GERD and SIBO: A circadian perspective

Most bowel disorders have some sort of circadian contribution, whether it be circadian disruption being one of the underlying causes of the disorder or a contributor to the persistence of it.  So, with that in mind, I thought I’d cover how circadian disruption may contribute to the progression from gastroesophageal reflux disease(GERD) to small intestinal bacterial overgrowth(SIBO) and how ignoring circadian disruption may contribute to the persistence of both.

Circadian disruption and GERD

In the mainstream healthcare paradigm, GERD is a problem of excess stomach acid production eroding the healthy tissue in the esophagus.  In the functional medicine world, the belief is that gastric acid is actually low but bacterial overgrowth somewhere further down the line in the gut causes pressure in the stomach forcing the gastric contents in to the esophagus.  So who’s correct?

Based on the data I’ve seen, I side more with the mainstream healthcare paradigm that increased acid contact in the stomach and esophagus is the cause of the problem.  But, I have to wholeheartedly disagree with reducing stomach acid as the solution to the problem.  In fact, that likely doesn’t even address the proximal cause of it.

There is ample mechanistic evidence that circadian disruption is a major cause of the damage associated with GERD and, therefore, addressing circadian disruption is a much wiser solution to the problem.  A study in mice found that sleep deprivation compromised the integrity of the gastric mucosa, the mucus layer that protects the lining of the stomach from contact with gastric acid.

A study in humans found that poor sleep caused an increase in gastric acid exposure the following day.  Symptoms of GERD also correlated with poorer sleep quality.  It’s not difficult to imagine how this combination could damage the stomach and esophagus.  Another study in humans found that people with irregular meal timings(>2 hr deviation 2x/wk) had 6.3x and 3.5x greater odds of acquiring H. pylori infection with gastritis and gastritis alone, respectively.

So how does all of this relate to circadian rhythms?  Well, sleep is partially dictated by circadian rhythms and circadian disruption leads to poor sleep.  Furthermore, peripheral clocks throughout the body are entrained by the feeding/fasting cycle.  Additionally, regular meal timing optimizes digestion through circadian rhythms.

When meal times are consistent, the hunger hormone ghrelin causes an increase in gastric acidity right before the schedule meal.  If this happens but no food comes, the stomach is exposed to gastric acid for a greater period of time, both during the regular meal time as well as during the time you actually ingest food.

Finally, digestion follows a circadian rhythm with digestive functions decreasing at nighttime.  This likely has to do with scheduling repair functions that can’t be accomplished when you’re eating.  If you eat right before bed, these repair processes never have a chance to be implemented and damage can accumulate over time.

Another problem with late night eating is that the lower esophageal sphincter, charged with preventing back up of acid from the stomach to the esophagus, doesn’t work well at night.  Thus, eating that late will disrupt sleep and likely allow acid from the stomach to creep back in to your esophagus while you’re lying on your back.

This is where using things like proton pump inhibitors(PPIs) can be problematic.  Sure, they reduce acid exposure and could, in theory, allow the stomach lining and esophagus to heal.  The issue is that with this symptom relief people often don’t change their behavior and, by reducing the acidity of their stomach and continuing to eat at irregular times or late at night, they may be priming the pump for SIBO.

I see no problem with using acid reducers other than PPIs in the short term to heal damage caused by a few days worth of bad decisions.  They’re also useful in combination with antibiotics to tamp down an H. pylori overgrowth.  Unfortunately, people use these medicines indiscriminately and long term without addressing the underlying issue, which allows things to progress down a road you don’t want them to.

GERD and SIBO: kissing cousins

There’s an established link between the use of PPIs and SIBO.  The mechanism behind this link is pretty straightforward.  Decreased acidity allows bacteria to survive in the normally acidic stomach, and increased bacterial exposure through the small intestine increases the risk of SIBO.

