The ultimate guide to fasting for gut health

In my last blog Bile, bacteria, and chronic inflammation, I went over the importance of bile in establishing and maintaining a healthy gut and improving chronic inflammation.  One of the primary ways bile and the enterohepatic circulation help decrease systemic inflammation is through the processing of endotoxin.  If you didn’t get a chance to check it out, read it here.

At the end of the article I promised to do 2 follow up blogs that cover improving the way you handle endotoxin.  In these blogs I’ll cover 2 important concepts: decreasing the amount of endotoxin in the gut and increasing the expression of alkaline phosphatase in the gut and liver.  Well, you just jumped in to the blog on reducing endotoxin.

There are numerous benefits to fasting that affect nearly every system in the body.  Rather than doing a 10,000 word blog covering tidbits on each of these benefits, I’m going to comprehensively cover a small portion of the benefits of fasting as they pertain to endotoxin.  I’ll do this by covering the following topics:

  • The evolutionary basis for fasting
  • How fasting affects endotoxin levels
  • How this and other factors affect systemic inflammation
  • The multiple ways to address fasting
  • Why I practice fasting the way I do
  • Choosing a method of fasting that meets your needs and lifestyle

By the end of this blog I hope you understand why fasting is important and find a way to implement it in to your lifestyle.  How you decide to do this is completely up to you.  Just realize that just as your brain and muscles need a rest, so does your gut.

In my opinion, fasting is something that should be looked at as a critical tool in optimizing gut health.  When you look at all of the evidence I think there’s strong support for this notion.  So let’s dig in and see why.

The evolutionary basis for fasting

Identifying and applying concepts from evolution can be very useful tools for improving health.  In fact, evolutionary biologists have put forth a “mismatch theory” of modern chronic disease.   This theory seeks to explain the increasing prevalence of diseases such as Type 2 diabetes, cardiovascular disease, arthritis, and other common ailments of modern life.

The mismatch theory postulates that modern chronic disease is a byproduct of a mismatch between our genes and the environment we currently live in.  This mismatch exists because the environment our genes evolved under is drastically different from the one they are currently participating in.

Think of it this way.  The environment selects winners and losers based on how well their gene set allows them to adapt to the environment.  The losers fall off while the winners make it to pass on their genes to the next generation.  This system works out great for the winners until the environment changes in a way that makes them the losers.

The attractiveness of the mismatch theory lies in the fact that people living in conditions similar to the ones we evolved under don’t experience the chronic diseases that we do.  An additional line of evidence is that these people do begin experiencing these diseases when they abandon their traditional lifestyle for a more modern one(1, 2).  When they switch back to their traditional lifestyle, things like Type 2 diabetes go away(3).

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Evolution and fasting

As you can probably guess, these tribes of modern hunter gatherers don’t typically experience gut problems like IBS, IBD, and SIBO.  At quick glance, it’s fair to say that this may be more due to the content of their diet rather than regular periods of fasting.  But upon further review I don’t believe this theory holds water.

There’s no argument that modern day hunter gatherers are exposed to far more microbes than we are.  They don’t wash their hands with soap, they don’t have antibiotics, and they don’t have the convenience of a sink to wash their produce in for 5 minutes. Basically, they yank their produce out of the ground, give it a quick rinse with water from a non-sterile water source, and eat some of the microbes from the soil they picked it from.  Don’t even get me started on how they butcher an animal.

If you think this through, the gut of a hunter gatherer is exposed to a large amount of bacteria on a daily basis.  This means they are probably exposed to far more endotoxin than we are.

An interesting hypothesis has emerged recently that indicates the chronic accumulation of endotoxin in the blood may be what’s causing the low grade inflammation associated with chronic disease(4).  But if modern day hunter gatherers are exposed to more endotoxin than we are, why aren’t they experiencing these chronic diseases?  They must be better at processing it and keeping it out of the blood.  Fasting helps tremendously in this respect, which we’ll cover in a little bit.

