How to improve gut health? Build resilience

People with gut problems often spend an eternity looking for how to improve their gut health. Many look to simple solutions such as supplements and cutting things out of their diet.

These approaches rarely work in the long term because they’re missing a large part of the equation. They don’t look at the body as a system.

We are all a collection of cells, organs, and tissues working together in synchrony for one common goal: survival.  For most of our evolution humans battled with the environment, other life forms, and sometimes each other for survival.  But now it seems for many of us, the battle is within.

For some people, rather than teaming up to battle nature, our organs are literally battling themselves.  Our gut, charged with preventing large proteins and microorganisms from accessing our blood circulation and organs, takes the night off. 

Chronic inflammation turns our own immune system against us.  The gut, liver, pancreas, kidneys, muscle and fat can’t get glucose out of our blood fast enough, causing free radical damage, literally caramelizing our nerves and small blood vessels.

But how did this happen?  And more importantly, how do we prevent or reverse it?

Where’d all the resilience go?

Our physiology works optimally under certain operating conditions.  Unfortunately, modern society presents the wrong signals to our body and this causes us to be more susceptible to dysfunction. 

This dysfunction leads to problems like metabolic syndrome, gut disorders, autoimmunity, and neurodegenerative diseases such as Alzheimer’s or Parkinson’s disease. Interestingly, as we get older, our risk for these chronic disease increases.

When we’re young we can hang.  You can throw challenge after challenge at us and we bounce right back. 

Drink socially until 3am and wake up at 7am for a Calc exam at 25?  No problem.  Have a glass of wine at 8pm and be up by 7am for yoga at 40?  Hahahaha.

It’s no secret that aging is the most important risk factor for all chronic disease. And there’s a reason that your ability to hang and bounce back decreases as your chronic disease risk skyrockets. 

To learn how to improve gut health, you must learn what resilience is and how to build it.

What is resilience?

Resilience is the ability to take a beating and bounce back.  It’s what makes a fighter take a beating for 10 rounds just to knock out their opponent in the 11th. 

But resilience also works at the tissue level.  When we exercise to build up our muscles, we are building resilience in them. However, this requires balancing tissue stress and recovery.

Apply a little bit of stress, let the tissue heal, and you come back stronger.  But we don’t have unlimited resilience, and if we apply too much stress or don’t allow our muscles to recover, they become damaged and fail.

This same concept also applies to the gut.  In fact, I believe this is a major contributing factor in people’s long-term battles with functional gut disorders such as IBS, IBD, SIBO, SIFO, and the like. 

When we’re young and resilient, it’s much more difficult for these disorders to take hold. Sure, young people do experience them.  It’s not like everyone with a gut problem is over the age of 40. 

But that’s because youth doesn’t have the resilience market cornered; resilience isn’t based solely on age.  Early childhood stressors can throw our entire system off, and this has a ripple effect throughout life. And chronic stress can really take a toll on the gut.

Once we destabilize the gut, we lose resilience and damage can accumulate.  And just like any other damaged tissue, applying stressors to a tissue with low resilience just causes inflammation and more damage to accumulate.

For people with gut problems, this results in what they call a flare.  But perhaps I’m a bit ahead of myself.  Let’s use a graphical illustration to pick this apart.

How to improve gut health?  Build resilience

Resilience: The difference between “Healthy” and “Susceptible”

While this image comes from a study on circadian rhythms and cardiovascular disease, it’s relevant to any tissue under circadian regulation, including the gut.  This chart gives us incredible insight into why people tend to stay susceptible to gut problems, and how they can address the problem in a way that optimizes the likelihood of successfully treating it.

At the top we see a generic chart of what is termed the resting physiological rhythm and rhythm during stressors.  The resting physiological rhythm is set by a number of factors including:

  • Circadian rhythms
  • Age
  • Accumulated damage
  • The microbiome
  • The overall health of the tissue 

The rhythm during stressors simply indicates how the tissue responds to immediate stressors. Obviously, the resting physiological rhythm is an important component of this.

On the bottom left we see an example of healthy local tissue function in the gut.  Having a low resting physiological rhythms makes us resilient to stress. 

Therefore, resilience is effectively greater when your resting physiological rhythm is further away from the risk threshold.  So, when someone who accurately represents this graph consumes something that stresses the gut, the rhythm during stressors rises, but it stays below the risk threshold that represents pathology or a flare.

