What Can I Eat to Improve My Gut Biome?

Written by Alex Reid
Posted September 6, 2018

gut biome header

Within all of our guts, there are two main types of bacteria competing against each other.1 You can think of them like two opposing armies.

In one corner, we have Firmicutes — lovers of everything sugar. In the context of this conversation, we can think of them like the evil empire, trying to invade your gut and twist it to suit their needs. In the other corner, we have Bacteroidetes. They’re the good guys.

YOU play an incredibly important role in this war. Because ONE of these armies will win. And YOUR choices determine who that victor will be.

To help the good guys — the Bacteroidetes — you have to give them the right fuel to help them run the war effort. This is where most sources would tell you to eat a diet rich in probiotics, things like sauerkraut, kimchi, yogurt, or kefir.

But There’s One BIG Problem With Probiotics

Probiotics Don't Work

They don’t do anything! At least not for the two largest groups of bacteria in your gut. Now, this is one of the most common misconceptions about your gut health, so listen closely to this next part: The whole idea that probiotics are all you need for a healthy gut is a side effect of savvy marketing.

What they won’t tell you is that there’s actually a much more nutritionally important group of foods than probiotics. You see, probiotics are good for feeding the aerobic bacteria of your microbiome — that is, the bacteria that use oxygen.

But the vast majority of bacteria present in your microbiome, including the two BIGGEST groups, the Firmicutes and Bacteroidetes, are anaerobic, meaning they don’t need oxygen to survive. These two bacterial phyla are the most important to balance for a healthy gut. But eating fermented foods or taking probiotic supplements does absolutely NOTHING for them.

What You REALLY Need to Enjoy a Healthy Gut Biome

So, what do you need to eat instead? I’ll tell you in just a moment, but the first thing to focus on is what you SHOULD NOT eat.

Sugars and processed carbs are a big no-no. Firmicutes loves sugars, so much so that sugar factories actually have to work hard to avoid blooms of Firmicutes in their facilities. Also, you’re going to want to avoid processed carbohydrates like white bread, pasta, sodas, snack food, and breakfast cereals. Because all of that gets gobbled up by your Firmicutes as well.

By eliminating these foods from your diet, you’ll deprive the Firmicutes of much of the energy they need to function. They’ll be weakened and injured, and you’ll be primed to deliver the knockout blow that will finally restore balance to your gut.

The ONE Type of Food That Will Dramatically Improve Your Gut Health

The Best Food for Your Gut

Now that the evil army of Firmicutes has been weakened, it’s time to lead the Bacteroidetes into battle. And you’re going to need more troops. Thankfully, there’s an easy way to increase the size of the Bacteroidetes army. All you have to do is give them the right food.

If you give them the nutrients they desire, the Bacteroidetes will grow and multiply. Then they’ll overwhelm the hordes of Firmicutes and create a long-lasting, healthy peace inside your microbiome. But remember, Bacteroidetes are anaerobic, which means you can’t just follow the same old advice and eat a bunch of probiotics.

Instead, you have to feed them prebiotics.

What Are Prebiotics?

Prebiotic foods are any foods that contain insoluble, non-digestible fiber, specifically a certain type of fiber called an oligosaccharide.2 An oligosaccharide is a small chain of carbohydrates, typically 3 to 10 molecules of fructose and glucose. When you eat oligosaccharides, they pass through your small intestine undigested. They then land in your colon, where they begin to ferment.

The fermentation process releases a number of short-chain fatty acids (SCFAs) that your good bacteria love, compounds like acetate, propionate, and butyrate.3 The Bacteroidetes feed on these fatty acids and use the energy to grow, multiply, and eventually overwhelm the bad bacteria lurking in your microbiome.

In other words, you can think of prebiotics like fertilizer for your gut. And the more of it you have in your diet, the more numerous your good Bacteroidetes will be.

So, which foods should you be eating?

Top 5 Prebiotic Foods

1. Onions


Onions are one of the best (and most delicious) prebiotics you can eat. That’s because they contain high amounts of oligosaccharides, specifically fructo-oligosaccharides (FOS). FOS compounds present in onions are responsible for their mildly sweet flavor. And when you eat onions, the FOS molecules travel through your gut undigested into your colon, where they can be broken down into the beneficial short-chain fatty acids we discussed above.4,5

Onions also contain inulin, a special type of plant fiber that cannot be digested. Like FOS, inulin lands in your lower gut, where beneficial bacteria use it as a food source.6 Bifidobacteria in particular love inulin.7,8 And they are one of your body’s best friends.

Bifidobacteria have been shown to protect against colorectal cancer, improve symptoms of irritable bowel syndrome (IBS), strengthen your immune system, reduce diarrhea, and even help you lose fat.9,10,11,12,13 Plus, onions simply make food taste better. So eat up.

2. Jerusalem Artichoke

Jerusalem Artichoke Improves Gut Health

Despite its name, the Jerusalem artichoke isn’t an artichoke at all. It’s actually a member of the sunflower family, and the edible portion looks like a lumpy, earthy tuber. It may not be pretty, but the Jerusalem artichoke is a powerful gut health aid. The tuber is extremely high in inulin, which, if you remember, helps feed good gut bacteria like Bifidobacteria.14

The growth of good bacteria in turn exerts a number of positive health effects on your body. In one study, Jerusalem artichoke was actually found to help prevent type 2 diabetes! The researchers of the study fed two groups of mice a diet rich in sugar. However, one group was also fed a small amount of Jerusalem artichoke. And the results were outstanding! The control group of mice developed type 2 diabetes as expected.

