Study: Nutrigenomics far outperforms Keto for weight loss.
Last updated on

Probiotics aren’t the only way to restore healthy gut bacteria

Ahh, the microbiome.

That mystery world of gut bacteria that helps us do everything from digest food, to regulate mood.

We’ve all read about its importance, and some of us have even had the DNA of the little critters colonizing our guts sequenced with services like uBiome.

However, we’re just scratching the surface of the myriad different ways gut health impacts overall health.

But, this much we know: diet and lifestyle can cause the balance of our intestinal flora to go out of whack, which can lead to nasty conditions like IBS.

This is why our healthy gut bacteria and probiotics are so important, they keep the system in balance. Species of bacteria like Lactobacillus Acidophilus (notice the word acid in the name) play a role in regulating the PH of our stomach, preventing the spread of bad guys like Candida.

But, probiotics aren’t the only way to rebuild healthy gut bacteria after a course of antibiotics, or a few months of bad food choices.

Below, I’ve listed some unconventional strategies for rebuilding a healthy gut.

11 ways to restore healthy gut bacteria

#1 – Go for a run

Studies have shown that aerobic exercise actually increases our microbial diversity, meaning going for a 20 minute jog every morning can actually go a long way to helping the good bacteria in your gut take back the wheel. For example, this study found that higher levels of cardiorespiratory fitness (measured by max VO2 levels) were associated with greater microbial diversity.


It appears that getting in good shape with some cardio training allows the body to better metabolize fatty acids. To quote the study:

The microbial profiles of fit individuals favor the production of butyrate.

Hmm, so the technical explanation of how running rebuilds the gut is that being in better cardiovascular shape increases our levels of butyrate, a short chain fatty acid that is associated with improved gut health. Butyrate is made when we eat fiber rich food that ferments in the gut. It appears running, and other forms of cardiovascular training, aid in this process, helping to create more butyrate, which in turn protects the gut lining from conditions like leaky gut.

#2 – Get your hands dirty

Some of you may have heard of Prescript Assist, a “soil based” probiotic that is now out of business that was all the rage in the functional medicine world. However, we may not need a soil based probiotic if we can get our hands dirty in the backyard. Sometimes health conversations become so focused on supplements that we forget about common sense. Go outside and work in your garden. Getting your hands dirty will expose your system to new, healthy bacteria. There is some controversy around soil based probiotic supplements, but one strain of bacteria commonly found in the dirt, Mycobacterium vaccae, has been linked with improved mood and stress response in some studies.

Getting out in the sunshine and regularly getting your hands dirty is an easy way to get exposure to soil based bacteria without the need for a mega dose probiotic supplement that could be dangerous for some people, especially those with immune system issues.

#3 – Get a dog

Dogs? Yes, dogs.

File this under the same category as getting your hands dirty in the garden. Dogs, like humans, have their own microbiome, and studies show that when we live with our pups, some of that good bacteria rubs off.

Of course, restoring gut health shouldn’t be the primary reason for getting a dog, as the current owner of an 8 week old puppy, believe me, it’s a lot of work. But there is research that shows that dogs can be beneficial to our health in many ways, one of which is improved gut health.

Note for you parents out there: the impact seems to be especially beneficial for children.1

For more, check out this NY Times piece: Are Pets the New Probiotic?

#4 – Limit traditional soap and shampoo

Wait, what? Did this crazy guy say to stop using soap and shampoo? Well, not altogether, I still use soap to wash my hands. But for the last few weeks, I’ve been moving away from soap and towards a product called Mother Dirt. I met the founder at a conference in Brooklyn last summer and was impressed. She created a line of skin care products that help us keep clean without stripping our skin of the natural bacteria it is supposed to have. No affiliate links to Mother Dirt anywhere in this post or site, I just think it’s an interesting concept, even if the science is still somewhat new.2

#5  – Eat fermented food and fermentable food

This one probably isn’t new to most of you. Fermented food, like sauerkraut for example, contains living strains of bacteria that can populate your gut. In some cases, these strains are said to be histamine producing, like L. casei for example, and may need to be avoided if you have histamine issues, but in many people fermented foods can be beneficial.