How to improve gut health? Move from susceptible to resilient!

When someone who represents the “Susceptible” graph on the right consumes something that causes tissue stress, the rhythm during stressors increases above the risk threshold.  For these people, the same exact type and amount of stress will throw their gut spinning in to dysfunction because they’re not resilient.

A great perceptual example of this come from a study looking at the effects of gluten. Researchers exposed gut tissue from different types of people to gluten. This included:

  • Humans with active celiac disease(ACD)
  • People with celiac disease in remission(RCD)
  • Those with gluten sensitivity(GS)
  • Healthy controls(HC)  

They found greater permeability in the ACD vs RCD, and HC; and in GS vs RCD. Oddly enough, the RCD group actually had the lowest intestinal permeability when exposed to gluten.

This occurred despite having the genetic predisposition to celiac disease.  Obviously some environmental factor is at play, and in my opinion, that factor is resilience.

I believe this same phenomenon likely plays a role in bile acid diarrhea.  Bile is released in to the small intestine when we eat. 

The bile acids circulate throughout the small intestine and 95% are reabsorbed in the ileum back to the liver.  Bacteria metabolize the remaining bile acids in to secondary bile acids in the ileum and colon.

But the receptors for bile acid recycling are under circadian control. If they’re not expressed in the ileum more bile acids enter the colon. 

There, they cause diarrhea and get converted in to toxic secondary bile acids that can damage the colon and promote tumor growth.  Coincidentally, the receptors that detoxify secondary bile acids are also under circadian control.

Building resilience in the gut

So right about now you’re probably asking yourself how you can build up this resilience I speak of.  Most people are doing at least something to build up resilience. 

More than likely, you’re trying to avoid things you’re sensitive to, which will decrease the inflammatory load in your gut.  That’s a great thing, but I don’t believe it’s enough.

In fact, I think most people’s anecdotal experience proves it’s not enough.  Those who start an elimination diet often end up eating a handful of foods or, at the very least, are never able to re-introduce foods that are stressors to them.  This in and of itself indicates to me that it’s not enough.

In fact, long-term elimination diets seem to back-fire. Yes, certain foods, particularly plants, have components that may stress digestion. Taking them out is the smart choice when having problems.

But these same components likely build up resilience in the gut when regularly consumed in a healthy gut. So long term elimination essentially knee-caps resilience in proportion to the number of foods removed.

Other people approach the situation with a much more aggressive tack, throwing an arsenal of antimicrobials at their gut in a kill protocol.  From what I’ve seen this also doesn’t appear to work.  Sure, it may boot out some bad actors temporarily and reduce symptoms for a short time. 

But I’ve rarely heard of a situation where someone’s done a kill protocol and not reverted back.  In fact, a lot of the time kill protocols can decrease resilience, particularly if they are hard on the gut.

If it happens with an antibiotic as powerful as Rifaximin, it’s happening with standard herbal protocols.

Important factors to improve resilience and gut health

I think the fundamental failure with these approaches is that they don’t address resilience to a significant degree.  You build resilience with your lifestyle, not from a kill supplement. 

Resilience relies on strong circadian rhythms. This optimizes communication between the gut, liver, and immune system, making us resilient to dysbiosis or a pathogenic assault.

Adequate high quality sleep also builds resilience.  We incur damage in the gut during the day when we eat and repair it during sleep.

Sleep loss causes gut dysbiosis, increases gastric acidity the next day, and makes the gastric mucosa thinner. The stomach loses resilience, and more susceptible to ulceration.  All of these things damage the gut.

Finally, physical activity is critically important to maintaining a healthy gut.  In fact, I would even lump in fasting/calorie restriction in to this equation.  Both of these factors play a role in resilience. 

Both physical activity and fasting/calorie restriction are our best ways to hedge against the loss of resilience that comes with aging.  Nutrient deprivation via either modality activates ancient pathways that make our cells, and us, more resilient.

Measuring resilience to improve gut health

Fortunately we have a pretty good measure of resilience that we can use to determine where we stand called heart rate variability.  Heart rate variability is a measure of your cardiovascular system that indicates how balanced your autonomic nervous system(ANS) is. 