Of course, this has led to a few potential fixes to the problem.  First, the risk of SIBO with PPIs can be reduced with high dose rifaximinProkinetics are also an option, as they’d likely keep things moving along.  But how much of this is a direct cause of suppressing acid production and how much is caused by not changing the behaviors that ultimately led to GERD, including circadian disruption?  A recent study may indicate behavior/circadian disruption is more likely the cause than simply the use of PPIs.

A study carried out by Dr. Mark Pimental’s team found that PPI use was similar between people with and without SIBO, so it’s unlikely that PPIs cause SIBO.   Being older than 60 years old, having IBS, and being Type 2 diabetic were strongly related to the presence of SIBO.  All 3 of these factors are associated with circadian disruption.  This supports the notion that the problem isn’t necessarily using acid reducers such as PPIs, it’s not addressing the low hanging fruit such as irregular meal timing and late night eating that can disrupt circadian rhythms.

My experience with the above

Truth be told, I’ve traveled down this road before which is why I’m familiar with it.  I started getting really bad GERD around 10 years ago and turned to Prilosec.  While Prilosec isn’t a PPI, it works by reducing stomach acid.  Of course, I experienced symptom relief which was great so I kept eating at irregular times, late at night, and doing things that promote circadian disruption and GERD.

This caused me to be dependent on Prilosec to manage the symptoms, and my digestive issues to progress past GERD.  Gas, bloating, and diarrhea became the norm.  It wasn’t until I corrected my behavior that my gut started working for me, not against me.

Of course, this didn’t happen overnight.  I spent thousands of dollars on supplements from digestive enzymes to biofilm disrupters, probiotics to gut support.  I tried Paleo, keto, and SCD but the didn’t work and I didn’t feel healthy.  I also gave up gluten, dairy, coffee, FODMAPs, and beer.  Due to poor sleep and adrenal dysregulation, I stopped exercising and decreased my physical activity.  My blood glucose was in the low diabetic range, and the dawn phenomenon was my every morning.

It wasn’t until I changed my behavior that my digestion moved from bad to better to normal, to better than normal.  Sleep also improved and my adrenal function normalized.  I was able to increase physical activity and gradually increased exercise.

It was a gradual process and it wasn’t easy, it took a lot of effort up front but now it’s just automatic.  I feel great, there are no food restrictions, and my hemoglobin A1c, a 3 month running average of blood glucose, is 4.8%.  This correlates to an average blood glucose of 92 mg/dL, which is phenomenal.


Lifestyle can play a pivotal role in your digestion.  Many factors common in the modern lifestyle conspire against us to make our digestion sub-optimal.  We eat at the wrong times, eat on an irregular schedule, live sedentary lives, and don’t get appropriate exposure to the Sun to help set our day/night cycle.

These factors disrupt our circadian rhythm, which helps set the tone of our autonomic nervous system.  The autonomic nervous system sets the “tone” of all automatic processes including the stress response, digestion, immune function, our mood, cognition, and energy levels.

Research in the area of circadian rhythms is currently exploding.  This is a paradigm shift from how we normally look at human health.  We’ve always focused on what and how much, but circadian rhythms address a new factor: when.  As it turns out, when matters.  A lot.

2 thoughts on “GERD and SIBO: A circadian perspective

  1. Jeffrey Rijsbergen says:

    Hi, I have a question
    Can you send me your day’s rhythm what you did in a day when and what time
    And what you used to improve your digestion
    Is that possible that I can receive that from you
    Kind regards Jeffrey Rijsbergen

  2. cincodm says:

    Hey Jeffrey, that’s not a cut and dry answer and is different for everyone based on lifestyle, genetics, and what they have going on. There really is no cookie cutter answer to this. In order to make recommendations on that order, I’d need to take a thorough history and even then there is some tinkering to be done. If you’re looking for a do it yourself way to optimize this stuff, I offer my Circadian Retraining Program, the details of which you can find here:

    I’ve been working with people doing the program for 18 months and they’re seeing fantastic results, but each one of them has an individualized plan that I helped them come up with. The program is almost 9 hours of video, so as you can probably tell it’s pretty time intensive to come up with a plan to optimize circadian rhythms. Thanks for reading!

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