Microbiome and Behavior
Article by Stefan Burns - Updated July 2022. Join the Wild Free Organic email newsletter!
If I may usurp the microbiome throne, I would bring attention to the profound effect toggling nutrients on/off has on the human microbiome. A microbiome is a characteristic microbial community which lives in a reasonably well-defined habitat with distinct physio-chemical properties (1). Without an influx of nutrients, microbiomes cannot exist.
Fasting, this is refraining from all nutrition besides water for a length of time, is capable of completly reversing gut dsybiosis and restoring proper digestive function. Fasting is our normal physiological state in-between feeding, and the longer you go without nutrition in any form, the more pronounced effects from fasting you feel. For example the lining of the intestines, the epilithium, heals increadibly fast by up to 20% a day, when their is little-to-zero lumen in the gut.
The human body and mind require nutrition to function, and it is important for overall wellness to stay well fed with ample micronutrients, macronutrients, and other more exoctic compounds like phytonutrients. That said, solving gut dysbiosis solely through dietary and supplemental measures will be inefficient compared to methods which incorperate toggling nutrients on/off. To heal, the body requires it, and additionally microorganisms multiple increadibly fast, and can survive without nutrition themselves for some length of time. Those pathogens survive even longer if they have eroded away the muscus lining of the gut and establismed biofilms. A period of fasting can completely eliminate pathogens, biofilms, and parasites faster than it can completely eliminate the symbiotic microorganisms we want preserved. With a nutrient dense refeed schedule of the same length of the fast after the fast, no new pathogens will be introduced into the microbiome while the body reuptakes nutrients and symbionts establish new territory and multiple.
We know that their exists a bidirectional gut-brain connection wired by the nervous, blood, and endocannabinoid system. The microbiome can trigger the vagus nerve and cause behavior adjustements to the brain (2). Likewise the brain can choose which foods to eat which determine the composition of the microbiome. With a healthy microbiome, the triggering of the vagus nerve might manifest as a thought or feeling to eat vegetables or for something else you body is deficient in, such as fiber, fats, and micronutrients. When the microbiome is pathogenic, you might feel triggered to eat unhealthily, or perhaps you experience food cravings. With enough self-consciousness, it is possible to ignore this behavioral commands from the microbiome, which wants to be fed with what it wants most, and instead make an informed decision on what is best to do for your overall wellness. But when awareness is not present, then thoughts can turn into actions and be repeated into behaviors. To use a metaphor, a microbiome that triggers the brain for low nutrient quality food, has effectively compromised the central processing unit of a computer with a virus.
The most effective way to reset the gut-brain connection is to reset the digestive system. A 48-hour fast will eliminate nearly all pathogens, and with a proper refeed schedule, the microbiome can evolve to synergism. This work also requires behavioral resets, for long term gut health success cannot be had without addressing this aspect of the problem. During a fast, behavior can be reset to a more holisitic mindset as low-quality triggers are removed and replaced. For behavioral resetting, the refeed after a fast is critically important, as it is also in refeeding the body after a period of zero nutrient intake.
High calorie foods, fruits, and vegetables that are all gentle on the stomach are best. Avocados and coconut are excellent in being very nutrient dense, while fruits and vegetables provide many micronutrients in addition to paired carbs and fibers. The refeed schedule should be as long as the fast that is undertaken, with an understanding that the longer the fast the more impressive the results will likely be but all the more important it is to follow a proper refeed.
With willpower and following precise instructions, the well-grooved signals from the vagus nerve firing for junk food can be easily ignored, as new more beneficial pathways between the brain and symbionic microbiome develop. Reseting behaviors and creating new habits requires time, and any loose signals from pathogens which slip through successfully could led to the feeding they require for survival. The trick in eliminating gut dsybiosis is to make sure you understand the human mind and behavior. Just as important as the gut health protocol being followed is the behavioral protocol that needs to be assigned.
Together the digestive system and microbiome are the foundation of health from which everything else is dependent on.
