This article may contain affiliate links. This means, at no additional cost to you, we will earn a commission if you click through and make a purchase. This helps to cover our costs and keep this site going. Thanks!

Probiotics, prebiotics, antibiotics… there are a lot of “biotics” to keep track of. From fermented foods to supplements and medications, it comes down to one thing: bacteria. More specifically, the balance of bacteria inside our body.

We’ve all heard of antibiotics and have likely taken them to fight infections when we’re sick. Antibiotics accomplish their job by killing the bacteria in our bodies, including those that cause these infections and make us feel unwell.

The thing is, not all bacteria are bad and antibiotics don’t really discriminate.

In fact, there are countless strains of good bacteria that we absolutely depend on to stay healthy… and alive. That’s where probiotics and prebiotics come in. Fermented foods, certain fiber-rich foods, and supplements all help us to increase the quantity and diversity of these beneficial bacteria in our gut.

And there are plenty of good reasons to do that. Let’s dig in to find out why and how.

This article covers:

Balanced gut bacteria: the good vs. bad

Our body is host to trillions of bacteria and other microorganisms that are (as mentioned) both beneficial and detrimental to our health. Most of these bacteria (good and bad) reside in our gut. From our stomach all the way through our colon, there are tons of places for these microbes to take up residence.

As the innkeepers, so to speak, we can (to a large extent) decide who we want roaming the halls and who we ask to leave.  We do this through our diet and lifestyle choices.

For example, by smoking and eating a diet high in sugar or processed foods, we provide an environment that invites bad bacteria to stick around. By contrast, getting outside in the sun and away from our devices, moving our bodies regularly, and eating a healthy diet are all choices that support the kind of environment that entices friendly bacteria to live there instead.

The effects of a balanced gut

When we provide a healthy environment for our beneficial gut flora to thrive, things tend to stay pretty peaceful at the inn (our gut). As a result, we are more likely to enjoy restful sleep, fewer colds, higher energy, clear skin, satisfying poops, lower incidence of disease, and overall healthier wellbeing.

But when our gut is off-balance, meaning the unfriendly bacteria outnumber the friendly, well, that’s when the bar fights start to happen and folks get hurt! An unhealthy gut biome has been linked to a variety of conditions including fatigue, depression, acne, digestive issues, weight gain and obesity, inflammation, allergies, autoimmune disease, diabetes, and more.

Shifting the balance toward a healthy gut biome

One significant way in which we negatively affect the health of our gut is by eating a diet that is high in sugar and processed foods, while not eating enough fermented and plant-based foods. We can make the choice to skip the packaged goods and, instead, prepare our meals ourselves from ‘real food’ ingredients.

Beyond food, other strong contributors to an unhealthy gut (and, by extension, a weaker immune system) include smoking, chronic stress and anxiety, and antibiotics. While we can’t always control the stressors in our lives (e.g., a mean boss, mountains of debt, a sick child), we can engage in activities that help our body to better handle them. Yoga, meditation, and breathwork are common examples we hear about. But even just stealing some time for yourself can help. Go for a walk in nature, sit in the park, visit an art gallery, or spend quality time with friends and family.

Believe it or not, all these things can have a positive effect on your gut. It all helps because our gut is resilient. A healthy diet and lifestyle can shift the balance of good-to-bad flora back in our favor fairly quickly.

Gut biome benefits - walking outdoors

A few things we can do to bring our gut’s microflora back into balance:

Let’s dive a little deeper into the fermented (probiotic) foods to include in our daily diet, the prebiotic foods that feed these healthy bacteria, and what to look for in a quality probiotic supplement.

Eat These Fermented Foods Daily

Probiotics are live microorganisms that help to restore and maintain the balance of beneficial vs. harmful bacteria in the gut, keeping it healthy. Eating cultured (fermented) foods is an easy and delicious way to fill your gut with healthy bacteria and balance your microbiome. You’ll find probiotic foods in most health food stores and you can also make them pretty easily yourself.