The ANS is the arm of your nervous system that controls automatic processes such as heart rate, blood pressure, the immune system and, yes, digestion. There are 2 arms of the autonomic nervous system: The sympathetic arm drives fight or flight responses while the parasympathetic arm drives rest and digest responses. 

People with greater sympathetic activity tend to have more of a hair trigger and become more stressed.  This type of imbalance negatively affects digestion due to lower parasympathetic activity. 

Things like meditation and vagus nerve stimulation activate the parasympathetic nervous system, which is why both seem to improve digestion.

Using heart rate variability to improve gut health

By measuring heart rate variability, we get a glimpse in to how our ANS is functioning.  If you have a gut problem, chances are pretty good that your heart rate variability is low, indicating poor rest and digest. 

Studies have shown that those with IBS have poor heart rate variability compared to healthy controls. Check a review here and a recent randomized clinical trial here.

Unfortunately, this is a rather roundabout way of getting to what we want to know as it is measuring the cardiovascular system.  Ideally we’d measure ANS responses directly in the gut, but we don’t have the technology to do that. 

Nevertheless, I’d more than likely test my HRV before trying any sort of kill protocol or adding back any new foods.  And if I had some social event I knew was going to substantially increase my rhythm from stressors, I’d do my best to increase my HRV to lower my resting physiological rhythm. 

Use the chart below and one of the common heart rate variability apps to see where you stand based on your age.

Image result for heart rate variability age
Image source

Clues from our hunter gatherer ancestors

While removing stressors from the gut is certainly a smart move, I don’t think it moves the needle on the resting physiological rhythm.  In fact, the only thing I’ve seen do that significantly are the 3 factors I discussed in the Building Resilience section. 

Based on this, you’d expect there to be little to no prevalence of these conditions in our hunter-gatherer brethren still floating around in the jungle who basically live this lifestyle, which seems to be the case. Obviously they’re more resilient than we are and they regularly fast, are physically active, have ideal circadian exposures, and get adequate high quality sleep. 

You can also imagine that the gut of a hunter-gatherer is exposed to far more pathogens than ours.  They don’t consume freshly washed produce, and butchering of their kills is unlikely to meet the stringent requirements that meat processing plants in the United States have to meet.

Additionally, they tend to respond quite well to the antimicrobial herbs that form the basis of the kill protocols most people with gut problems use.  In fact, they typically respond to teas and tinctures made by hand, not the ultra-concentrated versions that fail in us. 

None of this is really proof of anything, just an interesting tidbit.


When you’re trying to learn how to improve gut health, focus on the big picture. I’ve noticed a slow but emerging paradigm shift in the way people approach the treatment of gut disorders. 

What was once made up almost entirely of restrictive dieting and kill protocols is making way for a more holistic approach that involves things like circadian rhythms, yoga, meditation, exercise, time-restricted eating, sauna/steamroom, and sleep optimization.

Let’s face it, the results from restrictive dieting and kill protocols as primary therapies haven’t been all that great.  That’s not to say that using either can’t be helpful, but they should be looked at as adjunct therapies used to bolster a more pragmatic approach. 

An approach much like the holistic one that most practitioners are hovering towards. I think the way a member of my Circadian Retraining Program private group put it describes it best. 

Kill protocols and restrictive dieting move the needle momentarily but end up putting you back where you started, or worse.  When you build resilience by addressing critical factors like circadian rhythms, sleep, physical activity, and the feeding/fasting cycle you shift your susceptibility in a way that brings you closer to normal, healthy gut function.


Most people, when they encounter something similar to this flu-like state assume they’re entering a flare and that whatever they’re doing isn’t working.  But when we measure things like HRV, sleep, and heart rate we see we’re moving in the right direction. 

And with the proper variables to tweak and improve these measures, that builds resilience.

4 thoughts on “How to improve gut health? Build resilience

  1. Charles says:

    Hi Dave

    Concerning vagus nerve stimulation and parasympathetic balancing; I have been using this way of breathing in bed at night to help fall asleep faster and after exercise for better recovery.

    A variation of this is used by the military to help troops fall asleep even in combat zones wherein they inhale for account of 4, hold for a count of 7 and exhale for a count of 8. When I use this version, I usually add a hold after the exhale for a count of four with a stomach vacuum before the next inhalation.

Leave a Reply

This site uses Akismet to reduce spam. Learn how your comment data is processed.