How to heal gut flora


(scroll to How to alter a disease causing gut flora at the end)

Most western diseases/health conditions; obesity, type two diabetes, migraines, infertilitymiscarriages, acne, arthritis, cancer, autoimmune diseases, alzheimer’s, etc., originate from systemic inflammation. This usually due to a diet high in sugar, trans fats, omega 6 & low in omega3 and lacking in vegetables and soluble fibers etc., which promote a “bad /compromised gut flora”. I will below describe health conditions a low carb diet can reverse and how to transition your gut flora to a healthier one.
If you are worried about switching to a low carb/ketogenic  diet based on the “cholesterol theory” which has long dominated the health care industry, please find here a summary on recent (reliably set up) studies which provides strong arguments against this assumption. Or have a look to this documentary aired on Australian national tv some month ago, where several scientists and doctors are interviewed. Second documentary on how diet guidelines started the epidemic – “toxic sugar”.

A healthy gut flora consists of at least 200 different species of bacteria. Antibiotics disrupt a healthy gut flora, and kill of a large part of these. The standard american diet (SAD) of carbohydrates, fats and protein and possibly some grain fibers (which are not the fibers you are after) feeds no bacteria, people switching between different healthy/super foods – constantly starve their gut flora. Bacteria live off soluble vegetable fibers and there is a high specificity between a certain fiber and bacteria. Sugar and limited soluble fibers and the use of antibiotics – results in a damaged gut flora lacking in many of the species needed to degrade all the foods we eat and produce the many compounds we rely on our flora to make. We live in symbiosis with our gut flora, as the economist eloquently describes here.
A compromised gut flora is a major contributor to obesity, and this may be “cured” trough introducing a larger variety of species. – Alter gut flora, alter predisposed weight. Diseases that run in families are rather gut flora that run in families. The people you spend time with and are intimate with are the once you exchange flora with. Constant use of hand sanitizes etc. limits your exposure to a diverse and healthy flora. (Btw. Probiotics only contain a very small spectrum of bacteria – not by far enough).
You can read more here on how gut flora composition affects insulin resistance, metabolism and weight and how these conditions can be reversed with altered gut flora, and how you could manipulate mice weight trough alterin their gut flora.
Constipation is a sign of compromised gut flora.

Babies fed formula too early will develop an unbalanced flora and will be prone to e.g. autoimmune diseases later in life. Human breast milk is designed to help the child form a healthy flora and protect it from disease causing bacteria to colonize in too high extent. It is antimicrobial and selects for bifidobacteria (that’s why they smell like yoghurt until the day they are given formula). Cow milk is designed for calfs. “One bottle of formula kills the Bifidobacteria and replaces it with adult gut bacteria”, read more about the importance of breast feeding to establish a healthy gut flora here.

Grain fibers are not digested by bacteria and have a disrupting effect. Gluten is poorly tolerated by most people and wheat is the primary food to exclude form your diet. Humans have eaten grains through a fraction of its history. What we ate for the longest amount of time was ‘the hunter and gatherer diet’. We lived by water, fished, forged for berries, mushrooms, roots, greens, squirrels and bird eggs. We certainly did not eat french toast, high fructose corn sirup, drink milk or pasta carbonara. Our wheat grain has also evolved through farmers selection to favor crops with high gluten content as this flour creates tastier bread and thus higher financial return. 50% of the genetic material in the wheat has been lost during the last 2000 years and gluten content has sky rocketed mainly the last couple of decades when farming has become more efficient, forming a wheat with negative effects on health. Hence, one of natures example of GMO, due to random mutation and selection, in this case human selection. “Intestines produce an enzyme, transglutaminase (TG) that normally protects the gut from toxic plant proteins, such as grain gluten, but modern food processing and antibiotics corrupt digestion of gluten to produce intestinal inflammation and a series of related autoimmune diseases including celiac, thyroiditis, diabetes, baldness and atherosclerosis. ” The fine milling of todays flour also makes the gluten more difficult to tolerate. If you have to eat bread, have sourdough type bread (more details in link above).