Make it a goal to eat fermented foods regularly and help your gut biome to thrive. Here are some popular choices and what to look for when you’re buying them.


I eat so much sauerkraut, I’m practically turning into a cabbage. (You are what you eat, right?) I put it on my avocado toast at breakfast, over my salad at lunch, and on the side of whatever I’m eating for dinner. It’s just so good! I even bought a book (Ferment for Good: Ancient Foods for the Modern Gut) to learn how to make it myself. (I now make my own fermented pickles and kefir too! It’s crazy how easy it is.)

Homemade sauerkraut

One thing you should know when you’re buying sauerkraut is to always check the label to make sure what you’re getting is, in fact, probiotic — and unpasteurized. Most commercial supermarket brands will pasteurize their sauerkraut, which kills the beneficial bacteria. They may also add sugar, vinegar, and preservatives that we don’t want.

By contrast, the main ingredients in the beneficial (and OMG, so delicious) probiotic sauerkrauts are typically just cabbage and sea salt. Some brands may also throw in a few vegetables, such as carrots or onions, which is great. They also add some flavoring like caraway seeds or garlic. It’s all good.


A traditional Korean dish, kimchi’s main ingredient is often (though not always) cabbage, just like sauerkraut. It also tends to include more veggies such as carrots, radishes, onion, garlic, and ginger. But kimchi is usually spicy (sauerkraut traditionally isn’t ) and its brine is often made from fish sauce, instead of pure water and sea salt.

If you’re vegetarian or sensitive to fish, worry not. There are plenty of vegan versions as well.


Jun Kombucha by Wild Tonic
Jun Kombucha by Wild Tonic

Kombucha is a lightly carbonated drink fermented from black or green tea – not from mushrooms, as commonly believed. Why the widespread misconception?

An ingredient that is key to the fermentation process is yeast. And yeast is a distant cousin to mushrooms. Both yeast and mushrooms are fungi and it’s believed that this may be what prompted kombucha’s (wrongful) association with mushrooms. Some even refer to kombucha as “mushroom tea”. It is not.

All that to say, if you’ve been dismissing kombucha because you don’t like the taste of mushrooms, it neither contains nor tastes like mushrooms. And although it’s fermented from tea, it doesn’t taste much like tea either. Some folks think that pure kombucha (unflavored) tastes a bit medicinal, though I find that it tastes a bit like a tangy apple cider. If tangy isn’t your thing, you can easily buy or make it with honey or sweet fruits.

Do note that some brands pasteurize their kombucha. As mentioned earlier, pasteurization kills probiotics, so check the label to make sure it specifically says ‘unpasteurized’.

Also, please be aware that as kombucha brews, its sugars break down into alcohol and carbon dioxide. Home-brewed kombucha tends to have the highest alcohol content (as much as 4 or 5% by volume), while commercial brands usually have closer to 0.5%. You may see some brands labeled as “non-alcoholic”, which means it contains less than 0.5% alcohol… which may still be a concern if you wish to avoid alcohol altogether.


I looove miso. I make miso soup all the time, but it’s also amazing in salad dressings. To make the soup, just dissolve 1-Tbsp of miso paste in 1 to 2 cups of hot water, depending on whether you like it strong or mild. So simple.

Notice I said hot water and not boiling water. This is because boiling the water will kill the beneficial bacteria in the miso. I usually bring the water to an almost-boil before adding the miso — or a full boil, if I’m not paying attention. Either way, I’ll turn off the heat and let the water cool until it’s still hot, but not ‘kill the bacteria’ hot. (If you’d burn your mouth on it, it’s too hot.) Once it’s cooled a bit, THEN I add the miso paste.

I also use miso for full-on veggie soups, also adding the miso at the very end. There’s a little trick to adding the miso when you’ve got veggies in there. That’s because the miso paste doesn’t dissolve without a little help and if you just plop it into the veggie soup, you’ll end up with chunks of it. While the paste is delicious when it’s dispersed through a soup, it’s too salty and tart on its own.