The Holistic Gut Health Guide contains all the information you need to identify and understand the gastrointestinal and microbiome problems you may have while also providing you the most effective natural methods you can use to heal your gut. No gut health problems are unsolvable, give yourself every possible advantage along your gut health journey by reading an implementing the advice shared in the Holistic Gut Health Guide.
Some of the information in the Holistic Gut Health Guide isn’t common knowledge but when implemented it is highly effective in healing the gut and shifting the microbiome towards symbiosis. Give yourself every possible advantage along your gut health journey by reading an implementing the advice shared in the Holistic Gut Health Guide.
Fasting provides a neat set of instructions that gastroenterologists can issue to their patients, given proper safeties in place. As an example, if the patient is overweight, then fasting will switch the body to buring bodyfat, which may or may not contain stored toxins which will stress the liver, spleen, and kidneys. Fasting and autophagy (cellular cleanup) has been used to completely reverse auto-immune conditions, lower cholesterol and blood pressure, help patients suffering from neurological conditions such as narcolepsy, and is protective against chemotherapy treatment. Once the main systems of the body are in well-enough shape and/or controls are in place, then fasting can be prescribed clinically for people with gut-dsybiosis. Knowing the patient’s wellness situation is of utmost important before triggering such a big metabolic switch. Some questions asked may be uncomfortable, but knowing exactly what gut dsybiosis symptioms they are experiencing can be used to design the fasting and refeeding protocol. Diarrhea has to be treated differently than constipation. Mental health issues, inflammation, skin issues can all be linked to gut health issues. Bloating and gas are also signs that a patient has a microbiome dsybiosis.
Fasting removes all nutrients from the digestive system, with existing food/lumen typically emptying out completely after 48-72 hours. As the digestive system empties, the stress of digestion decreases and eventually all the organs which are involved in the digestive process can switch gears to cellular repair and regeneration. This regeneration process happens most meaningly during a fast of extended duration, with consistent intermittent fasting, or consistent OMAD (one meal a day, 24 hour fasting).
Typically after 2 days, the body switches ketogenic and bodyfat begins to be burned for energy exclusively. If toxins are stored in the bodyfat, then flu-like symptoms may be experienced, as known as keto-flu. Someone who is overweight, inactive, and with gut dsybiosis is likely to experience this, and should come prepared. There are certain herbal remedies which can increase the efficacy of a fast and also mitigate any negative symptoms experienced.
Green tea increases fat oxidation, levels out the brain into alpha wave lengths, and is rich in plant polyphenol antioxidants which aid in the repairing of the gut (3, 4, 5, 6).
Milk thisle flavonoids known as Silymarin support liver function by maintaining protective glutathione levels (7).
Turmeric curcuminoids and other turmeric compounds it possesses are rapidily taken up by the gut and are powerful antioxidant healers and more important powerfully anti-inflammatory (8, 9)
Sulforaphane has these functions too, being a powerful anti-inflammatory derived from cruciferous vegetables, targeting the bloodstream better than turmeric, improving immune functon throughout the body (10)
Papaya enzymes can aid in digesting food, especially for the first few refeed meals after a fast when the microbiome is still newly reshaped and growing.
Wormwood, clove, black walnut hull, and oregano oil are natural adaptogenic antimicrobials, killing pathogens and parasites while being gentle on symbiotic microorganisms.
Natural herbs like these can be used to assist in the evolving of the microbiome and behavioral transition from low-quality to high-quality vagus nerve triggers. The microbiome will always be able to influence the mind of its host, but it can be done symbiotically and cooperatively.
Beneficial behaviors need to be established to ensure minimal to zero gut-health issues continuing forward. Additionally, A well-rounded diet of fats, carbs + fibers, protein, and diverse micronutrients, from relatively unprocessed superior quality sources (organic, non-gmo, pasture-raised) will ensure the gut functions normally, and therefore all nutrients the body and mind receive henceforth are of the highest bioavailibilty. “You are what you eat”, and this truth has not changed.