Point is, as we often mention here at Gene Food, to watch your individual reaction to food and supplements rather than relying on the wisdom of the internet, your body will tell you if sauerkraut or kimchi sits well.

If you’re looking for genetic markers that could clue you in on histamine sensitivity, take a peek at the AOC1 gene.

Now on to fermentable food. This one is controversial, because not all people can digest this stuff. You may have heard of the low FODMAP diet. FODMAP stands for Fermentable Oligo-, Di-, Mono-saccharides And Polyols, basically a group of carbs that are tough to digest and absorb.

Some people thrive on a low FODMAP diet which excludes things like potatoes, apples, garlic, onions, bananas, beets, asparagus and more. However, here is the rub: as I pointed out in the butyrate discussion above, our colon needs some fermentable food to feed and grow the “good” gut bacteria. A diet with very little fiber will make it harder to rebuild the gut over the long term. The key is to understand what types of fiber your body can handle. And please do not interpret this as discounting the need to for many to go low carb to heal (see #6, below). I fully appreciate that some people need to significantly limit certain types of carbohydrates to beat back conditions like Candida. My point is only that zero carb, zero fiber is not sustainable, or healthy, for most people over the long term.3

#6 Limit carbs / no sugar

Wait, I thought you just said we needed fiber to produce the good gut bacteria. Well, that’s true. However, some of the carbohydrates we eat don’t just fuel the good guys, they also feed the bad guys. For example, it is well documented that carbs are essentially “Candida gasoline.” Eating large amounts of bread, rice, potatoes, etc will make an overgrowth worse. It is important to point out that the same effect from eating carbs was not observed in healthy people, presumably with non-pathogenic Candida.

The same “carbs are fuel” theory is true for small intestine bacterial overgrowth (SIBO), which as I wrote in my Candida post, might as well just be lumped into a larger category known as gut dysbiosis since it’s very difficult to diagnose this condition reliably.

Nevertheless, people suffering from gut issues do respond well to restricting carbs and FODMAPS, with this study showing a significant decline in bacteria in the small intestine on a low FODMAP diet. The problem is that butyrate levels also declined, meaning the good guys declined alongside the bad, which is why I am advocating for a balanced approach to carbs, with a more strict approach to sugar.4

#7  – Consider digestive enzymes

I’ve written before about the Urea cycle and how not everyone is born with the same ability to break down protein due in part to variants in the CPS1 genes.

The same principle applies when it comes to hydrochloric acid, the acid our bodies use to digest food, especially protein. As we age, our levels of stomach acid decline, which can result in poor digestion, and ultimately, a compromised gut and poor mineral absorption.5 The blood test diet has largely been debunked, however its one redeeming argument is that there does appear to be a link to blood type and stomach acid levels. Not everyone has the same ability to digest food, bottom line.

Enter digestive enzymes, a supplement long known to the bodybuilding community, that can help you break down and absorb more of the food you eat. Taken before a meal, enzymes like protease help to digest protein, while amylase breaks down starches, like bread. For our purposes here, the idea with digestive enzymes is they give an extra push to a weakened gut that isn’t doing a great job accessing nutrients from food.

#8 – Ditch the dishwasher

This study of over 1,000 children aged 7-8 years old in Sweden, found that children who lived in a household where dishes were washed by hand, as opposed to run through a dishwasher, had a lower rate of eczema as well as fewer allergies. The authors of the study hypothesized that the difference was based on exposure to greater microbial diversity in the families where dishes are washed by hand. So, I guess the lesson is we want our dishes clean, but maybe not too clean?

Get this, the risk was reduced further when the children were served fermented food and local food from farms. Of course, you already knew that from #5 on the list.

#9 – Glutamine

Glutamine has shown promise in helping to maintain the “epithelial” wall of the gut, and is one of the better supplements for treating leaky gut.6

But be careful.

