Why you need to fix circadian rhythms to prevent or reverse SIBO

Based on the way the research is heading on circadian rhythms and their impact on gut health, behavior is a completely neglected yet highly underrated therapeutic option for people addressing small intestinal bacterial overgrowth(SIBO).  Unfortunately, we’re not going to be seeing any human clinical trials on the topic any time soon.  There’s already a paucity of data on SIBO, let alone in an area of addressing SIBO that isn’t very profitable.

So much research is being pumped out on circadian rhythms and their impact on gut health that it’s hard to keep up.  A review came out earlier this year on the topic and there are some really cool takeaways.  You can find that open access review here.

Today I’m going to discuss a very small part of this review, which seems to lay the foundation that SIBO is probably best prevented or cured by addressing circadian rhythms.  Let’s dig in.

Circadian rhythms and the microbiome

I hope that it comes as no surprise to my readers that the microbiome has a circadian rhythm, often referred to as the microbial clock.  While we carry the same commensal organisms throughout the day, they change in abundance and distance from the intestinal wall.  Our circadian rhythms are synchronized through zeitgebers, environmental signals that help tell different organs and tissues of the body the time of day.

It’s important to have our clocks synchronized to one another because signaling molecules secreted from one tissue have physiological effects in another.  For example, bile acids are made in the liver, stored in the gallbladder, and secreted in to the duodenum of the small intestine during meals.

As bile acids make their way through the small intestine, they interact with the microbiome and get re-absorbed at the end of the small intestine, called the ileum, and sent back to the liver for recycling.  This causes the secretion of antimicrobial peptides and the small amount of bile acids that escape recycling are acted on by bacteria in the colon.  Some of the bile acids even escape out in to the blood and regulate metabolism in muscle and fat tissue.  Proper synchronization is a must.

Our master clock is found in the suprachiasmatic nucleus(SCN) of the hypothalamus of the brain and ties our internal clocks to the day/night cycle.  The predominant zeitgeber for the master clock is light exposure, specifically to the eye.  But throughout the body there are other clocks in every organ and tissue that are set by other zeitgebers such as the feeding/fasting cycle, physical activity, stress, temperature, and social interaction.

All zeitgebers are important for all clocks to some extent because all tissues communicate with one another.  But some tissues have a dominant zeitgeber.  The dominant zeitgeber for the microbiome, and one of the most well-studied, is the feeding/fasting cycle.

The feeding/fasting cycle and microbial clock

The predominant bacteria found in the human gut fall in to 5 major phyla: Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, and Verrucomicrobia.  Each of these phyla are enriched in different bacterial functions that cause the circadian variation in the microbial clock.

For example, Firmicutes increase in abundance during the feeding period to snack on our food while Bacteroidetes and Verrucomicrobia peak during the fasting period due to their metabolic flexibility and ability to snack on our mucus layer.  While snacking on our mucus layer, Bacteroidetes and Verrucomicrobia move closer to the intestinal wall in the colon; eliminating the loose, thin outer mucus layer and converting the thick, dense inner mucus layer in to the new outer layer.

This leads to changes in the types of short-chain fatty acids(SCFAs) produced by the microbiome.  During the day when carbohydrates are consumed by Firmicutes, there’s an increase in the SCFA butyrate.  During the overnight fast, there’s an increase in the SCFA propionate, which is produced when Bacteroidetes and Verrucomicrobia begin snacking on mucins in our mucus layer.

But what happens if we don’t have a proper feeding/fasting cycle?  Assuming a standard 12hr/12hr feeding/fasting cycle is balanced which studies seem to favor, what if we shift it to 14hr/10hr?  Certainly that would cause an increase in the Firmicutes:Bacteroidetes ratio over time, which is precisely what we see in obesity, who have between a 2-11x increased risk for SIBO depending on small bowel transit time.

SIBO and the microbial clock

Over time, skewing the Firmicutes:Bacteroidetes ratio will tip the balance in the colon to favor an abundance of Firmicutes.  In fact, the rhythm tends to be lost and rather than just having more Firmicutes, it seems that the circadian rhythm in the ratio is lost as well.  This means that they are always abundant, which is bad for 2 reasons.

First, Bacteroidetes and Verrucomicrobia are still around to snack on your mucus layer during your normal fasting period, but Firmicutes are still quite abundant, their rhythm is lost as they remain elevated throughout the day.  This can cause a bacterial overgrowth in the colon, particularly of Firmicutes.

But Firmicutes are supposed to decline during the “fasting” period, they aren’t supposed to come in to close contact with the gut lining.  Since they’re there, and the mucus guys are snacking away, they do get close and can set off the immune system, invade the dense mucus layer, and cause leaky gut.  This combo of increased abundance and a damaged colon could allow them to overgrow in to the small intestine.  They’d rather be there anyway, there are more carbs.

Second, what types of bacteria do we get overgrowing in to the small intestine?  Hydrogen sulphide and methane producers such as Desulfovibrio and Clostridiales, respectively…prime culprits in SIBO.

We don’t want these guys crawling around in the small intestine in abundance, they could alter bile acid homeostasis, cause inflammation or leaky gut, or just ferment the crap out of carbs and cause bloating.  But what does this all mean?


Whether you’re trying to prevent SIBO, get rid of it, or prevent it from coming back, you should absolutely practice time-restricted eating(TRE) where you are fasting at least 12 hours every day.  This should make it easier to return to a more “normal” microbiome and microbial rhythm.  Will this be enough to eliminate SIBO?

In some people, maybe.  If it’s going to work solo, it’ll probably only work that way for young people.  But the idea that time-restricted eating is the only thing you need to do to get rid of SIBO probably isn’t grounded in reality for most people over 40.  Even in younger people, TRE is probably something that should be used in conjunction with a short-term restrictive diet, antimicrobials, or a combination of the 2.

For older people, it’s absolutely essential to expose yourself properly to as many zeitgebers as possible.  Younger folk are more sensitive to zeitgebers so they may only need to modify light exposure and do TRE.  Many of the metabolic pathways that help regulate the clock just run better in younger people, and they’re also less likely to have Type 2 diabetes or experience regular hyperlgycemia that disrupt circadian rhythms.

Older people probably need to run the gamut and properly time their light exposure, feeding/fasting cycle, physical activity, stress exposure, and correct nutrient deficiencies that affect the circadian clock.  Some metabolites that help set the clocks decrease with age so correcting Type 2 diabetes and correcting nutrient deficiencies is an absolute must.

I think the science is clearly indicating that we all need to pay attention to our circadian rhythms for a healthy gut.  For those of us over 40, adjusting as many lifestyle factors as possible to optimize circadian rhythms sets the stage for a healthy, SIBO resistant gut.

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