The mind and body cannot function to their maximum possible potential when low-quality nutrients are being received, the culprit of which is behavior. Low-quality behavioral food patterns people have existed and relied on for years now can be difficult to reset. In this instance, a longer month-long period consiting of many shorter fasts, or a single long fast, can be successfull in repatterning behavior. A single long fast of seven days is shorter in total duration than a month from a patterning standpoint, but more difficult to execute safely and to the benefit of the patient. A month long period of intermittent fasting with 48 hour fasts once a week will be similarily effective in repatterning, but possibly be harder to execute as willpower drains over time.
In either setting, if the patient sticks to the protocol 80% effective and no medical emergency is encountered, then success will have been made in evolving the microbiome and repatterning food behaviors. The more precisely followed the fasting and refeeding schedules, the more effective the strategies will be. Conscious awareness of the gut must developed by the patient for long-term success, and it is the hope that a strict fasting/refeeding schedule, plus keeping a daily digestive system journal, establishes this long term gut-microbiome-wellness consciousness. Cannabis usage can assist with this, and when CBD dominant flower is dry-vaporized, it also calms inflammation in the gut (11), inflammation being a key ingredient in developing a systemic disease such as an auto-immune condition (12), heart-disease, or cancer. Most diseases begin in the gut.
Once gut consciousness is developed, then whatever further tools/protocols the patient has experienced and knows to work will be willingly reused to further improve the situation. Stabilizing the mind during the day (feeding hours) to alpha brainwaves from the L-theanine in green tea makes resetting food behaviors easier to accomplish as the brain is functioning at a higher cognitive level. When having green tea consitnetly for this purpose and its other benefits, it is then important to be mindful of the effects caffeine has on the body and circadian rhythm. Lastly alcohol is to be completely avoiding during any gut healing endeavor. Alcohol kills microorganisms indiscriminately, stresses the liver, and throws metabolism into haywire. Alcohol is not good for wellness and will not help the patient establish a healthy symbiotic microbiome.
With this information and theory now laid out, we will now establish the framework in more specific actionable details. Let’s start with a simple 48 hour fast and refeed schedule.
48-Hour Fast and Refeed Instructions:
Schedule
Day Zero - 3 meals, fast begins (after dinner)
The last meal eaten will be dinner, with no food happening after 6 pm. The meal can be what the patient decides, but with an emphasis on being healthy. Two servings of squash (~300 grams) will be included with this meal and is the last thing to be eaten, all together.
1 gallon (4 liters) of filtered water will be spread out and consumed daily. 16 oz before bed and immediately after waking are a good place to start.
At 6 pm day 0, the digestive system of the body is filled completely up. If the patient had 3 meals that day, then their stomach, small intestine, and large intestine will all contain food, lumen, and partly individualistic microbiomes. By 9 pm, the stomach is now empty and begining to repair from the stress of digestion. After sleeping a full eight hours, by 8 am the patient is now 14 hours into the 48 hour fast. A 16 hour intermittent faster would refeed at 10 am with this schedule.
Day One - Fasting, 1 gallon water
With a 48 hour fast, no food is eaten though at this 16 hour mark. Instead, a cup of green tea can be had anytime in the morning, from 6 am to 10 am. This is determined by every individuals unique circadian rhythm. The green tea assists the healing process in the stomach and also the small intestine as food moves out of there. Green tea also provides clarity of thought through alpha eave generation. If well-fed on day 0, day 1 of a fast is typically easy to achieve and of high energy. If feeding on day 0 was sporactic and lacking nutrients, then day 1 will be harder as the dysbiotic microbiome begins triggers the gut-brain connection for nutrients of any quality.
By 6 pm day 1, 24 hours have elapsed, and when performing a short 24 hour fast to control food cravings, you would refeed here. This is known as OMAD, or one meal a day. As night settles in, energy demands decrease, and with a little extra willpower, it is not difficult to begin getting ready for sleep and go to sleep without eating.