The immune system is regulated greatly by the intestinal flora. When the flora is unbalanced the immune system is either up regulated or suppressed. Leading to autoimmune diseases or general sickness. Certain foods (like wheat) are also associated with actively promoting certain disease-causing bacteria.

In studies with fecal transplants many conditions are substantially improved. This is an efficient treatment for conditions such as rosacea, arthritis, obesity, etc. Though the procedure is fairly costly and produce individuals with a much lower need for medications than before treatment. Which is not exactly the desired result for the medical companies, thus limited research investments.

Systemic inflammation can originate form a bad gut flora, and a bad diet, but also from dental problems and fat organ fat; i.e. fat deposits in the liver and around other organs a.k.a. inflammation caused by visceral fat. The later is caused by a sluggish liver. Organ fat is what constitutes that “middle age” belly which builds up with life and which tend to stick around even if you loose weight. To reduce your waist line the liver needs to be strengthen, so fat deposits in and surrounding it may be handled. This is not a natural place for fat to be deposited.
The liver processes sugar, vegetable oils, environmental toxins, plant toxins, stimulants , drugs and used up hormones such as insulin, etc.
Fructose is contrary to what the name indicates – far from “natural” or harmless. It was discovered in fruit but in modest amounts. Fruit is natural but naturally normally available during 1 or 2 months during summer. Fructose is toxic and kill microorganism feeding on them (evolutionary selection for fruit higher in fructose).  Fructose cause liver damage. “Fructose in sweeteners has now surpassed alcohol as the major source of liver disease. – Agave syrup contains fructose produced by industrial processing of the fructose polysaccharides, inulin, in agave extracts. Agave syrup is like HFCS on steroids.”
High blood sugar concentrations creates high insulin and suddenly there is a cue for the liver to process all these compounds. Refined carbohydrates such as in Pasta, bread, potatoes, rise consists exclusively of starch and starch is just very long strands on glucose units liked together, that is immediately degraded in the mouth and gut.  To purge the liver of fat deposits one need to reduce its may choirs so it has more time and energy for “cleaning” (burning fat) in the right places. This is done by reducing or excluding carbs, sugar, flour foods, stimulants such as coffee, pain killers, alcohol and also to eat calorie restricted during this period – to help with the fat removal.

But as for the gut flora. How to heal this.
1. Bacteria need to be replaced
2. Bad bacteria (if present) may need to be reduced
3. A large variety of bacteria need to be introduced
4. Create an beneficial environment for bacteria to settle

Probiotics can have some calming effect on gut flora momentarily but lactic bacteria cannot live in the gut, only transfer some of their genes/DNA for digesting lactose/milk sugar to the established gut flora. They are also a very small portion of all the bacteria needed for a healthy diverse gut flora. You need to introduce a range of different bacteria, specific to various food components and you need for these to settle and multiply. Lactose intolerance is the one food intolerance (note, not an allergy)  that can be cured very easily, by introducing a small amount of lactobacilli containing foods daily – such as a tea spoon of yoghurt or even better home grown fermented vegetables, sauerkraut etc.

You need to lower the inflammation “momentarily” to increase odds of bacteria settling. But in certain situation you need to remove some of the bad bacteria lodged in biofilms in the gut/intestines. This is done by anti microbial substances where whey protein powder is an efficient such material. Raw egg white is an other that also is anti microbial. By eating these together with a low carbohydrate vegetable and meat rich diet you can remove much bacteria and at the same time promote the growth of certain species growing on vegetable fibers, by making sure to eat these foods. To then continue eating a low carb diet, especially restricted in flour based foods and other refined carbohydrates.

If some bacteria have been eradicated by inconsistent eating habits, antibiotics and over consumption of milk, then the missing species are not present and are not going to appear out of thin air. The missing species must be introduced and fed. At the same time the systemic inflammation levels must be managed to create an environment encouraging “new inhabitants”.

Vitamin D is contrary to what its name implies a hormone. It is highly involved in regulating bodily inflammation and in people with auto immune diseases or just acne for that matter, the blood serum levels are usually very low. Vitamin D is usually produced in summertime when the sun stands high(closer), but where there is inflammation no Vitamin D is produced in sunniest Sahara. Catch 22. These people need to supplement to get their levels up to where they can start producing vitamin D again.