Another potential dietary factor for more chronic disease in Western civilization is low diversity in the diet.  However, a lot of modern day hunter gatherer tribes really don’t have that diverse of a diet either.  Most have a couple of staples foods that make up most of their calories and have for hundreds of years(5).  You’d also have to figure that the large amount of fiber some tribes consume would make them more susceptible to small intestinal bacterial overgrowth(SIBO), not more or less immune to it.

A final candidate for the cause of gut problems in people living a modern lifestyle could be sugar consumption.  You definitely can’t argue that we eat far too much sugar in the modern diet.  However, honey is a substantial component of the diet of many modern hunter gatherer tribes including the Hadza.  The Hadza consume 30% or more of their calories from it.

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Not only is this a high sugar load, honey is higher in fructose percentage-wise than high fructose corn syrup.  Even if you assume that the Hadza consume 25% less calories than we do, their daily sugar consumption would still be greater than ours.

We also eat way too much.  But is it the calorie load or the amount of time we spend eating vs fasting?  While the jury’s still out on this stuff, there are a number of mechanistic factors that make regular fasting a pretty solid candidate for why modern day hunter gatherers don’t experience our gut problems.  So let’s dig in to those mechanisms.

Fasting, the migrating motor complex, and bacteria

As I said above, I look at fasting as an integral part of the digestive process.  While most people focus on what happens when we eat something, equally important functions occur when we’re not.  This includes a housekeeping mode called the migrating motor complex.  If you’re really interested in the science behind the migrating motor complex, check out this blog.

The migrating motor complex is a phase that occurs in the small intestine when we are no longer digesting food.  Like an all night kegger, the party isn’t over once everyone leaves.  The fun part gives way to the burdensome clean up the day after.  In the same way, the migrating motor complex cleans up your small intestine when you’re done eating by sweeping undigested food particles and bacteria from the stomach and small intestine in to the colon.

As you can imagine, your gut isn’t a very clean place.  You definitely want to tidy up after a meal and the migrating motor complex does an excellent job provided you let it.  And here’s how you do that…

Turning on the migrating motor complex by fasting

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The basics of turning on the migrating motor complex are pretty simple.  Approximately 3 hours after your last meal, it begins.  Your stomach begins moving and you get a nice squirt of stomach acid.  This mixes with bacteria left over in the stomach as well as incompletely digested food particles.  The acid helps kill any bacteria that may still be alive and the contractions help mobilize bacteria and the food particles for removal.

Next, the pylorus opens and the contents of the stomach move in to the duodenum.  The pancreas and gallbladder squirt in some pancreatic enzymes, bicarbonate, and bile for good measure to neutralize the acid.  Just a note, during this first phase, the pylorus stays open, making this an opportune time for trapped gas to get burped out.

From there it’s a cakewalk.  Your small intestine propels the digestive enzymes and loose bacteria gradually toward the colon.  All along the way, the antimicrobial effects of bile kill bacteria and keep it from slipping across the gut wall into the blood.

Once bile makes it to the ileum, bile acids get reabsorbed, sent to the liver, and re-stored in the gall bladder.  The process of bile absorption also brings another welcomed effect: the release of antimicrobial peptides to kill most of the live bacteria remaining.  The bacteria get pushed in to the colon and you’re ready for the next round of the migrating motor complex, or your next meal.  This entire process takes approximately 90 minutes.

An important concept to understand here is that movement is good.  While most people have a 2-D image of bacteria interacting with the gut wall, this isn’t the case.  There’s a loosely adherent mucus layer that keeps bacteria a distance from the enteroyctes that make up the intestinal wall. This mucus layer plays a big role in keeping your gut healthy.

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The mucus layer prevents a large immune reaction every time you eat.  By keeping bacteria away and requiring them to travel to enterocytes, your mucus layer gives your immune system time to take out bacteria before they can become a problem. Space Invaders is a good analogy here.

