The secret to eliminating small intestinal bacterial overgrowth

Small intestinal bacterial overgrowth (SIBO) is a condition where excess bacteria grow in the small intestine. While there are normally trillions of bacteria in the gut, their numbers are low in the small intestine of healthy people.

Different areas of the gut contain varying amounts of microbes, expressed as log colony-forming units per gram(CFU/g). In the colon, bacterial numbers are on the order of 1,000,000,000,000 CFU/g. However, in the small intestine, numbers are between 10,000-10,000,000 CFU/g, depending on the segment.

Local environmental conditions regulate the amount of bacteria that grow in each segment, along with different species. Therefore, changes in environmental conditions can play a major role in the development of SIBO as well as dysbiosis.

One determinant of bacterial numbers is gut motility. A big environmental difference between the small intestine and colon is how long digested food sits. Food passes through the healthy small intestine in about 4-6 hours. In the colon, food can sit for up to 36 hours.

As a result, if motility slows to a halt in the small intestine, the microbiome there will more closely resemble the colon in species and number. We covered the importance of small intestinal motility and it’s relevance to SIBO in a blog you can check out here.

Environmental conditions that protect against small intestinal bacterial overgrowth

While motility is an important environmental factor to control against SIBO, there are other important factors as well. Consequently, SIBO may be the product of multiple failures within the microbial defense system.

Motility is a target for SIBO because we have therapies that address it. Prokinetics are drugs or supplements that increase the strength and frequency of contractions in the gut. One approach to treating SIBO is to use antibiotics to decrease bacterial numbers, while using prokinetics to maintain remission via increasing motility.

Relapse is one of the unfortunate aspects of SIBO. This may be driven, at least in part, by the way it’s treated. If we look at SIBO as an “infection”, the above antibiotic/prokinetic therapy makes sense.

Unfortunately, this approach isn’t all that logical when you look at SIBO for what it is: An injury or failure to defense mechanisms within the gut. To clarify, this doesn’t mean this treatment approach isn’t worthwhile, it’s simply insufficient.

The American College of Gastroenterology recently updated it’s treatment guidelines for SIBO. Within these guidelines is a table containing the various mechanisms that maintain homeostasis in the small intestine.

As you can see, motility is simply 1 out of 6 factors that regulates homeostasis in the small intestine. Interestingly, all but one of these mechanisms is directly regulated by circadian rhythms.

We covered how circadian rhythms regulate essentially all functions in the gut in a blog you can check out here.

Lifestyle and circadian rhythms

Just like environmental factors regulate the bacterial numbers and species in each segment of our gut, they also regulate our physiology. Environmental cues called zeitgebers optimize our physiology to help us function optimally in our environment. This is the basis of circadian rhythms.

With respect to the gut, this creates time of day changes in digestion, absorption, motility, immune function, and the microbiome. Changes in light exposure, core body temperature, and feeding times all play an important role in setting time in the gut.

But circadian rhythms are a little more complicated than that. While environmental cues alter our physiology and behavioral patterns, the opposite is true as well: Our behavioral patterns also impact our circadian rhythms.

For example, we are active during the day and sleep at night, but poor sleep hygiene messes up our sleep. When our sleep becomes disrupted, this impacts other systems, including the digestive system.

Disrupted sleep is known to impair gastric motility, intestinal motility, and causes dysbiosis of the microbiome. In fact, the microbiome and sleep physiology are bi-directionally related.

A number of behavioral factors including physical activity, timing of exercise, meal timing and spacing, and nutrient quality are all important factors that regulate our circadian rhythms.

Lifestyle and small intestinal bacterial overgrowth

As you can tell, our circadian rhythms strongly regulate the environmental conditions in the gut. As a result, they play an incredibly important role in regulating our microbiome, which is dependent on the gut environment.

This is the same in all segments of the gut, including the small intestine. If the goal is to reduce bacterial numbers in the small intestine, building strong circadian rhythms is essential to recovery and permanent remission.

The problem is, an antibiotic and prokinetic have no substantial long term effect on circadian rhythms. In fact, using a prokinetic is an attempt to circumvent the circadian rhythm of motility, and something you’ll have to do ad infinitum.

So even if the antibiotic removes the overgrowth, the prokinetic is simply a band-aid if you’re not making an attempt to address circadian rhythms. And while it addresses motility, it doesn’t address pH, enzyme secretion, absorption, and the various other factors in the gut regulated by circadian rhythms.

Therefore, it’s crucial to address behavioral factors that regulate circadian rhythms to hop off the SIBO roller-coaster. This includes proper light exposure, getting adequate physical activity, maintaining a consistent feeding schedule, prioritizing sleep, managing stress, and getting adequate nutrition.


Small intestinal bacterial overgrowth is ultimately a failure of the factors that regulate homeostasis in the small intestine. Treatment approaches often include the use of antibiotics and a prokinetic to maintain motility. Unfortunately, relapse is incredibly common.

Since circadian rhythms regulate most of these defense mechanisms, an effort should be made to practice good circadian hygiene to help prevent relapse. Despite substantial evidence to the importance of circadian rhythms, it is rarely addressed in SIBO protocols.

Make an effort to build strong circadian rhythms whether you are currently battling SIBO or in remission. There is a strong case that it will make the difference between success and failure.

2 thoughts on “The secret to eliminating small intestinal bacterial overgrowth

  1. Monica says:

    But also, not snacking between meals. SIBO is often a dysfunction with the migrating motor complex (MMC) which is shut down by eating.

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