In these cases supplements are very useful to get the levels up to where it should be. Namely around 60 nmol/L at least. Following  the anti inflammatory diet which Dr Ayers advocates helps reduce inflammation.


Reduce carbs  & sugar
No grains
No high fructose corn syrup
No trans fats
Lower omega 6 /3 quota (omega 6 is found in grains and is inflammatory, eat more omega3) – eat fish and grass-fed meat/wild meat.. – Do not fear saturated fats, it is a safe food that help reduce LDL and also help absorption of omega3.
No vegetable oils, only olive oil (cold) or coconut oil (for frying) (or fruit oil like avocado oil)
Eat saturated fats – these aid absorption of omega 3
Eat supplements of omega3, vitamin C 1000 mg, Vitamin D 2000-4000 IU, Glucoseamin 800..
Eat a little extra (e.g. himalayan mountain) salt in the beginning of all this as you will release water weigh, which is water containing minerals.
Vegetable antioxidants, (some fresh fruit if insulin sensitive to handle the sugar), coffee, chocolate and wine great in moderation
Sprinkle all your foods with fresh (non heated) herbs – Always have something raw with your meal
Further details on general eating guidelines; what to eat and avoid..

If you switch to a low carbohydrate diet the main points of importance is to limit flour based foods and fructose/ refined sugar. Table sugar contains 50% fructose, so does honey and agave often contains up to 80% fructose. As you transition to eating more vegetables instead your flora will slowly adapt. If you want to speed up this transition and also “clean out” some of the current “bad” gut flora you can also add in components such as  antimicrobial foods such as whey protein powder and raw egg whites. Eat the protein powder fora few weeks and when you stop start focusing on re-building gut flora (vegetables, meat, and new bacteria from your surrounding) and strictly avoid flour based foods and sugar that feed the wrong kind, etc. Further details below.

How to alter a disease causing gut flora:
This is based on the book The 6-Week Cure for the Middle-Aged Middle by Drs. Eades (Mary Dan and Michael), here reviewed by Dr. Art Ayers. Here you can listen to Dr. Ayers in an interview (he is the second speaker in the episode).
Eat shakes for 3 weeks – 3 shakes a day and one low carb meal.
Shakes recipe: 40-60 grams of whey protein powder,  1 raw egg, 1 Tbsp coconut milk or cream, 2 dl water, some flavour/sweetener (stevia or Erithrytol), some ice – in a single serving type personal blender.
The whey protein powder should be less than 4 grams carbohydrates per 100 gram.
To clean out liver; do calorie, alcohol and stimulants restricted diet for two weeks.
Drink plenty of water in this period and potentially supplement with magnesium and potassium or eat extra mountain salt with your food.
Low carb meals. Here is some nice recipes for inspiration I breath I’m hungry recipe blog and I can really recommend these very lovely cookbooks three cookbooks.

Follow the anti inflammatory diet with all the supplements
Chose a few “bulk” vegetable ingredients that you believe you will be able to stick to and eat regularly
Example of some I use a lot of: Cauliflower, Cabbage, Zucchini, onions, garlic (inulin source), coconut flour, flax meal, olives, citrus peel /zest (pectin source). – This to keep feeding the same complex bacteria species mix so do not jump from food to food, chancing “super foods”.. Plants contain a lot of toxins so there is no harm in cooking the majority of them, it is the plat fibers that feed our gut flora and some fibers in meat, so have a lot of veggies.
Try to introduce missing bacteria. This is done by contact with other people and kissing animals and babies. Eating raw organic veggies that has not been thoroughly cleaned. Sprinkling everything with fresh herbs and have something raw (and dirty) at every meal. By daily introducing some bacteria with “potential” and feeding these with a antiinflammatory diet and fibers, odds increase that your health will improve.  – More on introducing a wider population of gut flora here. Avoid contamination of sick people and healthcare workers.
More details here on how Dr. Ayers found the “six week cure”.