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During the early levels of Space Invaders, the bad guys drop slowly giving you enough time to peck away at them.  As you move up in levels, they start coming down much faster, becoming progressively more difficult to eradicate.  This gradual increase in speed would be similar to having a less viscous or smaller mucus layer, which underscores its importance.

Along with the integrity of the mucus layer, constant motion in the direction of the colon prevents the mucus layer from accumulating too much bacteria just like water from a moving creek has less bacteria than a standing pond.  Motion is good, stagnation is bad.

How to keep the bacteria moving

Now that you see how important it is to keep things moving, you’re probably wondering how you do that.  It may seem counterintuitive, but the best way to do this is to fast.  If you only look at digestion from an eating perspective you’d think that eating again would be the best way to keep things moving.

When you include the migrating motor complex and understand how it works, you can see why this isn’t the case.  Once you eat, wherever the waves of the migrating motor complex are occurring, they just stop dead in their tracks.  This diverts attention from clean up to the digestive process in the stomach.

From an evolutionary perspective, not giving preference to digestion and absorption of nutrients when food becomes available would have tragic disadvantages in an environment where food is scarce.  However, in an environment where food is plentiful it could have severe consequences on keeping the gut clean from bacterial overgrowth.

This break in the migrating motor complex effectively brings stagnation to wherever it is.  Probably not a huge deal if you’ve already gotten in a cycle or 2 or it just so happens to stagnate near the duodenum.  However, if you’re pretty far down the digestive tract or you chronically interrupt it because you eat every 3-4 hours, your mucus layer is going to gradually become loaded with bacteria.  Not good…Does this look familiar?

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Armed with the science and average timescale of the migrating motor complex, we can make decisions to best maintain a low bacterial count in the small intestine.  Since we know how long after a meal it usually starts and how long each cycle lasts, we can guesstimate as to how long we should take a break from eating.

Determining how long to fast

We know that the migrating motor complex typically starts around 3 hours after a meal so we know we should fast longer than that.  Add in the time it takes for a single cycle, and we’re already at 4.5 hours.  Of course, these times are just averages, so adding another half hour to an hour gives you room to work.

Other aspects of the migrating motor complex stretch this period out even longer.  First, not all cycles of the migrating motor complex begin in the stomach.  Some begin in the small intestine and these cycles aren’t as effective at killing and moving bacteria.  This is because you don’t get that squirt of gastric acid and the gallbladder puts out less bile.  Taking this in to consideration, adding in a second cycle is probably ideal.

Now we’re at 6+hours between meals for effective cleaning of the small intestine.  To put this in to perspective, this would mean you eat breakfast at 6am, lunch at noon, and dinner at 6pm with no snacks in between.  Who actually manages to do this?

Another factor that needs to be taken in to consideration is sleep.  The migrating motor complex is less effective when you sleep so I tend to assume that fasting cycles while asleep aren’t adequate.  So if we wake up at 6am, getting 2 full cycles of the migrating motor complex means we eat our first meal no earlier than 9am which moves our meals to 9am, 3pm, and 9pm.

If you’re a square like me, you’re in bed by 10pm.  In general, to avoid situations like GERD, you want to stop eating 3 hours before bed.  This would put your last meal at 7pm which messes up your eating schedule if you’re trying to get a couple of cycles in before each meal.  For me the solution is simple, but there are a few ways you can get the benefits of fasting.  Let’s look at those and I’ll tell you what I came up with for myself.

Methods of fasting

When people think of fasting, they typically think of going a full day or two without eating.  This is the standard approach but it’s not very fun.  To get the full benefits of doing it this way, you need to do it a few times a month.

A drawback of this method is that you also need to carefully reintroduce food on the days you come off your fast, particularly as it pertains to carbohydrate consumption.  Rapid reintroduction of carbohydrate without being replete in the vitamins needed to process them can lead to the refeeding syndrome.