Organic Fermented Miso

Here’s the trick to dissolving the miso in a veggie soup:

First, you have to make the soup. Toss the veggies into a soup pot, cover them with water, then bring it to an almost boil. Lower the heat and let the veggies simmer on low for about 20 minutes. Turn off the heat and let it cools a little, before adding the miso.

Dissolve the miso:

  • Throw the miso paste into a coffee mug.
  • Dip the mug into the hot soup water, trying not to capture too many veggies in the process.
  • Stir the miso to dissolve as much as you can in the mug.
  • Carefully pour only the liquid back into the soup.
  • Repeat this a couple of times until the paste is fully dissolved. (It only takes a minute or two.)

(Shout out to Christy Morgan, the Blissful & Fit Chef for teaching me that trick!)

Soy-Free Miso

Most miso is fermented from soy… and most soy in the U.S. is genetically modified. You can easily find soy-miso that is non-GMO at most health food stores. However, if you want to skip soy altogether, these same stores usually offer miso that has been fermented from barley, rice, or chickpeas. Just be sure to check the ingredients, because (oddly) some of these alternatives still include soy, even if they’re labeled ‘rice miso’.


For those who can tolerate dairy, kefir is similar to yogurt. But while yogurt is cultured bacteria, kefir also contains beneficial yeast. They end up tasting the same (at least, I think so), but kefir has a greater diversity of beneficial bacteria than yogurt. I eat kefir the same way I do yogurt: I mix it with fruit and sprinkle it with seeds (specifically, sprouted pumpkin and sunflower seeds, hemp seeds, and chia seeds).

Kefir can be made from either cow, sheep, or goat’s milk. The cow’s milk tends to have a thicker consistency, closer to yogurt, while the sheep and goat’s milk is quite a bit thinner.

Probiotic Kefir with Fruit

Many commercial kefir brands (and this goes double for yogurt) contain sugar and preservatives, so always check the label. Or consider making your own — it’s surprisingly fast and easy.

If you do buy kefir, check the label to also see that it’s made from unpasteurized milk, as (again) the pasteurization will kill the probiotics.

It’s also worth noting that while all kefir is probiotic, not all yogurt is. Further, many commercial yogurt brands often contain high fructose corn syrup and other unsavory ingredients, which you don’t want. So at the risk of sounding like a broken record… always check the label, check the label, check the label.

Making Your Own Kefir: starter kits vs. kefir grains

Kefir grains kind of look like tiny cauliflowers up close, but they’re actually a thriving colony of beneficial bacteria and yeast. A little goes a long way and you can encourage the grains to multiply over time. You can also buy large grains, to begin with, if you plan to make large kefir batches right out the gate.

Kefir grains

Starter kits, by contrast, typically come as small packets filled with a powdered version of the grains. Fermentation books will often tell you that using a starter kit for kefir is cheating. I don’t necessarily disagree, but if you’re a newbie, it’s a fantastic way to get started. That’s what I did! Once you’ve practiced a few times, you can graduate to fresh kefir grains. Or if you’re confident enough (it really is easy), just dive right in. The grains require a bit of care but are just as easy to use as the starter kit packets.

Good to know: The starter kits can only make a few batches per packet, so you’ll have to buy a new kit every so often. By contrast, you only have to buy the kefir grains once and then you can use them indefinitely. And as I mentioned earlier, you can even nurture the grains so that they multiply. This way, you can share them with friends or make larger batches.

Coconut kefir

Coconut kefir is a dairy-free alternative to milk-based kefir. The coconut version has some of the same bacteria as regular kefir, but with fewer probiotic strains. Kefir recipes are just a Google or Amazon search away, so you can make them pretty easily at home. Or if you buy it, look for brands that do not contain added sugar or preservatives and do contain beneficial probiotic strains.