Day Two - Fasting plus first refeed meal (dinner)
After another 8 hours of restful sleep, by 8 am on day two 38 hours of fasting have been completed. With zero food intake, the brain has begun its own cellular cleanup, pruning synapses associated with the low-quality behaviors we’re selecting against. 10 more hours o no food and just water takes the patient to their first refeed meal.
By 8 am day 2, one or more bowel movements will have occured since the start of the fast, and now the stomach and small intestine are completely emptied of lumen. The large intestine may or may not have fully emplied yet depending on the patients gut motility. Another cup of green tea has the same helpful benefits as before on day 1, and now also sulforaphane and milk thistle can be added for liver and blood support. A dsybiotic gut typically has weak tight-junctions, and therefore inflammatory particles and microorganisms can slip into the blood stream, causing a base-load immune response.
Energy and behavioral volatility may be experienced during the final 10 hours of the fast from 8 am to 6 pm. Ensuring the patient has a low-stress easy routine set for the duration of the 48 hour fast helps the patient stay on-track and safe with their fasting schedule. Walking helps to energize the body and stablize energy levels, while some downtime focused on simple mental activities like meditation, writing, reading, or watching educational content are easy to pass the time with, requiring little calories. For fasting to be maximally successful and safe for resetting the digestive system and gut dysbiosis, these lifestyle factors need to be communicated to the patient and understood for their importance. Heavy exercise is best avoided during a fast, though certain types of yoga are fine, like yin yoga.
At 6 pm of day 2, the first refeed dinner is eaten. The food ingredients for the breakfast, lunch, and dinner refeed meals are below. This refeed dinner is light and easy to digest, easing the digestive system back into work and reestablishing a more productive symbiotic microbiome. Papaya enzyme is used here to help break down the food. Eating small bites and chewing each bite thoroughly will reduce food particle size and therefore reduce the demands on the microbiome to process the nutrients down into sizes that can pass into the bloodstream. No food after the dinner refeed, just water if thirsty.
Day Three - Refeed
The 48 hour fast has been broken by the first dinner refeed meal, but this meal also marks the beginning of a 16 hour fast, from dinner to brunch. This intermittent fast will make it very clear to the patient how they respond to the dinner they ate since their will be no food before or after it for 16 hours. Intermittent fasts are benifically healthy in numerous ways (13).
From 10 am to 12 pm the patient can refeed with either a large breakfast or lunch. This meal will be the primary caloric replenishing meal for the patient after the fast, as the first refeed dinner was small in order to ease the patient back into digestion.
After brunch, no snacks are consumed other than some nuts or pumpkin seeds. Pumpkin seeds are calorically dense with healthy fats, contain appreciable fiber and protein, and are high in commonly deficient minerals. Pumpkin seeds are also good at killing parasites.
1 gallon of filtered water is consumed evenly throughout the day.
At 6 pm the second refeed dinner is eaten. This meal is the same as it was on day 2 just larger in volume. No food is consumed after dinner.
Day Four - Refeed
Now the patient can decide to resume a 3 times a day eating schedule (breakfast, lunch, dinner) or a 2 meals a day feeding structure, breakfast + dinner or lunch + dinner being the most common. If the 2 meal structure is preferred, then day three can be repeated. For the purpose of this guide, we will guide the patient back to a 3 meal food schedule.
At 8 am a refeed breakfast is eaten, with no snacking in-between breakfast and lunch.
At 12 pm a refeed lunch is eaten, with some snacking of nuts or pumpkin seeds allowed in-between lunch and dinner.
1 gallon of filtered water is consumed evenly throughout the day.
At 6 pm the final refeed dinner is eaten, and then the patient can begin making their own food choices hopefully guided by increased gut-health consciousness and better behaviors. If following a month long plan, then this 3 meals a day or intermittent fasting schedule focusing on food quality and no food alergens is followed until the next 48 hour fast, one week later.