In my article titled the MSG in your supplements, I talk about the role of glutamic acid in various supplement formulas, a problem because glutamic acid is a precursor to glutamate, which is an excitatory neurotransmitter. Now, glutamine is actually a different amino acid than glutamic acid, and it’s glutamine that shows promise in repairing gut health,6 but there are supplements marketed for their glutamine content that actually contain high levels of glutamic acid, and therefore could have an adverse effect on people with “mutations” in genes like GAD1, and GRIA3.

When it is in balance with GABA, glutamate is helpful, in fact our bodies need it to think and function. However, elevated glutamate levels have been linked to a wide range of diseases ranging in severity from simple anxiety to neurodegenerative disease. Our bodies can recycle glutamate into GABA, however, the common genetic variants listed above can disrupt these pathways, causing glutamate to take a harder toll on some people, and a very hard toll on others.

For an article on glutamate in food and the problems it can cause, see this excellent blog post by the team at Mission Heirloom.

The bottom line here is to make sure that you’re getting glutamine and not glutamic acid.

#10  – Collagen

This is a sensitive one as collagen is high in both histamine and glutamate, so not everyone will respond favorably. That, and I couldn’t find a good study on collagen repairing gut health. There are lots of anecdotal stories of collagen’s benefits, but not a direct study looking at healing leaky gut. If you have a good one, please share in the comments.

Having said that, I have on occasion used Bulletproof collagen protein and have noticed improvement in joint health when I have. In addition, stress reduces collagen levels, and since stress and gut issues are tied together, perhaps collagen does have a role to ply here.7

For a different take on collagen, see our recent podcast episode discussing dissenting opinions on popular supplements.

#11 – Zinc

Zinc is essential to the proper functioning of the immune system so it makes sense that this important mineral would play a role in maintaining gut health as well.8

For more, see my post: Zinc has many health benefits, but don’t overdo it

Final thoughts

Well, there you have it, 11 actionable ideas for rebuilding a healthy gut that don’t include probiotics. Of course, high quality probiotics, used under the right circumstances, can be beneficial in healing the microbiome. My point with this post is that it may be necessary to think more comprehensively if you want the best results.

John O'Connor

John O'Connor is the founder of Gene Food, a nutrigenomic startup helping people all over the world personalize nutrition. John is the host of the Gene Food Podcast and a health coach trained at Duke's Integrative Medicine Program. Read his full bio here.

The very latest on genetics, nutrition and supplements delivered to your inbox!


Leave Comment

  1. Philip Moreau says:

    What a life-affirming article. We not only have 1 brain. We have 2 brains. The first is in our conscience. The 2nd is in our gut. The gut let’s the mind know whether everything is either A-OK or totally Out-Of-Whack. I truly Thank You.

  2. John Holland says:

    Your statement, “No affiliate links to Mother Dirt anywhere in this post or site.” is incorrect. There was an embedded link to in this sentence: “I’ve been moving away from soap and towards a product called Mother Dirt.”

  3. Melanie Hayes says:

    My husband has took chemo by mouth for rectal cancer. About a year later he had an sinus infection and was prescribed an antibiotic. Then he started having lots of gas and problems with bowels being sometimes hard and sometimes soft. He has no cramping or pain just will feel the need to go. He’s taking probiotic twice a day. They are 112 billion a capsule. We don’t know what else to do. His gas problem is the most problem. Are we doing the right thing.
    We have two dog and no dishwasher.

  4. James Kong says:

    Hey.. I hear you on the L Glutamine. It has caused me anxiety.. can you recommend any that won’t do that?

    • Lily says:

      L Glutamine cannot cause anxiety, its in your head, you listen to your body too much after you take it. That happens to some sensitive people, and they cause anxiety to themselves. Or there is something else other than L Glutamine in the supplement you are taking. L Glutamine has no impact your nervous system or brain so it can’t cause anxiety at all.

  5. Brea says:


    Thanks for this article, I really found it helpful. I’ll look into adding glutamine. Would kombucha fall into the fermented group?

Leave a Reply

Facebook icon Twitter icon Instagram icon Pinterest icon Google+ icon YouTube icon LinkedIn icon Contact icon Info icon