Note: You can use the milk kefir grains to make coconut kefir, but the grains won’t really feed on the coconut the way they will the milk. That means, you’ll have to make milk-based kefir every few rounds; otherwise, the bacteria in your kefir grains will starve and die. (Interesting, right?)

Probiotic Coconut Kefir


Kvass is a drink fermented from barley or rye and it is definitely an acquired taste. I can barely handle the smell, but I’ve met people who swear by its benefits and by the fact that it’s “not so bad once you get used to it.

I’m trying, I really am.

Those sensitive to grains can also find kvass fermented from carrots, beets, or other root veggies. I haven’t tried veggie kvass yet, but I’m guessing you may not need to hold your nose quite as tightly to take a shot of it.

Fermented Kvass
Mr.Icon (Mricon) [CC BY-SA 3.0 (]

Probiotic Supplements

In addition to fermented foods, you can also get your probiotics from a supplement.

You’ll often see probiotic brands bragging about how many strains they include in their product. They’ll say things like “most other brands use only 5 or 6 strains, but we have over a dozen!“. As is often the case, this ‘more is better’ mentality misses some very key points.

Bacteria strains: quality over quantity

When it comes to probiotics, it’s the quality of the strains that count, as well as how well the strains interact with each other (vs. compete with each other) in the gut. So having billions of bacteria across a dozen strains can be great. Or not. It depends on the strains.

Think about this: If those bacteria are not strong and healthy, or they have not been properly fermented, or the quality of how they are manufactured has otherwise been compromised, or the strains compete with each other, then they are not going to support your gut in the way you need them to. Strains and quality matter.

It’s worth noting that whether a probiotic requires refrigeration is not a determining factor of its quality. Many high-quality brands can be found on the shelf in the non-refrigerated section of the supplements aisle.

Overdosing on probiotics

Apparently, you cannot overdose on probiotics. However, you can experience some uncomfortable symptoms if you take too much, as well as when you’re just starting out. People typically report temporary reactions such as gas, bloating, diarrhea, constipation, headaches, acne breakout, and/or a rash.

These side effects, unpleasant as they may be, are often a sign that the probiotics are starting to work. The good bacteria are overtaking the bad bacteria and the battle can be a bit intense at first.

If the symptoms are mildly uncomfortable, the recommendation is typically to ride it out. If they last longer than a couple of weeks or are too uncomfortable, the advice I’ve seen says to lower the dosage until your gut acclimates, then slowly increase until you reach the recommended dosage.


Prebiotics are a type of soluble fiber that passes through our digestive system without being digested. The undigested fiber ends up in our colon, where it becomes food for our beneficial microflora. In other words, the beneficial bacteria we add to our gut, whether through food or supplementation, are probiotics. The fibers that feed and nourish those probiotics are prebiotics.

Prebiotic fibers are found in vegetables (usually raw) such as chicory root, garlic, onions, leeks, dandelion greens, jicama, asparagus, and Jerusalem artichokes, which are also known as sunchokes… or lovingly referred to as ‘fartichokes’ thanks to their high fiber content. 😉

Prebiotic Garlic

Prebiotics are also found in psyllium husk, in whole grains such as wheat, corn, and barley, in under-ripened bananas and plantains, prunes (dried plums), the skin of apples, and in yacon syrup.

Depending on your diet, you may get enough prebiotics from food. But you can also supplement to promote even stronger gut health.

Good to know

Fermented foods often contain both prebiotic fibers and a variety of probiotic strains. Some supplements, such as Dr. Ohhira and Dr. Mercola also have both prebiotics and probiotics, so you don’t have to buy them separately.

Your gut will thank you

As you make these changes to your diet, remember that your body may take a little while to adjust. It can get a little chaotic at first, so start gently and give your friendly bacteria the time it needs to establish some law and order. And while you’re waiting, make yourself a batch of sauerkraut — I’m telling you, it’s addictive.

[accordions] [accordion title=”Research” load=”hide”]


Comments are closed.