In this way, after multiple repititions, the microbiome will have been sufficiently reset to symbiosis, the brain will have pruned bad synapses, and food behaviors will have been changed. Within this framework is the task of making sure the patient consumes enough calories and required macro and micronutrients over the entire duration of the digestive reset. If the patient is carrying excess bodyfat, then the caloric concern is not as warranted, but stored toxins in the bodyfat, and the potential flu-like symptoms that might be encountered during detoxifying must be considered clinically.
By the end of the full month, or even just after a single four day bout, especially if journaling all aspects of gut health, symptoms, experiences, feelings, and thoughts was done, the patient will now be much more cognisant and mindful of their gut health, diet, mental state, and how they are all connected. Journaling for 1-2 months is typically successful in identifying any food intolerances or allergies they might have without the need for an elimination diet. For patients with these or suspected having these issues, intermittent fasting is more effective in intolerance/allergy diagnosis than a 3 meals a day schedule, as there will be less blurring of the effects between different meals.
Refeed Meals
Dinner
10.5 oz (300 grams) squash (butternut, zucchini) lightly roasted
2 oz (55 g) of raw mixed salad greens and/or spinach. No additions or dressing
1 large avocado
3 oz (85 g) Cassava chips
Notes: The first refeed meal on day 2 will be half the amounts above. Avocado and cassava chips are eaten first providing the body with much needed fats and elecrolytes. After 48 hours of fasting the body will now be ketogenic so the fats from the avocado will be processed efficiently. The carbs from the cassava chips will begin shifting the body back out of ketosis gently. Next the bulk of the meal is eaten, which is squash. Zucchini and butternet squash contain good fiber, helping to scrub the intestines clean, and is a natural food source for symbioic microorganisms which otherwise might exist in nature on the vegetable itself or in the soil. Eaten last are the salad greens, containing ample water-soluable micronutrients as well as fiber and protein. Food timing is important.
Note: Buying all organic non-gmo foods is important for the refeeding process. Whoever undergoes this fasting schedule is not just refeeding themselves with food but also the makings of a new microbiome. The patient is best served consuming the lowest amounts of pesticides possible and food grown from healthy soil. Washing fruits and vegetables with a baking soda rinse helps to remove pesticide residues. Organic food from a farmer’s market is ideal and still cost-effective.
Lunch
1 orange
1 cup of cooked brown rice
Protein - Either 4 oz (114 g) of mushrooms, beans, or fish protein. No beef, poultry, or pork.
1 oz (28 g) of a fermented food like kimchi, pickles, sauerkraut, kombucha, or others.
2 oz (55 g) of raw mixed salad greens and/or spinach. Olive oil and soy sauce can be added as a dressing.
Notes: The orance is eaten first in order to grow the microbiome, improving its ability to digest the incoming meal. Then the rice, protein, and fermented food is eaten. The salad is eaten last. Chopsticks are best used for this meal, as it forces smaller bites to be taken and lengthens the time it takes to complete the meal, improving digestion. Raw unpasteurized nuts or pumpkin seeds can be snacked on to satiety after this meal through to dinner, also contributing their microbiome communities to the symbiotic one you are establishing in your gut.
Breakfast
2-3 large pasture-raised eggs
1 potato (homefries, hashbrowns, baked), using butter or avocado/olive oil. Ketchup may be used.
Fruits or a fruit smoothie (1 orange, 1 banana, 1 lemon, 10-15 strawberries).
Notes: For vegans, the eggs can be replaced with mushrooms, beans, or lentils. The strawberries can also be used with or replaced by other berries like blueberries. Organic strawberries have signifigantly less pesticides and are the recommended purchase. The potato contains resistant starch, carbs, and many micronutrients. These 3 foods can be eaten simultaneously and will provide a very solid base of nutrition and energy for many hours. Eat to satiation but don’t stuff your stomach till you’re unconfortably full. Listen to your body and stop eating when appropriate. Therefore these recommended amounts of foods are variable based on individual needs and wellness preferences.