It should be mentioned that when changing once diet  this may result in indigestion and constipation, as the gut flora is not adapted to digesting the new fibers, and thus it can be good to move into this gradually. The shakes helps facilitate the process by making room for the required bacteria to multiply and clean out portions of the “bad” flora.  Certain condition which are caused by “bad bacteria” feeding on a SAD diet high in wheat and sugar, will seem to get worse when you swith to a low carb diet, this as the die off rate increase and more toxins are relased when the flora is killed off and cleaned out (remember to drink a lot of water). In conditions like rosacea the symptom can get significantly worse before they get better. The whey protein shakes again facilitates this by moving things along quicker. It is important to try to avoid constipation during this process as this will make toxins from cell death accumulate and symptoms to worsen. When I did this treatment I experienced worsening of my symptoms and then a significant improvement when I finished. I had for more then 10 years struggled with a rash on my chin and had to eat antibiotics in high concentrations to keep it under control. I had for a few years noticed that this condition would be improved when I stuck to the antiinflammatory diet, but when I tried to restrict all carbs  the rash would instead get worse and get agitated red and pussy and I would get terrible head aches. When I added the shakes to my low carb diet I predicted this to get worse for a period of time, and so it did. And when I finished (shakes and extremely strict low carb diet) 5 weeks later, the rash was gonne! I have previously always had to eat heavy antibiotics to manage this. The extensive use of antibiotics would kill both the bad and good bacteria and further  compromise my gut flora.

During the diet (further details explained here I constantly used Voltaren T gels on my face to reduce some of the worst breakouts. Anti inflammatory pills are unfortunately very tough on the stomach and do more harm then good on the intestinal flora but could be useful during the whey treatment period to mange inflammatory symptoms caused by die off reaction. Read more on NSAIDs here.
Sweeteners that are fine to use are Stevia and Erythritol. Further explanations why etc.
In addition to this, try to get some sun, excercise and if stress is a major factor in your life, check out these two links on clinical trials on how to induce stress relief.

Other ways to feed the population in your gut. The main groups of food for bacteria are soluble fiber, some fibers in meat, inulin (found in onions) and pectin found in the peal of apples and tomatoes in moderate amounts but in high quantities in citrus fruit. Thus a good idea could be to use (organic) Citrus zest on food, and potentially make your own stevia sweetened lemon/orange marmalade!

This have really helped for me. I did the strict low carb diet together with the whey protein and raw egg shakes and while I was doing the treatment my symptoms worsened, and when I finished the chronic rash on my chin was gone. Also my headaches are much less frequent after the diet. Tip: I used Voltaren T/an antiinflammatory gel on my chin during the treatment just to keep the inflammation based break outs somewhat under control.

MAIN POINTS of importance after the 3 week whey treatment:
Avoid carbs (worst is bread, pasta, potatoes rice) and sugars
Expose yourself to bacteria
Kiss you loved once and animals
Avoid over cleaning and hand sanitizes
Have something raw with every meal and avoid over cleaning these organic herbs and veggies
Recruit healthy gut bacteria by eating a variety of homemade fermented vegetables
Choose staples (veggies) or gradually change what you eat with the season to not have too quick changes in nutrients
Avoid four foods but if you have to eat bread eat fermented bread/sour dough
Avoid vegetable oils eat butter, olive oil and coconut oil
Supplement with omega3, Vitamin D, Vitamin C, glucoseamin

For further inspiration on why a low carb is beneficial for many health conditions and weight loss listen to Dr. Dwight Lundell explain it for you (advanced), or Dr. Andreas Eenfeldt, Swedish MD (for a general review).



2 Responses to “How to heal gut flora”

  1. Breakfast of champions – low carb high protein paleo porridge | MatFysik Says:

    […] powder or rice, pea protein powder. (I’m using whey protein powder here as I am doing a bad gut flora clean out and whey has anti microbial properties, “high in lactoferrin, a protein found useful in […]

  2. Förstoppning? Barn och vuxna | by Anna Sparre Says:

    […] Min vän Anna-Karin (AK) har skrivit bra om mag-/tarmflora här: […]

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