A low fiber diet may be disrupting your circadian rhythms

A low fiber diet is often used by those with gut problems to manage their symptoms, particularly those with IBS, IBD, and SIBO. This isn’t necessarily a bad approach in the short-term.

But current practices show this approach may not be suitable in the long term(>2 months). There are a number of reasons for this being the case. 

First, they limit a lot of otherwise healthy foods and can lead to nutrient deficiencies.  I wouldn’t consider this a low fermentation diet specific issue since most people eat a horrendous diet anyway. 

The primary issue with using these diets long term is a lack of fermentable carbohydrate. Though this is how they work, there are drawbacks.

Fiber is known to be the munchie du jour of many of our resident microbes. They transform fiber in to compounds that protect against things such as:

  • Leaky gut
  • Type 2 diabetes
  • Obesity
  • Cardiovascular disease

By removing their food via a low fiber diet, this could increase your risk for these conditions.

As a result of this, these diets shift the microbiome and reduce some of the beneficial things our microbes make.  As a byproduct of microbes munching on fiber, they produce short chain fatty acids(SCFAs).

SCFAs are the preferred fuel to the cells that line our gut, called enterocytes.  This low energy state could throw enterocytes in to dysfunction. And this can cause leaky gut, increased inflammation, and impaired motility.

Well, you can add another potentially negative effect to the chronic use of low fermentation diets: disrupted circadian rhythms.

Image result for circadian clocks peripheral
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Circadian rhythms and a low fiber diet

Circadian rhythms are daily fluctuations in organ and tissue function that follow an approximately 24 hour period.  Every one of our organs and tissues has their own circadian rhythm. This circadian rhythm matches tissue function to the environment. 

In turn, circadian rhythms help synchronize our tissues with one another. The ultimate goal is to increase the chances of biological success.  First to find food and survive, then to ultimately pass our genes on to the next generation.

Our microbiome is often thought of as another organ. And given the abundant number of genes it contains, an incredibly important one.  Despite the genes in the microbiome not being our own, our microbiome does follow a circadian rhythm. 

Much like the other peripheral clocks throughout the body, it’s set primarily by the feeding/fasting cycle.  The master clock and other peripheral clocks affect the rhythm of the microbiome, and vice versa. Thus, disrupting any of them is problematic.

There are a lot of low fiber diets to choose from.

  • The Specific Carbohydrate Diet(SCD)
  • The Fast Tract Diet
  • The Low FODMAP Diet

The goal is to decrease the amount of fermentation in the gut to reduce symptoms such as bloating and inflammation.  This absolutely gives symptomatic relief in the short-term.

But, it can disrupt your circadian rhythm, as research in mice has recently pointed out.

Microbiome in a low fiber diet
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The microbiome and circadian rhythms

A major concept in circadian rhythms is that all tissues and organs communicate environmental factors with one another.  We know that the master clock in the suprachiasmatic nucleus uses melatonin and cortisol.

These hormones relay environmental information on light to the peripheral clocks in other tissues.  The pancreas releases insulin, the gut bile, muscles different myokines, and fat tissue triglycerides and leptin.

For the microbiome to participate, it must utilize some form of communication molecule(s) with other tissues.  The most likely candidates are the short-chain fatty acids(SCFAs) butyrate, propionate, and acetate.

And the microbes in our gut produce these SCFAs when they ferment fiber.  The very fiber most people limit in these low fermentation diets.

In order to be a valid candidate, SCFAs would themselves need to follow a circadian rhythm.  A study published earlier this year investigated if this was the case. 

Both butyrate and acetate follow clear fluctuations from day to night, obviously dictated by feeding. Feeding them to mice in the middle of the day, when they normally sleep, causes a shift in circadian rhythm.

It’s not difficult to see how this could have an effect on human physiology.  The circadian rhythm of butyrate and acetate caused peak concentrations in the cecum at the beginning of their active period.

In mice, this is shortly after they wake up.  Having higher SCFAs in the cecum would dramatically lower the pH there, making it more acidic. 

It would also provide enterocytes with adequate butyrate prior to acquiring food.  In theory, this should make the colon less hospitable to foreign invaders.

Antibiotics, the microbiome, and a low fiber diet

Another interesting finding of this study was that using antibiotics caused the same effect as a low fiber diet. Disrupting the SCFA circadian rhythm prevented the kidney and submandibular gland clocks from entraining to the feeding/fasting cycle. 

In case you didn’t know, the submandibular gland produces saliva that contains salivary enzymes and antimicrobial peptides. This sets the stage for digestion and killing of pathogens that may be on your food. 

So this isn’t an insignificant problem.

A low fiber diet, epigenetics, and circadian rhythms

In addition to the gut, both acetate and butyrate have an effect on a large number of tissues.  This includes the brain as well as the liver, muscles, and fat tissue

Part of this may come down to other tissues using butyrate and acetate as a fuel source. But both have some pretty interesting epigenetic effects through their function in histone acetylation/deacetylation.

