenting. Within a short period of time, you have sauerkraut.


A crock is the most widely-used, as well as common term, for the stoneware or ceramic vessel we ferment foods in.

What amazes me is that during this process, multiple strains of probiotic bacteria are growing and multiplying invisibly in the crock. The finished product of raw, unpasteurized sauerkraut contains around 13 different kinds of friendly bacteria. One example is Lactobacillus plantarum , which is renowned for its ability to keep pathogenic bacteria at bay. It also breaks down histamine, which is great for allergy-sufferers.

Some fermented foods require starter cultures in order to transform them.

Kombucha, water kefir, dairy kefir, and red wine vinegar are examples of fermented foods that use starter cultures, which are called a Symbiotic Community Of Bacteria and Yeasts (or SCOBYs).

SCOBY’s cannot be created by humans. We discovered them and subsequently handed them down for thousands of years. For example, Kefir SCOBYs were passed down from generation to generation among the tribes of Caucasus and considered a source of family wealth. Other examples of SCOBYs include the kombucha mother or the vinegar pellicle, which most people get from a friend or family member because it’s been passed down, hand to hand, for generations until it got to you.

Delicious Functional Ferments

We’ve mentioned Kefir and sauerkraut already, but there are a ton of delicious functional ferments that you can experiment with, including:






Pickled Carrots

Dilly Beans


Legume Ferments




Soy sauce

(A fermented rice and bean paste that’s turned into a fermented biscuit)

Grains Ferments


(An Ethiopian flatbread)


Fermented Beverages


Coconut kefir

Water Kefir

Dairy Kefir

(A fermented Slavic and Baltic beverage commonly made from rye bread.)

Incorporating these foods into your diet, whether you make them at home or buy them, is a great way to make sure that your gut ecosystem is fully supported with beneficial bacteria.

Microbes and Humans: An Invisible Friendship

In order to understand how the ferments above impact human health, let’s take this conversation out of the microscopic realm and talk about something we can see…wolves. An unexpected result occurred in Yellowstone National Park when the once-endangered wolves were reintroduced to the forest. Prior to the reintroduction of wolves, the deer population had overtaken the park.

Due to the overpopulation of deer in the park, rivers and creek banks were eroding, because the animals were over-grazing the grass. Turns out the grass roots hold the soil in place. As a result, the rivers were getting wider and wider, as the soil was displaced downstream, and beavers no longer were able to build dams. Basically, adding the one predator — wolves — had caused a massive shift in the balance that kept the Yellowstone ecosystem in harmony.

Shortly after the wolves were released back into the wild, the rivers changed. The erosion reversed. All because the wolves were keeping the deer population under control, and the beavers came back.

Probiotics are like wolves. They keep the other organisms in check. In the gut, certain bacteria (like the deer) are normal inhabitants of the gut, but if left unchecked, they can grow out of control and cause problems. For example, Lactobacillus plantarum, one of the important strains of bacteria found in raw, unpasteurized sauerkraut, is one of the wolves of the gut…keeping “deer-like bacteria” E. coli and Candida albicans under control.

Human Gut Ecosystem Comparison

Your gut is basically an ecosystem that functions symbiotically in much the same way as bigger ecosystems do.

You will never be able to fully see the magic that is happening inside your gut when you eat fermented food. But I’m going to do my best to help you appreciate the magic and wonder of it all this month. Through knowledge of the invisible world of bacteria in our food, Fermentationists learn to appreciate the magic of the relationships that humans have with microbes.

In part two of this series, I’ll break the fundamental rule of magic and pull back the curtain to let you see exactly how the trick is done. Next week, you will learn the benefits of fermentation, which ferments are best for you and which ones you might want to limit or avoid altogether. 

And if you can’t wait to start fermenting foods so you can improve your gut health, alongside the Happy Gut® Programs Dr. Pedre has put together to restore the gut microbiome and reverse leaky gut, then you can get started right away!

You can also learn more about The Fermentationist™ Certification Program to go to the next level when ready.

Edward Farnworth, the author of a book titled The Handbook of Fermented Functional Foods, put it best when he wrote that “Fermentation consists of the transformation of simple raw materials into a range of value-added products by utilizing the phenomena of the growth of microorganisms and their activities on various substrates. This means that knowledge of microorganisms is essential to understand the process of fermentation.”

How amazing we can take the process of food spoiling and use it to our advantage for its incredible health benefits! Stay tuned to learn more in the next blog post.

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