Study shows circadian disruption damages the gut and microbiome

Circadian disruption increases the risk of many health problems. Most of the chronic health issues plaguing us today are either caused or made worse by circadian disruption. And since modern life essentially promotes circadian disruption, this is bad news for team human.

Circadian rhythms help coordinate physiological processes within the body. Therefore, things like blood glucose regulation require timely and proper communication between organs and tissues. The liver, pancreas, gut, muscles, fat, bone, adrenals, brain and kidneys to name a few.

Each of these organs contains its own clock that helps it tell time. And when the clocks are on the same time, there’s circadian synchronization and physiology hums along nicely. This promotes a state of health.

But when they all march to the beat of their own time, this is circadian disruption. As a result, our physiology is thrown off. This is bad for every aspect of health. And tissues that are regulated outside our conscious control suffer badly, including the gut. I’ve covered this in many blogs including one you can check out here.

A new study in rats shows us how one of the most common habits we have causes circadian disruption. Eating late at night in an environment similar to ours altered the microbiome and caused circadian disruption in many tissues. Let’s take a look.

Image result for circadian disruption microbiome

Mimicking modern life in rats to induce circadian disruption

For this study, researchers wanted to mimic the modern human lifestyle as closely as possible. Rats are active during the night and sleep during the day, the opposite of humans. So to extend their active period, they put them on an 8/16 (light/dark) cycle instead of 12/12. Consequently, this more closely mimics our extension of the active period with artificial light.

The rats were separated in to 4 groups, all eating the same amount of food. The groups were:

  • Free-fed-Free access to food during the dark period
  • BLD-Breakfast, lunch and dinner
  • BLN-Breakfast, lunch, and nighttime snack
  • LDN-Lunch, dinner, and nighttime snack

Lights on, marking their sleep/inactive period, was ZT0 while light out, marking their active period, was 8 hours later at ZT8. Meal timing was:

  • Breakfast from ZT8-10
  • Lunch from ZT13-15
  • Dinner from ZT18-20
  • Nighttime snack ZT 22-24

Consequently, these times line up in a human awakening at 7am to:

  • Breakfast at 7am
  • Lunch at noon
  • Dinner at 5pm
  • Late night snack at 9pm

As a result of the layout, this study effectively created 2 separate late night eating conditions. The first consumed breakfast & lunch, skipped dinner and had a snack(BLN). The other skipped breakfast, had lunch, dinner, and a snack(LDN).

Late night eating induces circadian disruption and changes the microbiome

Overall, both late night eating groups saw greater weight gain and a decrease in activity. Seems like this behavior promotes others common in modern life. This doesn’t surprise me because circadian rhythms regulate motivation.

There were other metabolic problems that popped up as well. Both late night eating groups saw increased:

  • Serum and liver triglycerides
  • Total cholesterol
  • Liver inflammation
  • ALT(A liver enzyme indicative of dysfunction)

And in the gut, late night eating caused:

  • Gut inflammation
  • Decreased mucus secretion
  • Lower antimicrobial peptides

Therefore, late night eating effectively damaged the liver and gut while making the gut more susceptible to dysbiosis. However, late night eating didn’t affect the master circadian clock. And while this may sound like good news, it’s not. Because it caused a 4 hour phase delay in the liver, fat, muscle, colon, ileum, and jejunum.

In other words, it de-synchronized the peripheral clocks from the master clock. This is a huge problem that decreases resilience in the gut and predisposes to dysbiosis.

Circadian disruption and the microbiome

Inducing circadian disruption via late night eating also altered the microbiome. Each groups saw separate changes:

  • LDN only saw decreased diversity
  • LDN had decreased Bacteroidetes(31%) & Verrucomicrobia(61%) and increased Spirochaetes(74%) & Proteobacteria(26%), Actinobacteria(88%), and Tenericutes(300%) compared to FF & BLD
  • BLN had decreased Firmicutes(12%), Spirochaetes(18%) & Verrucomicrobia(42%) and increased Proteobacteria(89%), Acidobacteria(52%), Actinobacteria(85%), Tenericutes(70%) & Deferribacteres(24%) compared toFF & BLD
  • Both had upregulated microbial pathways of fatty acid synthesis and the glyoxylate cycle.

I don’t think the specific strains are really that important here. Although, as a result of poor gut defense, Proteobacteria increased. A note on Proteboacteria:

In human gut, interaction between microbiota and the cells plays an important role in digestion. However, it also helps shape and modulate the immune system. In cases of increased disease (gut), Proteobacteria are often found to have increased in number, which is evidence of instability of microbiota.