Epigenetic regulation effectively pulls the strings for the circadian clock.  In order to alter function on a daily cycle, genetic expression must change throughout the day. 

One form of epigenetic regulation, histone acetylation, adds an acetyl group to a histone. This relaxes a structure called chromatin that normally prevents DNA from being read.  Thus, histone acetylation increases genetic expression.

During histone deacetylation, the acetyl group is removed from the histone. Next, the chromatin condenses and prevents the gene from being read and expressed. 

Histone acetylation/deacetylation is a core component of the circadian clock.  Acetate can be converted to Acetyl CoA which is used in acetylation. 

Butyrate, on the other hand, is a histone deacetylation(HDAC) inhibitor.  Since both follow a circadian rhythm and alter epigenetic regulation of the circadian clock, abstaining from fiber may have a negative effect on your circadian rhythms due to epigenetic changes.

SCFAs, epigenetics, and a low fiber diet
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How epigenetic changes affect the gut

The implications at just the level of the gut are pretty significant.  Exposing resident immune cells of the gut(Macs/DCs=Macrophages and Dendritic cells) to increased acetylation or HDAC inhibition via SCFAs reduces the inflammatory response to LPS.

LPS is something you have in spades in your gut and is highly inflammatory.  Thus, the SCFAs may function as a brake on LPS-induced inflammation in the gut via epigenetic mechanisms. But the effects extend well beyond the gut.

Many other tissues get access to SCFAs from the blood including the liver, kidney, and brain. Possibly every other tissue you can think of. 

The wide range of tissues impacted by a loss of the circadian rhythm in SCFA production is definitely concerning. It also indicates that long term use of a low fiber diet may not be a good idea. 

I would steer clear of using these diets long term,. Though, there are a few things that could limit the damage for the short period that you use them.

Limiting the damage of a long term low fiber diet

First, it’s important to put this in to perspective.  There is a high amount of individualization when you reintroduce, so you’ll have to find things that work for you.  One man’s meat is another man’s day full of bloat, so it’s important to find fiber that works for you.

Ideally, this comes from whole, unprocessed food with other beneficial nutrients such as lentils, brussels sprouts, and wild blueberries.  I would stay away from powders and stick to whole foods if you are coming off one of these diets.  Start slow, very slow, and work your way up.

Second, based on the study above, time-restricted eating seems to be able to mitigate some of the negative effects. And fasting probably does as well if put at the proper time. 

This likely has to do with increased beta-hydroxbutyrate in the fasted state, which also functions as an HDAC inhibitor. Though a much weaker one.

Finally, realize that circadian rhythms are essentially a way for your body to solve the puzzle that is the environment.  So best practices indicate that you should be dialed in everywhere else in terms of circadian entrainment. 

  • Properly time your light exposure
  • Perform time-restricted eating
  • Get adequate physical activity throughout the day(>10,000 steps)

You should do this during the 2 months you do one of these diets. Continue following these principles when you reintroduce new foods as well. In fact, you should just be doing these things all the time anyway.

A couple of studies show why this is important. Circadian disruption caused by jet lag alters the circadian rhythm of the microbiome. In addition, disruption of the microbiome causes circadian disruption in the liver

It works in both directions.  So if you do a low fermentation diet for a couple of months, make sure you also prevent circadian disruption.


Many people take to low fermentation diets to reduce the symptoms of IBS, IBD, and SIBO.  These diets are great in the short term to manage symptoms.

However, most experts in the area don’t recommend long term usage of these diet.  Part of the disruptive effects of these diets over the long term likely comes from circadian disruption.

If you do one of these diets for the recommended 2-3 month period, take your circadian rhythms in to consideration.  And just a heads up, it’s probably not sufficient to just do TRE and block blue light. 

Based on the above study, a low fiber diet made it more difficult to entrain to TRE. So get outside during the day and block blue light at night. Set a feeding window < 12 hours long and stick to it.

Finally, get adequate physical activity and your circadian clocks will be in harmony with one another. As will your digestion.

2 thoughts on “A low fiber diet may be disrupting your circadian rhythms

    • cincodm says:

      That’s neither well thought out nor evidence-based. That’s not to say that I think a carnivore diet isn’t better than what most people eat. It’s that there is a complete absence of evidence for that and there’s no mechanism for it that can’t be reproduced via an evolutionarily correct process, aka fasting. Plus, tons of data that a high fiber omnivorous diet promotes both healthspan and life’s span. If you have that type of data I’d love to see it.

      Also, mice being nocturnal doesn’t disqualify all data based on them. All of the molecular mechanisms behind the circadian clock were discovered in lower organisms, and mice played a big role. Now shoo and go troll somewhere else.

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