6 Foods That Feed The Gut Microbiome

Microbiome Kate Chury RD calgary.jpg

There has been a lot of talk about the bacteria and microbes in our gut (or colon) lately. The study of the gut environment which contains all these microscopic organisms (called the gut microbiome) is an emerging science but is still in its infancy. There is so much that we don’t know about it. However, some of the things we do know are encouraging enough that we can pretty confidently say that having a healthy mix of microbes in our gut is a factor of good health.

Some of the things we do know (or sort of know) about the gut microbiome are:

  • There are more bacteria in (and on) our body than cells in our body. Some estimates are around 40-100 trillion microbes living in/on our body!

  • There are thousands of different types of microbes living in your gut.

  • A greater diversity (i.e. the more different types) of bacteria and microbes in our gut is associated with better health.

  • Some bacteria and microbes in our gut are friendlier than others (i.e. there are “good guys” and “bad guys”).

  • Our gut microbiome is dynamic. It changes with time. It can be influenced by things like stress, dietary changes and medications.

  • Our microbiome may influence our blood sugar levels.

  • It may influence our mental health.

  • Changes in the gut microbiome have been found in both irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD).

  • The gut microbiome is involved with the metabolism of neurotransmitters, such as serotonin.

  • Certain microbes may be able to influence our blood lipid (or cholesterol) levels.

  • Everyone’s microbiome is different.

There is honestly so much research into the gut microbiome that it can’t be covered in a simple bulleted list or even one article. Scientists are learning more and more each day but are still pretty far from having a complete understanding of it. One thing that is certain is that a healthy gut environment does play a role (somehow) in maintaining optimal health. Since there are so many different microbes that populate the gut (or could potentially populate the gut), it’s hard to know exactly which ones or in which combinations we need to maintain or improve our health. While there are still plenty of pieces of the puzzle that we don’t know, we do have some idea of what we can do to create a more beneficial gut environment. The most obvious thing that you and I can do it is to feed our gut foods which cause these beneficial microbes to thrive.

The following are 6 foods that help create a happy gut environment:  

My Post (2).jpg

Leafy greens, such as spinach, kale, Swiss chard, arugula, and collard greens are not only a great source of nutrients like folate, magnesium, potassium, and vitamin K but it turns out that they also may play a special role in maintaining our beneficial gut bacteria. Leafy greens contain a particular type of sugar molecule (called sulfoquinovose, or SQ for short) which has been found not only to feed the good bacteria but also limit growth of bad bacteria.


Many dark blue, red and purple fruits and veggies (think berries, beets and red cabbage) contain a special kind of molecule called anthocyanin. Not only does anthocyanin provide a beautiful hue to these fruits and vegetables, it likely is used by the gut bacteria to decrease inflammation and to positively influence microbe growth. While more research is still needed in this area, it does appear that eating those gorgeous blue, red and purple fruits and veggies is a great thing to do for your gut!  

prebiotic micro.jpg

Prebio-what? If you’re like many people, the word prebiotic doesn’t mean much. In very simple terms, prebiotic fibers are the foods which feed the microbes in our gut. Just like you or me, microbes need to eat for energy. That’s where prebiotic fibers come in.

Like all fiber, prebiotic fibers are not able to be broken down by the human digestive tract. The same is not true for the microbes in our colon as they can utilize these prebiotic fibers by fermenting them.

So, what kind of foods contain these prebiotic fibers? In general, plant foods (because remember fiber only comes from plants). More specifically, here’s a list of some foods rich in these prebiotic fibers (this is a just a short list, many fruit and vegetables not listed here also contain prebiotics):

  • Jerusalem Artichoke/Sunchoke

  • Asparagus

  • Garlic

  • Onions

  • Leeks

  • Apples

  • Jicama

  • Dandelion greens

  • Potatoes and rice (especially when cooked and cooled)

  • Wheat

  • Barley

  • Legumes/beans

  • Cashews

  • Pistachios

What to learn more about prebiotics? Check out this article Probiotics vs. Prebiotics: What’s the difference?

A note for those with IBS - If you noticed that a lot of the above listed foods are those rich in FODMAPs, you are correct. Many FODMAPs do act as prebiotics. This is why it is not recommended to stay on the low FODMAP diet long term. Long term avoidance of FODMAP containing foods results in changes to the gut microbiome. If you have been on the Low FODMAP diet for greater than 6-8 weeks, it is likely time to start the reintroduction (re-challenge phase). If you need some assistance with this step, contact a Registered Dietitian with experience in the Low FODMAP Diet. If you’d like to learn more about the Low FODMAP diet, check out my post: What the FODMAP is a FODMAP?

fermented microb.jpg

While the prebiotic foods provide nourishment for the bacteria and other microbes in our gut, fermented foods actually contain the beneficial organisms (called probiotics) that populate our gut. At first thought, eating microbes might not seem appealing but it is actually quite common. In fact, you’ve probably already been consuming food products that have used bacterial fermentation in their production - like yogurt. Consuming foods with these bacterial cultures can help populate your colon with the same beneficial microbes. The follow foods contact some probiotics:

  • Yogurt (look for active bacterial cultures on the ingredient list)

  • Kefir

  • Sauerkraut (non-pasteurized/must be stored in fridge)

  • Miso

  • Tempeh

  • Kimchi

  • Kombucha

  • Homemade pickles (lactic acid fermented pickles)

  • Homemade fermented vegetables


This one isn’t exactly a single type of food that benefits your gut microbiome but it still deserves some attention. Research shows that consuming a variety of plant based foods is associated with a more favourable profile of microbes in your gut. In simple terms, the more different types plant foods you consume the better. Data from the American Gut Project (that studied over 15,000 stool samples from 11,336 people) found that those eating the more than 30 different plants (fruits, veggies, grains, nuts, legumes, etc) each week had a greater diversity of microbes in their gut than those eating less 10.

Now, eating 30 different plant foods does sound like a lot but it is a worthy goal to work towards, isn’t it? Perhaps grab a pen and paper and list out all the different plant foods you’ve had over that last week or so, you may actually be surprised how many you do consume. If 30 different plant-based foods sounds like a challenge, why not start at trying to get above 10, or even 15. The point here is that the more diverse your diet, in terms of plant foods, the better off your gut environment will be.

You may also be wondering if this means that you have to be on a plant-based (i.e. vegetarian or vegan) diet to see benefits to your gut environment. Not exactly. What this means is that a “high plant diet” (plus or minus meat) is needed to create a healthy gut environment.


Whenever I come across a potential health benefit of eating chocolate, I feel like it’s my duty to report back to you. Not like you need an excuse to enjoy chocolate, but it sure is nice to know that it might have some health benefits, right?

A small study (i.e. more research still needed) found that a particular type of compound in chocolate (called flavanol) is fermented by the gut bacteria. As a result of consuming these cocoa derived flavanols for 4 weeks, subjects showed an increase in friendly gut bacteria, as well as, lower inflammatory markers.

Your best bet, if you want to capitalize on the potential benefits of chocolate, is to choose a fairly high percentage dark chocolate (maybe 70% or higher). This way you’ll get a higher amount of cocoa and less sugar.

As mentioned above, our knowledge of the gut microbiome is still in its infancy. It’s very likely that we have only uncovered a small fraction of what we need to know about its role in human health. So, while we patiently wait for more info to come, one thing we can do is feed ourselves in a way that also benefits those important microbes in our gut.