Supplemental Help (natural herbs)
For the herbs prescribed above, here is the dosage information and high-quality sources you can purchase. Not all these need to be used, though at a minimum the green tea is highly recommended as it makes fasting signifigantly easier.
1-2 cups a day inbetween 8 am and 4 pm.
200-300 mg Silymarin daily, taken with lunch.
1-2 servings of papaya enzymes, taken with dinner. Can be taken with other meals too if desired.
2-3 grams of turmeric powder, with or without standardized curcuminoids. Taken with breakfast or incorperated in food (avocado is a good choice, the fats present improving the bioavailibility of the curcuminoids).
50 - 100 mg a day, taken with lunch. Easy sources include brocolli sprouts, cabbage, or in supplemental form.
Wormwood, Clove, Black Walnut Hull
5-15 pills of SCRAM taken after dinner
300-400 mg taken after dinner.
In the context of a 48 hour fast and 2 day refeed, these herbal supplements are fine to take and will improve outcomes, but should not be taken daily forever. For a gut flareup, SCRAM, oregano oil, and turmeric work well. Papaya enzymes can be used to help food digestion. Sulforaphane is a powerful anti-inflammatory which can be used for any reason (gut flareup, headache, viral infection, injury). Milk thistle should only be used when placing the liver under stressful conditions (drinking alcohol, fasting if overweight/obese, prescription or commercial drug use).
4 Days to Success
With this theory of the digestive system, microbiome, behaviors, and neurology established, it is easy to understand the power of fasting in reversing gut dsybiosis. Fasting intelligently prescribed toggles the nutrient on/off master switch, from which cascades a series of important biological events such as autophagy, ketosis, and synaptic pruning. Once this reality of health is experienced and understood by the patient, then they have a powerful tool they can use to favorably alter their gut health at any point in the future given certain safety precautions best discussed with their primary care physician. Sometimes a 16 hour fast is all that is needed, other times longer duration fasts are more effective in healing the digestive system and guiding the microbiome to a more symbiotic state.
Our health is our responsibility, and it is up to us to make the most important health desicions there are to make. If you have a suspecicion that something is wrong with your gut, then you’re probably right. Normal gut function is 1-2 regular wipeless poops a day with no gas or bloating. Yes that is possible. No one can do for you what you need to do to establish a healthy digestive system, but clinicians, doctors, and natural health practitioners can guide you along the way. When not in a state of dire need, natural alternatives are safer than prescription drugs and much more gentle on the detoxifying organs of the body.
Fasting is one of the master switches for wellness, and much care must be taken when undergoing any fasting technique. If at any point blood sugar drops dangeously low and the patient feels dizzy, stablilize by sitting down and consume the refeed diner asap, no matter the time. It takes practice to improve your ability to fast without nutrients for extended periods of time, this is especially true for increase fat oxidation and metabolism. Once stabalized and healthy a few days later, the 48 hour fast can be attempted again, hopefully more successfully. The average 1st world citizen has never gone without food for more than 24 hours, and while the biology of the human body can go without food potentially for months, it is best to take the exploration of fasting for health cautiously and patiently. Green tea fasting is highly recommended as it increases the odds of success by aiding in the gut healing process, altering brain wave activity, and increasing fat oxidation.
The tea I use for my green tea fasts, from intermittent to 72+ hours, is Pique Tea. Pique Tea uses cold brew extracted green tea leaf products from pesticide-free sources for maximum potenency (antioxidant capability, polyphenols) and reduced risk of chemical exposure. They sell green tea blends specifically for fasting, of which I prefer their matcha and ginger Green Tea Power Bundle, as well as a variety of other green teas, herbal teas, and immune support products. If you use the coupon code WILDFREEORGANIC, you’ll receive 5% off your order and help support Wild Free Organic in funding operations. Amazon referral links also help support Wild Free Organic.
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