All Disease Begins in the Gut

Hippocrates. He was a pretty smart guy who said some pretty interesting things for his time. A couple thousand years ago he was considered to be the “Father of Western Medicine”. He was the first person to acknowledge that perhaps diseases were not caused by god, superstition, or religion, but rather by environmental factors, diet, and living habits. Boom! Smart man! So when he was quoted saying that “All diseases begin in the gut” it really made people think twice. And only now, 2,000 years later, are we really starting to get it. We’re starting to realize that having an unhealthy gut contributes greatly to a myriad of many different diseases.

                                        Nature itself                                        

When we talk about having an unhealthy gut, this can mean a lot of things. Autoimmunity disease rates are going through the roof and we’re starting to realize that with every autoimmune condition lies a deeper problem of gut health, usually including intestinal permeability (“leaky gut”). This is because when your gut flora is impaired you become inflamed, which leads to autoimmunity (and vice versa). 80% of your immune system is located in the gut, which makes addressing gut issues a critical first step on working on any autoimmune disease. Other gut issues such as IBS, SIBO, parasites, hypochlorhydria, food allergies, and general gut dysbiosis (constipation, bloating, gas, etc) are all too common as well. Within having an unhealthy gut lies much more potential for issues such as obesity, diabetes, acne and other skin issues, and even depression.

hippocrates food medicine

Unfortunately, in today’s modern world it’s more the norm to have an unhealthy gut than it is to have a healthy gut. There are just too many ways our beneficial gut flora are constantly being killed. We know that antibiotics kill both the bad and the good gut bacteria, but we’re now starting to learn that perhaps it’s much more difficult to gain back the good bacteria after their use than we thought. Other common medications such as birth control pills and NSAIDs contribute to unhealthy gut flora, as does the Standard American Diet that many of us are used to. Dietary contributors are primarily sugar, refined carbohydrates, processed foods, and industrial seed oils. Knowing these triggers for killing the beneficial bacteria may help you make more informed choice about using them.

When I was in school studying to be a Nutritional Therapist Practitioner, I learned about the importance is maintaining the ratio of about 85% good bacteria and 15% the bad. Usually this means we should always be focused on inoculating our guts with more good bacteria- in this day and age, it’s hard to have too much of the good. There are three different types or microbes of bacteria: Bacteriocides, Prevotella, Ruminococcus. There are many different brands and types of probiotic supplements available today, all with varying ratios of microbes. While taking a probiotic supplement is a good idea for someone who has no interest in eating fermented foods, it doesn’t have the same benefit as fermented foods, since there is a much wider range of different bacteria found in lacto-fermented foods. One day in class, a local fermented foods company called Firefly Kitchens came in to talk to us about fermentation, what they do, and how we can easily do it too. We had learned all the details about why having beneficial bacteria is necessary for good gut health, and we were ready to learn the how.

I came into that talk open minded as always, but wasn’t expecting it to make as much of a lasting impression on me as it did. At the time, I hadn’t had much of a history with eating fermented foods, and from whatever experiences I did have, I wasn’t too thrilled to create more. The thought of fermented foods made me uneasy, but after learning about their importance, I was willing to give them another chance. Firefly Kitchens had brought samples of all their different sauerkrauts, and based off their flavor suggestion I tried the Yin Yang carrots first. I was honestly impressed! It tasted like sweet, gingery carrots. I got brave and tried a few other types. Even the more traditional sauerkraut flavors were not as bad as I was expecting. While that probably doesn’t sound like the most amazing review ever, it led me to where I am today, which is a true fermenting machine- so I am grateful for my first real experience with fermented foods. Within a couple months of that class day, I was vigorously chopping tons of different types of vegetables and experimenting with various herbs and seasoning. It’s so easy to create your own various fermented concoctions! The top of my kitchen cabinets turned into a rainbow of mason jars.

Cultured and fermented foods have traditionally been made all around the world. Kefir from the Middle East, Natto from Japan, Tempeh from Indonesia, Kimchi from Korea, the popular Sauerkraut from Germany, and of course- even beer. The basic traditional reason for fermenting makes complete sense- many years ago, most cultures did not have access to a plethora of different vegetables throughout the year. They ate what was in season where they lived. The introduction of grocery stores and international produce shipping is relatively new phenomenon, so when people wanted to make use of what was plentiful and in season, they would ferment it to have for later. From a health beneficial stand point, it also makes great sense. Fermenting produces enzymes that make the food easier to digest- this is why I recommend soaking and sprouting nuts and grains. It also brings out and heightens the nutrition already available in the vegetables. You may have heard me mention before that beets are highly nutritious- once you ferment them, their nutrients are out of this world! Those enzymes also make the nutrients tastier, something that takes some getting used to for many people who have lost touch with the natural zestiness of fermented foods.

My go-to sauerkraut recipe is from Diane Sanfilippo’s book Practical Paleo. It’s easy and fun to make, and at the rate we go through fermented veggies these days, it saves us a ton of grocery money each month. I’ve been making kombucha regularly for months now, and feel wildly successful every time a new batch is ready and my husband takes his first sip with a big grin on his face. Recently, I made a few new fermented foods (shown below)- beet kvass, fermented radishes, sweet pickle relish (from “Fermented” by Jill Ciciarelli) and perhaps my new favorite, sprout kraut. The sprout kraut is the only one that is ready and it is going fast.

lots of ferments3 fermentssprout kraut pre fermentsprout kraut

I’m still a beginner at fermenting but can’t wait to create more wonderful, nourishing, gut healthy concoctions. Please share your favorite recipes and fermenting tips!


  1. Devyn

    Emily, what do you use for weights when fermenting in mason jars? The couple times I tried Diane’s recipes for long fermenting (as opposed to Sally Fallon’s recipes which only take a couple days), my jars just went moldy– even with the little weight contraptions I used to keep everything below water-level. Your jars looks beautiful and I would love to give fermenting another go!

    • Emily

      Hey Devyn,
      Have you tried putting a cabbage leaf on top of your fermenting veggies to act as a barrier between them and the air? I use that on ferments other than sauerkraut as well. When it’s done fermenting you just remove the leaf (gets the mold) and hopefully the veggies under it were kept submerged and are all fine.

  2. Gayle

    Emily- you’ve inspired me to get fermenting again and also to try some different vegetables in addition to my favorite tried and true sauerkraut. Your jars are beautiful! Good job.

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  6. Jeanne


    Zack is a fermenting machine. Sauerkraut beer kimchi. You name it he ferments it. I didn’t realize how beneficial it is. How does yogurt fit in this picture. Btw. Love your blog. I often link to it through face book. Does this post get me linked in directly?

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