Healing the gut: What you need to know

If you’ve ever dealt with a chronic functional gut problem, you know that healing the gut is a monumental task. So much can go wrong in the gut, because there are a lot of moving parts.

One of the most important concepts for a healthy gut is synergy. Healthy behaviors promote a healthy gut, which secretes factors that attract a healthy microbiome that makes a happy you.

Members of a healthy microbiome, in turn, secrete factors that attract other healthy microbes and keep our gut healthy. The fermentation of fiber into short chain fatty acids is a wonderful example.

A recent paper illustrates how this synergy is essential to healing the gut and having optimal gut health. But first, let’s talk about synergy.

Synergy between the gut and microbiome

Over the last few decades, we’ve learned a lot about the gut, particularly as it pertains to the microbiome. The microbiome is the collection of microscopic organisms that live in and on us, including bacteria, archea, fungi, and viruses.

We have a microbiome on our skin, in our nose and mouth, and throughout our entire digestive tract. In each little niche, there is bi-directional communication between the host(us) and the microbes that live there.

The microbes that inhabit a niche are selected by the environmental conditions of that niche. Furthermore, when a microbe pops up, it tends to bring friends through the different metabolites it makes. This creates a microbiome that promotes health.

For example, a healthy gut selects for a different microbiome than an unhealthy one. A healthy gut secretes factors that bring healthy microbes, which beget more healthy microbes. An inflamed gut brings unhealthy microbes, which further inflame the gut.

Different behavioral traits such as circadian rhythms, diet, sleep, exercise, alcohol, and antibiotic use alter conditions in the gut. Thus, there is an unspoken social contract between us and our microbiome:

Take care of them, and they’ll take care of you.

Healing the gut: Create synergy

Our gut has a number of ways to prevent the presence of bad microbial actors. Bile, created in the liver and stored in the gallbladder, has a strong antimicrobial effect.

However, certain beneficial microbes in our gut are bile tolerant. These commensal organisms outcompete others who may feed on the same food but are not tolerant to bile.

There is also a mucus layer that keeps microbes from getting too close to the cells that line the gut. Some beneficial microbes attach to this mucus layer, and others can snack on it.

Cells of our gut also secrete antimicrobial peptides, or AMPs. AMPs accumulate in the mucus layer and prevent pathogenic bacteria from overgrowing there. As a result, all of these factors help create a healthy microbiome that creates synergy within.

One particular antimicrobial peptide that’s important for maintaining a healthy microbiome is Regenerating islet-derived protein 3 (Reg3). This AMP plays a role in crushing pathogenic bacteria, and keeping bacteria out of the blood.

As you’ll see in a moment, it’s incredibly important for creating a healthy gut.

Healing the gut: The role of Reg3g

Reg3g in mice, which is equivalent to human Reg3A, is an antimicrobial protein found throughout the gut. A new paper indicates that Reg3g is important for attracting beneficial bacteria, repelling pathogenic bacteria, and coordinating the circadian rhythm between the mouse gut and microbiome.

In a low fat, high fiber diet, there is a circadian bloom of Lactobacillus species that interacts with the cells of the gut. This causes the secretion of Reg3g, which certain Lactobacillus strains(rhamnosus, johnsonii, and intestinalis) are resistant to.

This creates a competitive advantage for the good guys. As these Lactobacillus strains increase in numbers, they stimulate the production of Reg3g via an increase of metabolites generated via the diet.

So, in essence, we do things that help promote a healthy microbiome. When we do this, our microbiome creates heath-promoting metabolites that inhibit inflammation, prevent leaky gut, and increase the thickness of the mucus layer.

As a result, the environment of the gut promotes beneficial Lactobacillus species, and inhibits pathogenic bacteria. In addition, this creates a healthier environment in the mucus layer of the small intestine.

But it’s important to point out that this bloom eventually wanes during the day, keeping these Lactobacillus strains from overgrowing and causing chaos.

You can definitely have too much of a good thing, as anyone with SIBO will tell you.

Reg3g and diet

Another finding of this paper is that a high fat/low fiber diet(HFD), the standard American junk food diet, decreases the circadian rhythm of Reg3g in the gut. To be clear, this was driven by the poor microbiome created by the poor diet.

The Lactobacillus strains identified in this study increase in a high fiber, low fat diet. Then, during the fasting period, they gradually decrease to create the Reg3g rhythm. As a result of high fat diet-induced dysbiosis, this rhythm was lost.

Interestingly, alcohol causes the exact same effect. In a paper looking at the effect of alcohol on Reg3g, researchers found that alcohol causes Reg3g deficiency. Furthermore, Reg3g deficiency in mice causes bacterial overgrowth in the mucus layer.

As a result, bacteria breached the intestinal barrier, entered the blood, and damaged the liver. Increasing Reg3g production in mice protected against this effect, preventing alcoholic liver disease.

Interestingly, Lactobacillus rhamnosus granules, essentially secretions from one of the probiotic strains that increases Reg3g, protect against the negative effects of alcohol consumption in mice.

Therefore, consuming a high fiber diet, limiting alcohol intake, and eating fermented foods using L. rhamnosus such as kefir may be useful for creating synergy between our gut and microbiome.

Of course, it’s important to point out that healing the gut is much more complex than taking a probiotic supplement. It requires adopting a lifestyle that creates an environment where said probiotic can flourish and do its dirty work.

Synchronizing the microbiome and gut

Based on this data, these 3 beneficial Lactobacillus species help maintain harmony in the gut. Of course, there are likely dozens of microbes that simply weren’t studied. But that doesn’t change the primary point: Take care of your gut, and your microbiome will take care of you.

It’s an essential give and take that we absolutely need to take advantage of for healing the gut. It’s the perfect tenant/landlord relationship: We’ll give you a clean place to stay, you keep it clean and pay rent.

If we don’t uphold our end of the bargain, the relationship will sour. Us, the slumlord not staying on top of things, our microbiome, the slacker tenant who won’t pay rent and trashes the place because conditions aren’t liveable.

Ultimately, no one benefits from a strained relationship like this. So it’s best to uphold our end of the bargain, so our microbiome upholds its end.


Healing the gut is a daunting task, and much more complex than most people would believe. Early research into the microbiome laid forth promises of personalized probiotics with the potential to be gamechangers for things like IBS and SIBO.

Unfortunately, things are never that easy. For probiotics to work, we have to fulfill our end of the bargain. We have a fighting chance if we:

  • Maintain a healthy weight
  • Reduce sedentary time
  • Prioritize sleep
  • Eat a higher quality diet. (A Mediterranean diet seems to be optimal, but can be done poorly)
  • Manage stress
  • Oh yeah, and limit alcohol

If we do these things, we may be able to turn the corner by creating synergy between us and our microbes. Probiotics, probiotic foods, and other supplements may help give us a chance.

But unless we’re willing to uphold our end of the social contract, none of those things will move the needle enough to matter

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