The Proteobacteria phylum contains a number of opportunistic pathogens including:

Tenericutes was also highly upregulated and contains Mycoplasma. Mycoplasma is a genus of bacteria with members that cause walking pneumonia, bacterial vaginosis, pelvic inflammatory disease, male infertility, and spontaneous abortion.

It’s not the least bit surprising to see an increase in Proteobacteria with late night eating. All of the above are opportunistic pathogens. Circadian disruption creates an opportunity for them.

Wonder if the decreased antimicrobial peptides and thinner mucus layer play a role here?

Circadian rhythms improve resilience to opportunistic pathogens

What is an opportunistic pathogen? An opportunistic pathogen normally exists in our gut without causing problems. But how and why?

When our gut operates the way it should, the digestive process and immune system keep pathogens in check. But when either of those systems break down, opportunistic pathogens overgrow and cause problems. It’s not that the free-fed and BLD mice didn’t have any Proteobacteria, they just had less. Because their gut kept it in check.

Candida albicans is a great example of this. C. albicans is actually a healthy part of our microbial garden when in low numbers in the yeast form. Therefore it’s not a problem in a healthy gut. It doesn’t become problematic until environmental conditions promote yeast to fungal transition and the immune system can’t hold it in check. That’s why it’s more common in immuno-compromised populations.

This study suggests that circadian disruption from eating late at night impairs gut, liver, and immune function. And by doing so, gives opportunistic pathogens the right opportunity to destabilize the microbiome.


Circadian rhythms help stabilize the microbiome by promoting a healthy gut. At the cellular level, optimizing circadian rhythms promotes gut health by organizing cellular repair and replacement. It also helps other organs that work with the gut promote health by synchronizing peripheral clocks in each organ.

The microbiome also has a circadian rhythm, changing throughout the day based on our behavior. But when our behavior causes circadian disruption, our microbiome works against us. Opportunistic pathogens can gain a hold and cause more damage in the gut and beyond.

This study suggests that eating late at night disrupts circadian rhythms and destabilizes the microbiome. This is likely due to decreased resilience from damage to the gut. Further studies in humans are warranted to see if the same holds true for us.

We have a new module coming to the program scheduled for the end of the month. This module is a quantum leap forward for gut health and synthesizes the 2 main topics of this blog. I’m talking about Syncing the gut clock to your circadian rhythms. So far I suspect it will be beneficial for:

  • Enhancing deep and REM sleep
  • Decreasing the urge to urinate at night
  • Improving electrolyte balance
  • Decreasing pain/Breaking the pain cycle
  • Improving bowel regularity and stool consistency
  • Improving the cortisol awakening response
  • Improve mood/anxiety
  • Improving fat absorption
  • Decreasing leaky gut and neuroinflammation
  • Optimizing blood glucose regulation

This will add more great material to the program. Additionally, we’ll start a challenge for members to make some tweaks to their current plan and measure their progress.

Of course, we’ll report here on the blog, so stay tuned!

4 thoughts on “Study shows circadian disruption damages the gut and microbiome

  1. Sherry L Lassin says:

    I get up at 9. I eat breakfast at 10, lunch at 3, and dinner at 8 when my husband can join me because that is the time he gets home from work. I go to sleep between 12 and 1 . I wonder how that this rhythm would be interpreted. I thought I was doing well with intermittent fasting.

    • cincodm says:

      It depends on the individual. I have people in my programs measure things like heart rate variability and glycemic control. You also have to take in to consideration your individual circumstances. For me, that schedule simply wouldn’t work and definitely wouldn’t be ideal even if my job/schedule allowed it.

  2. ME says:

    How would this information line up with the studies that have been done showing that a snack right before you go to bed can help with adrenals and waking up in the middle of the night? I often wake up around 4 a.m. and find that if I have snack right before bed I am less likely to wake up in the middle of the night.

    • cincodm says:

      There haven’t been studies showing eating at night helps the adrenals. I know people often experience relief in doing so, but I suspect this is something that is better addressed working on circadian rhythms and managing stress.

      I don’t think having HPA axis dysfunction would prevent the negative effects of eating at night on the microbiome. If anything, I think it would make it worse. That’s why it’s not a practice I’d recommend. If you have issues with your blood glucose tanking at night, fixing your light exposure to increase melatonin and/or working to improve insulin would be a much wiser approach.

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