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Fermentation: tend your microbial “garden” for better health

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In this fermentation article, we’re going to try to take a complex subject and boil it down into something accessible and useful. We hope our efforts translate into you learning something interesting and inspire you to incorporate fermented foods and beverages into your diet!

You are a microbial garden — and that’s a good thing 

Living things are complex. There was a time when human beings were thought of as single, solitary beings. Bacteria and all those other critters only visible under a microscope were gross, and if we wanted to be healthy, we needed to live in sterile, sanitized environments and eat sterile, sanitized foods.

Then various fields of science started to notice that we’re actually covered, inside and out, with a massive complexity of microbial lifeforms. In fact, for every human cell in your body, there are about 1.3 microbial cells. Yes, you’re outnumbered.

What are all these organisms and what do they do? Thankfully, there are very smart people with very advanced computational equipment who are devoting their lives to figuring out the answers to these questions. And what they’ve already found out is beyond amazing…

Gut biota: the garden of life inside your GI tract

You probably know that your immune system is your body’s defense system: the thing that keeps you from getting sick/infected and helps you recover when you are sick/infected. But where and what is the immune system? In your mind, can you picture your immune system like you can a heart or a brain?

No. The reason why is that your immune system is distributed, not centralized; layered, not single-function. And it’s not just your immune system – you’ve got help.

Neutrophil with anthrax.jpg

Roar! A neutrocyte (a type of white blood cell) engulfing anthrax bacteria. CC BY-SA 3.0, Link

Even though your immune system is distributed, about 70% of it is found in your gastrointestinal (GI) tract. Given this high percentage, you might guess that what happens in your GI tract is rather important to your health and wellness. You’d be right.

The GI tract also happens to be home to the highest density of microorganisms in your body. If you’re healthy, there may be 100 trillion microbial cells and upwards of 1,000 different species of bacteria in your gut microbiome (collectively weighing about 2-3 pounds).

Are they good or bad? If your gut ecosystem is in equilibrium, the percentages should be about 85% good microbes to 15% “other” (which means either benign or bad). An interesting side note, this is the same ratio of beneficial insects to pest/benign insects in an healthy outdoor ecosystem (perhaps an emergent biological pattern?).   

Florida predatory stinkbut eating Harlequin bug

A Florida predatory stinkbug (“good” insect) eating a Harlequin bug (“bad” insect) at Tyrant Farms.

What are all those microbes doing in our GI tract? For starters, without your microbes, you couldn’t fend off pathogens, produce antibodies, or even access much of the nutrition in your food.

As Lita Proctor, Ph.D., the Human Microbiome Project’s program manager at the National Human Genome Research Institute says,

“Humans don’t have all the enzymes we need to digest our own diet… Microbes in the gut break down many of the proteins, lipids and carbohydrates in our diet into nutrients that we can then absorb. Moreover, the microbes produce beneficial compounds, like vitamins and anti-inflammatories that our genome cannot produce.”

The brain in your gut

Another recent and rather revolutionary finding is the “brain in your gut,” aka the enteric nervous system (ENS). As it turns out, what you eat – and what you feed to the microorganisms that digest your food for you – has a profound impact on your mood, health, and the way you think.

No, the brain in your gut doesn’t do math calculations or plan your garden, but it does communicate with the brain in your head via your central nervous system (CNS). Interestingly, the conversation is somewhat one-directional, since 90% of the fibers in the vagus nerve (the nerve that connects your gut brain to your head brain) carry information from your gut to your brain, but not the other way around.

Now, given the fact that the microbes in your gut make neuroactive compounds that your head brain uses to communicate and regulate mood (serotonin, norepinephrine, dopamine), how might various compositional changes in your gut flora impact your state of mind?

One tantalizing result: scientists recently inoculated the guts of healthy mice with bacteria from depressed human beings. The result? The previously healthy mice began showing signs of depression and anxiety. But when the vagus nerve was snipped, thus cutting off communication between gut and brain, the bacteria no longer had an impact on the mice’s behavior. Woah.

How might your diet and microbes be impacting your thoughts and behavior?

Bad news then good news

If you’re reading this article, it means there’s a high likelihood that you eat the “Western diet” characterized by lots of refined sugar, highly processed starches, and “bad” fats. It also means you have high levels of synthetic pesticide residue in/on your food.

If you’re looking for a perfect recipe to be overweight, sick, diseased, and reliant on increasingly expensive healthcare to stay functional/alive, then the Western diet is a good match.