The refeeding syndrome presents as a micronutrient deficiency even though you’ve eaten enough because stores of the particular nutrients are low but demand for them is high.  This is typically only a problem if you enter the fast already under a mild nutrient deficiency.  Symptoms include electrolyte disturbances that can lead to arrhythmias.  Supplementation of the B vitamins, particularly thiamine, are useful to prevent or correct refeeding syndrome.

Another common approach to fasting is called 5/2.  In 5/2 fasting, you eat however you like for 5 days out of the week and then fast on 2 other days.  This way is a little more flexible, allowing you to eat 500 calories on your fast days if you’re a woman and 600 calories if you’re a man.  Theoretically speaking, you could still interrupt the migrating motor complex too much doing it this way if you spaced out your calories, but it’s unlikely.

The final way is called 16/8.  In this method, you fast for 16 hours every day and restrict your eating to an 8 hour window.  This way is much easier to introduce yourself to fasting because you don’t have to go an entire day without food.  If you time it right, you can eat your last meal at 7pm, be in bed by 10pm, and eat your first meal of the day at 11 am.

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How I made fasting fit my lifestyle

As you may have guessed, I do the 16/8 method because it fits my schedule.  It also seems to me to be the best way to optimize the housekeeping system of the gut based off the timing of the migrating motor complex.

I’m not super rigid on this.  Some days I fast a bit shorter and other days I go a bit longer.  Every now and again I’ll throw in a 24 hour fast and for the most part I make a concerted effort to push my first meal off until 3-4 hours after I wake up.  On most days it’s actually closer to 6 hours.

I think another benefit of doing it this way is I can get more cycles in without having to go a full 6 hours between meals.  The bulk of the time-suck from the migrating motor complex is the 3 hours you need to wait after a meal.  Getting 4 cycles in first thing in the morning allows me to cut the time between meals to 4.5 hours rather than 6 while getting the same number of cycles daily.

On many days I graze during my 8 hour eating window and some days I expand my eating window to 12 hours.  I don’t think you need fasting to consume your life, I just think it’s beneficial to use it as a tool for better digestion.

Evidence for the gut benefits of fasting

There’s a lot of evidence that shows fasting to be very good for reducing levels of inflammation throughout the body.  Recent studies show fasting to have many inflammation fighting mechanisms(6) and to reduce inflammation in the central nervous system(7) as well as the gut(8).  But what about endoxotin levels?

While the effect of fasting on endotoxin levels hasn’t been studied extensively, a new tightly controlled study shows some pretty encouraging results.  In this study, participants were fed exactly the same food but under 2 different conditions: one day spread over 2 meals and the other over 5 meals.  One of the study measures was serum endotoxin.

The results of the study found that after just 1 day, serum endotoxin levels were significantly higher in both lean and obese subjects when they ate the food over 5 meals versus 2 meals(9).  The results are strong because each subject experienced both conditions.

This means that over the course of a single day, when people eat 5 times per day they accumulate more endotoxin in their blood than when they eat the same amount of food over 2 meals.  I’d love to see what happens after eating 5 times a day for many consecutive days.

Another interesting aspect of this study is that it somewhat overturns a long held finding.  Earlier studies indicated that a high fat meal induces low grade endotoxemia.  The thought was that people with low grade endotoxemia were simply consuming too many high fat meals(10).

In this study, when subjects were eating 2 meals per day they were eating more fat at each meal than when they spread it out over 5 meals.  During each meal they were probably absorbing endotoxin, but the periods of fasting between each meal were sufficient to clear it before it accumulated in the gut and blood.

While this study is small(24 subjects), it supports the notion that fasting can lower the absorption of endotoxin from the gut.  Digging in to the potential mechanisms at play, it seems that the housekeeping effect of the migrating motor complex may be keeping bacteria moving out of the small intestine.

In those eating 2 meals, there’s less stagnation in the small intestine than in those eating 5 meals per day.  Less stagnation leads to lower accumulation of endotoxin in the small intestina and, thus, less absorption.

Given that the contents of the diet were identical, the change in endotoxin is due to a non-nutritional component.  Since these were high fat meals, and high fat diets increase the absorption of endotoxin, these results support the notion that fasting has a substantial effect on decreasing the absorption of endotoxin from the gut.


