What SIBO teaches us about healing the gut

SIBO, short for small intestinal bacterial overgrowth, is a condition where bacteria overgrow in the small intestine. While we normally find bacteria in the small intestine, the numbers pale in comparison to the large intestine, or colon.

As you can see, the amount of bacteria in the small intestine ranges from in the 1000s to the 100,000,000s depending on the segment. In contrast, the colon harbors bacterial numbers in the 1,000,000,000,000s.

So what drives the difference in numbers between the small intestine and colon? Simply put, it’s the environmental conditions. And when the environmental conditions in the small intestine change to resemble that of the colon…well…you can guess what happens.

Environmental conditions in the small intestine vs the colon

The living conditions in the small intestine are night and day when compared to the colon.

First, digestive enzymes and bile in the small intestine inhibit bacterial growth. Furthermore, immediately prior to entering the small intestine, food must go through the stomach. There, gastric acid does a great job of dramatically reducing the amount of bacteria found in the food bolus.

Next, the passage of food throughout the small intestine is much more rapid than in the colon. Food typically passes through the small intestine within 6 or so hours. In the colon, contents can remain for up to 2 days. Stagnation, whether in a body of water or in your gut, allows for greater bacterial growth.

In addition, the mucus layer in the small intestine is quite different than the mucus layer in the colon. The mucus layer in the small intestine is only one layer, thinner, less dense, and not attached to the cells there.

Bacteria live within the mucus layer, so a thinner and less dense mucus layer houses fewer bacteria. On top of that, since the layer in the small intestine is not attached, it carries bacteria with it into the colon during peristalsis.

Finally, cells in both the small intestine and colon secrete antimicrobial peptides that populate the mucus layer. Antimicrobial proteins are higher in the small intestine, and since the mucus layer is thinner there, it is a more concentrated source.

These environmental factors make the small intestine a less suitable environment for bacterial growth.

SIBO: When the small intestine acts more like the colon

So what happens when the small intestine begins to behave like the colon? As you can imagine, conditions begin to favor greater bacterial growth.

One common misconception with SIBO is that the bacteria are moving from the colon into the small intestine. However, SIBO doesn’t always happen in the ileum, which is the segment of the small intestine adjacent to the colon.

It can happen anywhere in the small intestine, so it’s simply a matter of environmental conditions. One important consideration is the presence of bile and digestive enzymes. But probably the most important is motility.

When the food bolus stagnates in the small intestine, there’s greater opportunity for bacterial growth. An additional consideration with stagnation is that lower motility generally leads to more mucus in the small intestine and greater bacterial growth.

This is for 2 reasons. First, the mucus layer in the small intestine continuously renews throughout the day. Under normal operating conditions, motility propels this loose mucus layer through the small intestine and into the colon. Slower motility gives bacteria a chance to grow in the small intestine.

Another consideration is that the enteric nervous system controls motility, digestive enzyme and bile output, antimicrobial peptide secretion, and mucus production. So if you have a problem with motility, you likely have a problem with multiple aspects of small intestinal bacterial defense.

When the small intestine begins acting like the colon, bacterial numbers increase there.

Factors affecting the enteric nervous system

Many factors go in to proper function of the enteric nervous system. First, a healthy microbiome plays an important role, as does a proper microbial circadian rhythm. The microbial rhythm interacts with our circadian rhythm to optimize function of the enteric nervous system. (Learn how to start improving your circadian rhythms in this video)

Maintaining proper blood glucose regulation is also crucial. The enteric nervous system is particularly sensitive to high blood glucose levels. Diabetes re-wires the enteric nervous system and damages enteric neurons.

Pathogens can also play an important role in enteric nervous system function. In mice, infection with viruses that infect the gut cause temporary damage to the enteric nervous system. Though the damage to enteric neurons does heal, an unfortunate consequence of this initial hit causes the mice to be more susceptible to damage from viral reactivation or other inflammatory stimuli.

Ultimately, the data in SIBO clearly indicates that the most important factor for preventing or reversing it is to restore the environmental conditions in the small intestine that inhibit bacterial growth. This is also the key to maintaining a healthy gut.


Approaches to addressing SIBO have primarily focused on the use of antimicrobials to clear the overgrowth. There are clear drawbacks to this approach, particularly since many cases of bacterial overgrowth involve bacteria that you don’t want to completely annihilate from the gut. Doing so could create instability in the microbiome.

But the primary drawback to this approach is that it doesn’t address what caused the overgrowth in the first place. Bombing microbes addresses the symptoms, not the cause. While this approach may yield initial benefit, relapse is almost sure to happen.

This is likely why SIBO relapse is very common. If you don’t address the instability in the small intestinal environment, overgrowth is sure to reoccur.

Addressing factors that regulate function of the enteric nervous system is critical to eliminating SIBO and building a healthy gut. This centers around fixing lifestyle, diet, and circadian rhythms. Furthermore, if you are a type 2 diabetic, you must get your blood glucose under control. If that’s you, we have a program for that you can check out here.

If you’d like to learn more about addressing SIBO, we covered it in a couple of blogs you can check out below:

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