Fast food 01 ebru.jpg

It’s truly a mystery as to why everyone is sick and overweight… Burger and fries photo by ebruFlickr, CC BY 2.0, Link

The Western diet has also wreaked havoc on the non-human part of you: especially, your gut microbiota. Research has shown that the Western diet starves or kills many of the species of good bacteria you need for optimal health while encouraging the bad microbes to over-proliferate.

Improve your microbial garden and your microbial garden can improve you

The good news is that by learning about these problems and how to fix them, you can start choosing what you feed to your gut microbes more wisely. When you do, you might be shocked at the difference it makes in how often you get sick, how you feel, your mood, your mental clarity, energy levels, etc..

Perhaps the single best way to quickly and dramatically improve the quantity and diversity of beneficial bacteria in your gut flora is to consume high quality fermented foods/beverages.   

veggies for sauerkraut - probiotics

Cool season, organic garden veggies chopped and ready to be made into sauerkraut. Sauerkraut is one of the best fermented probiotics available. There are hundreds of delicious fermented foods and beverages you can make at home, and we highly recommend getting The Art of Fermentation by Sandor Katz to learn how..

As a study published in the Journal of Physiological Anthropology concluded:

…we argue that the consumption of fermented foods may be particularly relevant to the emerging research linking traditional dietary practices and positive mental health. The extent to which traditional dietary items may mitigate inflammation and oxidative stress may be controlled, at least to some degree, by microbiota. It is our contention that properly controlled fermentation may often amplify the specific nutrient and phytochemical content of foods, the ultimate value of which may associated with mental health; furthermore, we also argue that the microbes (for example, Lactobacillus and Bifidobacteria species) associated with fermented foods may also influence brain health via direct and indirect pathways.

Susan’s (as in Susan The Tyrant) sister is Dr. Lisa Durette, MD, DFAPA, a Board Certified Child and Adolescent Psychiatrist, and the Medical Director at Healthy Minds in Las Vegas, NV. This topic area is of particular interest to her as well, so we thought we’d add her statement:

“The American Psychiatric Association recognizes the connection between mood and food. Several researchers conducted symposia at the 2014 annual meeting highlighting the evidence between psychiatric illness severity and diet. In my own practice, I have found the benefit of discussing daily diet with my patients-and the benefits from dietary changes on mood. For example, eliminating frequent fast food consumption as well as cola, and the addition of probiotic rich fermented foods, has led to reduction in anxiety symptoms in some of my patients more so than medication intervention.”

What Is Fermentation?

Simply put, fermentation is the chemical breakdown of a given substance by bacteria, yeasts, or other microorganisms.

Fermentation is not a new hipster discovery, and you don’t need a beard or skinny jeans to enjoy fermented foods/beverages.

In fact, humans were “intentionally” fermenting their food at least as far back as 10,000 years ago. Archaeologist unearthing the Neolithic village of Jiahu in Henan province in China found that a mixed fermented beverage made of rice, honey, and fruit was being produced and consumed there.

Long before that, our pre-agricultural ancestors were likely to have benefited from “unintentional” fermentation in various wild fruits, veggies, and honey. A funny non-human example of this is animals in South Africa getting drunk off of fermented marula fruit (see video below):


Types of Fermentation

The intentional fermentation techniques that human civilizations around the world have developed can generally be categorized as follows:

  1. textured vegetable protein / example: tempe
  2. high salt amino acid-rich sauces / example: soy sauce
  3. lactic acid fermentation / examples: sauerkraut, cucumber pickles, olives, yogurt, milk kefir
  4. alcoholic fermentation / examples: wine and beer
  5. acetic acid & vinegar fermentation / example: apple cider vinegar, kombucha
  6. alkaline fermentation / example: Japanese natto
  7. leavened breads / example: sourdough bread

There are some types of fermented foods/beverages that fall into multiple categories. One thing that all fermented foods/beverages have in common is that they are “probiotics.” Some are also “prebiotics.”

Fermentation. One of our favorite summer beverages is tepache, aka Mexican pineapple beer. We make it from the skins of our homegrown pineapples and our neighbor's honey - it's delicious, slightly alcoholic, and very pleasing to our gut flora (so they tell us).

One of our favorite summer beverages is tepache, aka Mexican pineapple beer. We make it from the skins of our homegrown pineapples and our neighbor’s honey – it’s delicious, slightly alcoholic, and very pleasing to our gut flora (so they tell us).

Probiotics and Prebiotics: What’s the Difference?

  • Probiotics already have beneficial microorganisms in them, usually beneficial bacteria. Think of probiotics as an “inoculant” you can use to help establish and maintain colonies of beneficial bacteria in your digestive system.
  • Prebiotics are relatively sterile fibrous carbohydrates that your body can’t digest, but help feed the beneficial microorganisms already in your gut. For example, fiber found in whole foods (whole grains, veggie & fruit skins) are excellent at feeding/promoting the beneficial bacteria already in your gut.
Whole foods like this anthocyanin-rich napa are great building blocks for kimchi, which is amazing for your gut health.