Fasting is a useful tool for those experiencing chronic inflammation.  It’s important to look at the digestive process from the bigger picture.  This bigger picture includes the tidying up that needs to be done between meals.

Over time, not allowing full cycles of the migrating motor complex can lead to the accumulation of bacteria in the small intestine.  This increases the amount of endotoxin in the gut and increases the absorption of endotoxin in to the blood.  Both can lead to increased systemic inflammation.

But…I left out an important factor.  In my last blog I went over how important alkaline phosphatase is for processing endotoxin in the gut and liver.  When we fast, alkaline phosphatase levels go down.  This makes sense because you’re sweeping the gut of endotoxin so there’s less that needs to be processed.

However, we definitely want to optimize alkaline phosphatase levels, particularly in the gut.  But how do we do this?  Well it turns out there may be a nutrient that’s particularly important in this regard.  A nutrient that’s been a crucial part of our diet even before we became hunter gatherers.  A nutrient that plays multiple roles in gut homeostasis that’s also low in the modern human diet.

In my estimation, getting enough of this nutrient is probably one of the first steps you should take in healing the gut.  It sets the stage for better processing of endotoxin and decreased sensitivity to it.  It also sets the stage for proper processing of bile, environmental toxins, and pharmaceutical drugs.

In my next private blog I’ll cover this nutrient, how it works, and why you should be getting enough of it in your diet.  This blog will only be available to members of the facebook page, so request to join here if you want this valuable information.

UPDATE: I’ve been tinkering with the fasting stuff and developed a program based on research in circadian rhythms.  Circadian rhythms help control much of your physiology including appetite, digestion, metabolism, the sleep/wake cycle and more.  Check out what happened when I adjusted things in a way to optimize these circadian factors in this blog.

7 thoughts on “The ultimate guide to fasting for gut health

  1. Meredith Coughlin says:

    Are you able to drink liquids other than water during the fast? Or does anything other than water cause the MMC to halt?

    • cincodm says:

      From an MMC perspective I’m not sure. Anything caffeine related will definitely change motility and anything other than water including herbal teas could cause the gut or liver circadian clocks to start. There is evidence that stuff like autophagy continue despite things like coffee. But that’s never been studied from the perspective of the MMC. Having said that, caffeine stimulates gallbladder contraction so I’d assume it affects the MMC.

      • Cristina says:

        I think there are some studies that say coffee is ok.but you can test that.for me, with sibo, coffee alone doesnt stop it but if i add milk , it does.btw this is a very good blog.ive been fighting with sibo for years.also, studies show a high balance of good bacterias helps mmc. What i do also i take ginger with lunch and that speeds up food going through.the next dose of ginger i take 4 hours after eating when in stage 3.studies shows ginger affects the length and amplitude of mmc.anotherthing afecting mmc is the intestine being basic ph. So maybe thats why lowering inflammation helps with mmc.

      • cincodm says:

        Glad you enjoyed the blog! It’s important to point out that different areas of the intestine operate differently wrt pH. Lowering inflammation improves the MMC because inflammation messes with neurotransmission and metabolism.

  2. Joe says:

    I have undergone a colonoscopy and a gastroscope before. Although the images of my gut were normal, the biopsies showed signs of moderate inflammation throughout my gut, including stomach, ileum, and rectum. Unfortunately, I didn’t get a definite diagnosis from my doctor.
    My main problems are diarrhea, fatigue, abdominal pain and multiple food intolerances. I’ve tried restrictive diets like SCD but only had limited benefits. I want to try 16/8 fasting, but I’m afraid of losing too much weight, since I’m currently nearly underweight . Do you have any suggestion on how to get enough calories when doing fasting? Thank you.

    • Cristina says:

      But this you can fix.there is small intestine inflammation and colon inflammation.this can be fixed independently. Try at least partially hydrolised guar should help with both.can explain the science…

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