But the group that was fed Jerusalem artichoke did not. The plant seemed to protect the mice from the harmful metabolic effects of high sugar consumption.15 Not only that, but incorporating Jerusalem artichoke into a diet may be able to improve immune function and help your body fight off disease.16

While scientists are still trying to figure out the exact mechanisms behind the effects of Jerusalem artichoke, they all believe it has to do with the powerful prebiotic properties of the little root vegetable and its ability to nurture a healthy microbiome. Depending on where you live, Jerusalem artichokes may be hard to find. But you can see if any nearby local farms grow them by going to www.localharvest.org and typing in “Jerusalem artichokes” and your zip code into the search bar at the top.

3. Garlic

Garlic is Potent Prebiotic

Remember, great health doesn’t have to be expensive. And garlic is one of the most cost-effective ways to nourish your microbiome.17 17% of the total fiber content in a garlic clove comes from beneficial inulin and fructo-oligosaccharides. Like the other probiotic foods on this list, garlic promotes the growth of healthy Bifidobacteria. But it also actively fights a group of disease-causing bacteria known as Clostridium.18

Clostridium are nasty little organisms that can cause botulism, food poisoning, gangrene, and tetanus. Additionally, garlic also possesses antimicrobial and antifungal properties, both of which can help tame rampant invasive organisms in your microbiome.19

4. Leeks

Leeks Prebiotic

Like garlic, a large part, 16%, of the fiber content in leeks is in the form of inulin.20  As we’ve shown previously, inulin is crucial if you want Bifidobacteria and other healthy strains of gut microorganisms to flourish. Leeks are also rich in kaempferol, a unique type of flavonoid that significantly reduces the damage caused by free radicals and oxidation.21

What’s more, leeks are a very versatile vegetable that you can enjoy in a number of ways. You can saute them, toss them in a salad, or use them in soups and stews.

5. Cocoa

Cocoa Prebiotic

Much more than just an ingredient in sweet treats, cocoa is increasingly proving itself to be a veritable superfood.

Especially for your gut.

Cocoa has been shown to have extreme prebiotic properties in a number of different studies. In one of those studies, conducted at the University of Reading in the UK, researchers found that after just four weeks, cocoa increased healthy Bifidobacteria and Lactobacilli, while reducing the population of unhealthy Clostridia.22

There are two compounds that seem to be behind the incredible prebiotic effects of cocoa: epicatechin and catechin. They are powerful flavanols, and both epicatechin and catechin are present in a number of different superfoods, especially green tea.23

Even though scientists have long known about the health benefits of the two catechins, they were at a loss as to how or why the two compounds exerted their effects. However, now the majority of the world’s scientists agree that catechins are healthy mainly because they improve the composition of our gut flora.

This is why cocoa has been shown to reduce insulin resistance, decrease blood pressure, and even slash LDL levels.24 It isn’t the cocoa itself that gives you all the benefits. The real heroes are the healthy gut flora that the compounds in cocoa help feed.

But warning:

This isn’t an excuse to eat a bunch of high-sugar chocolate snacks and desserts. To give your microbiome the nourishing cocoa flavanols, you need to find chocolate that fits the following parameters:

  1. At least 70% cacao: Anything less, and it won’t have meaningful amounts of catechin and epicatechin.

  2. Low amounts of sugar: Try to find chocolate that has at most 5g of sugar.

  3. Organic: Chocolate is grown in dense jungles with a lot of bugs and pests. Consequently, regular chocolate tends to be sprayed heavily with pesticides and other chemicals. Avoid brands that don’t have the organic certification.

  4. Fair trade: Because chocolate is grown in the developing world, all too often the manufacturers take advantage of the workers. When you buy fair trade, you send a signal that moral capitalism and sustainability are the ways of the future.

Wrap Up

5 Best Prebiotics

  • Two types of bacteria make up the majority of your microbiome: Firmicutes and Bacteroidetes.

  • Too many Firmicutes have been associated with weight gain, insulin resistance, diarrhea, heart disease, and many other diseases, while more Bacteroidetes is associated with increased health and longevity.

  • Probiotics don’t do much to change the profile of your gut. Most gut flora is anaerobic, while probiotics are aerobic.

  • So, to actually make meaningful changes to your gut composition, you need to eat a diet rich in prebiotics, such as onions, Jerusalem artichokes, garlic, leeks, and cocoa in the form of dark chocolate.

To your health,

Alex Reid
President, Longevity Insider HQ

1 https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-14-788

2 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3705355/

3 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4756104/

4 https://www.ncbi.nlm.nih.gov/pubmed/25498616 

5 https://pubs.acs.org/doi/abs/10.1021/jf070623x 

6 https://www.ncbi.nlm.nih.gov/pubmed/15877886 

7 https://www.ncbi.nlm.nih.gov/pubmed/12088518 

8 https://www.tandfonline.com/doi/abs/10.1080/08910600310002091#preview 

9 https://www.ncbi.nlm.nih.gov/pubmed/8910918/ 

10 https://www.ncbi.nlm.nih.gov/pubmed/10468688/ 

11 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5722804/ 

12 https://www.ncbi.nlm.nih.gov/pubmed/15815206 

13 https://www.ncbi.nlm.nih.gov/pubmed/23135760 

14 https://nutritiondata.self.com/facts/vegetables-and-vegetable-products/2456/2 

15 https://www.ncbi.nlm.nih.gov/pubmed/24968200 

16 https://www.ncbi.nlm.nih.gov/pubmed/25123678 

17 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4103721/ 

18 https://www.sciencedirect.com/science/article/pii/S2213453013000311 

19 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4103721/ 

20 https://pubs.acs.org/doi/abs/10.1021/jf070623x 

21 https://www.ncbi.nlm.nih.gov/pubmed/19549512 

22 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3566565/ 

23 https://www.ncbi.nlm.nih.gov/pubmed/17977475

24 https://www.ncbi.nlm.nih.gov/pubmed/16027246