Whole foods like this anthocyanin-rich napa are great building blocks for kimchi, which is amazing for your gut health.

7 recommendations for improving your gut flora (and health)

Now that you know a bit more about the link between the health of the microbial communities in your gut and your own health plus the benefits of fermented foods/beverages, we’d like to leave you with these seven tips:

1. Eat a diversity of homemade fermented foods/beverages.

Nope, this doesn’t mean go buy a bunch of unregulated pills which claim to have probiotics and prebiotics in them. Make or buy actual living fermented foods or beverages. Sauerkraut, kimchi, pickled daikons, kombucha, tempeh… just to name a few.

Consuming a diversity of fermented foods and beverages ensures you’re getting quality fermented products with high beneficial bacteria and yeast counts, and you’re introducing a diversity of different species of beneficial microorganisms. Just as in a forest or other ecosystem, biodiversity in your gut flora is a good thing.

2. Learn to make fermented foods/drinks that you and your family enjoy.

Yes, food is medicine, but it shouldn’t taste like medicine. We LOVE the way our ferments taste, not just the way they make us feel.

There are thousands of fermented goodies you can make. The best book we know of to teach you how-to’s and useful recipes is The Art of Fermentation by Sandor Katz. And for Pete’s sake, get a good German crock pot, which will more than pay for itself after a few batches of sauerkraut.

Some of our favorite fermented recipes we’ve published on Tyrant Farms:

3. Eat prebiotics in your diet.

Eat whole foods, not refined/processed foods. Basically, picture a fast food “value meal” – yeah, don’t eat any of that stuff.

Meals made with whole grains, tubers, fruits, veggies, herbs, roots – these foods help feed the beneficial microorganisms in your GI tract. Conversely, processed foods encourage pathogenic microorganisms which directly impact how you think & feel, and your body’s ability to fight microorganisms that cause sickness and disease.

Since the most commonly consumed processed food in the US is white bread, here’s a 5 minute whole wheat artisanal bread recipe that will rock your world (and thrill your beneficial gut microbes).

4. Use organic foods in your fermented products (and non-fermented products).

The American Academy of Pediatrics noted that by switching to organic diets, children were shown to drastically decrease the amount of pesticides in their urine. We’re not sure if there is much research out there as to how various types of neonicotinoid, pyrethroid, and organophosphate pesticides that are commonly found in conventional foods (but not allowed in organic production) might impact your gut flora, but our guess is the answer is not good, especially for babies/children undergoing rapid development (and microbiome development).

So, if at all possible, switch to organic foods.

5. No more sodas, diet or otherwise.

As you probably know, regularly drinking sugar water isn’t great for your health, so we won’t bother to go into the reasons why here. What you may not know is that drinking diet soda probably isn’t any better.

It appears that the artificial sweeteners in diet soda alter your gut microbiota such that you may end up with: 1) increased intestinal permeability, and 2) glucose intolerance (e.g. higher than normal blood glucose levels).

This may explain why people who regularly drink diet sodas actually put on weight without increasing their caloric intake. (More on the topic of diet sodas.))

6. Only use antibiotics if absolutely necessary.

Got a cold or flu? Truly sorry about that. But antibiotics can’t do a thing about it – they kill bacteria, not viruses.

If you take antibiotics every time you get sick, you’re simply increasing the odds that your body becomes a breeding factory for antibiotic-resistant pathogenic bacteria, aka superbugs. Instead, let your body heal and inform your immunological memory, allowing it to better fight off bugs in the future.

If you want to reduce the severity and duration of your cold or flu, get some high quality elderberry syrup.

7. Expecting a baby? Plan for vaginal birth & breast feeding.

When/how does your microbiome form? As it turns out, having a vaginal birth inoculates your baby with a range of important beneficial bacteria that immediately inform/charge up its immune system. 

Studies are conclusively showing that people who were born via c-section have an elevated lifetime risk of various metabolic and immune diseases, so if at all possible have a vaginal birth… or take these measures if you have to have a c-section.

The same thing is true with the living milk that your body produces for your baby. Breastfeeding is a beautiful, essential step to ensuring your baby has optimal health – don’t let anyone shame you into thinking or doing otherwise.

Now go forth, ferment, and nurture your microbial gardens! The human parts of your body will be well-served for your efforts.


Fermentation: how to tend your microbial garden for better health. #microbiome #guthealth #probiotics #prebiotics #tyrantfarms

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