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Heal Your Gut now – HUG it!

Micobiome, gut bacteria, rebuild, yeast infections, pathogens, fecal transplants, fecal enema, commensal bacteria, Heal Ur Gut, Heal Your Gut, Heal Your Body, HUG protocol, Thomas Borody, Dr Colleen Kelley
Heal Your Gut now - HUG it!

All illness starts in the gut and this article tells you how to heal your gut; whether you have Crohn’s, colitis or IBS, or chronic fatigue syndrome, fibromyalgia, persistent cystitis, urinary tract infections, or the start of something worse like blood pressure problems, early Alzheimer’s, diabetes or even a cancer.

The Power of the microbiome

There are 90 trillion bacteria in your gut microbiome –  but you only have 7 trillion cells yourself. They outnumber you 13 to 1.

They have at least 75,000 genes, you have just 25,000. They ‘make’ three times more proteins, enzymes and messages than you make yourself. 

Their mRNA messages can stand in for yours when you have a lack, for example, none of us can process lactose – our gut bacteria may do it for us.

However, the opposite is also true – the mRNA from pathogens or parasites can override our healthy RNA messages in our cellular microenvironment, making us ill.

At any one time, 38 per cent of the small molecules circulating in your bloodstream were made by your gut bacteria, not you. They control your physical biochemistry and your mental biochemistry.

All illness starts in the gut

Research is consistent: The Human Microbiome Project (40 Medical Schools, 200 scientists, 3 years, $178 million) concluded, they get ill first, then you get ill. And you can’t get fully better, until they get better.

They get ill? What does that mean? Typically, you lose the volume of the good bacteria; and you lose strains of good bacteria. We call it volume and diversity. When this happens, your Adaptive Immune System (your antibodies) declines. There is clear reciprocity between your microbiome and your immune system (1). And when your good bacteria and your immune system decline, your pathogens come out to play. 

Look at any chronic illness – from IBS to Colitis, or from Alzheimer’s to cancer, or from fibromyalgia to chronic fatigue syndrome  – and you will see a loss of the good, and an increase in the bad. It’s like a see-saw; the good go down, the bad rise.

If you are fully healthy, you might normally have 800 to 1000 families (species, genus) of bacteria in your gut. Within each family you can have up to 250 different strains – the family members, cousins, brothers, aunts. 

How you damage your microbiome

There are three ways you can upset the healthy balance of your gut.

1. You take a drug:

Drugs, especially antibiotics or Proton Pump Inhibitors like omeprazole, damage your microbiome. Even a seemingly harmless 5-day course of antibiotics can cause dramatic effects (2). The commensal bacteria start to die off after just two days – they are fragile. Some become extinct – gone forever. But pathogens are more hardy – some can survive 8 weeks of antibiotics. The net result? Drugs and antibiotics cause the loss of good bacteria and the rise of the bad bacteria and yeasts. A 2022 study showed that antibiotics ‘scar’ the microbiome (16).

2. Self-inflicted:

You eat poorly. For example, your good bacteria love soluble fibre, like oats, psyllium, nuts and seeds, vegetables and pulses (legumes). Do you eat those foods? (3) 

Perhaps, instead, you eat too much glucose, high fructose corn syrup (fizzy soft drinks), dairy (lactose), and/or you eat fruit immediately after a meal, and feed their enemies.

Maybe you binge drink, smoke or are stressed – all stop the good from growing and multiplying, and this allows the bad to take hold. There is clear research on the effects of stress on the microbiome (4).

3. You have a parasite:

A parasite is much easier to pick up than people realise. Do you remember the food poisoning you had for a few days, 12 years ago? Maryland Medical School have shown that pathogens and parasites can live in us for 20 years or more before they come back out to play. Some parasites don’t even give you diarrhoea or sickness. Blastocystis hominis, Helicobacter pylori and a liver fluke would be just three examples. 

A parasite can screw up the whole microbiome (5) and you might not know it was still there until too late.

Bacteria – who needs them?

You do. 85% of your immune system and your immune memory is made in response to your gut bacteria. Destroy the good guys and you destroy your immune system. You also need a strong gut wall, or compounds (small food molecules, chemicals) can pass straight into your bloodstream causing inflammation. You also need a strong gut lining – attacks on your gut lining then prompt a healthy immune response. In fact, research shows that your gut microbiome controls your immune response. 

Your healthy bacteria also provide a defence against foreign invaders – it is called the ‘barrier effect’, or colonisation resistance. When your defenders are depleted, you get more infections (6). It is called Dysbiosis.

Your gut feed and their metabolites are essential to your health (7). For example, they make your B vitamins, vitamin K to strengthen your bones, and serotonin to brighten your mood and increase melatonin production. Certain bacteria also ferment fibre to produce important Short Chain Fatty Acids (SCFAs), propionate, acetate and butyrate, which help control your cholesterol levels or control inflammation in your gut or keep the gut acidic, which is what a healthy gut should be. Butyrate, heals the gut wall, activates vitamin D, crosses the blood brain barrier, restricts colitis, reduces inflammation and even attacks cancer cells in the gut wall. Butyrate significantly improves your health.

At night your commensal bacteria consume yeasts that have come into your body on the food and drink you consume (8). If the good bacteria are absent, the yeasts can take over the gut. Like mushrooms, they have roots which make small holes in the gut lining and wall, through which food molecules or chemicals can pass. It’s the start of ‘Leaky gut’. Consume gluten and the holes get bigger, via an enzyme, zonulin. Now yeasts can pass into the bloodstream – they sit on cell membranes and block messages and chemicals such as insulin moving in and out of cells; they colonise areas of the body – they are anaerobes and deplete oxygen levels; they like to sit on areas of slightly lowered oxygen, for example, scar tissue and this can even cause cancer recurrence.

What are the most common signs of dysbiosis, or microbiome disruption? Flatulence, bloating after meals, thrush, cystitis, skin problems, eczema, acne, allergies, diarrhoea, constipation, bad breath, fatigue, loss of appetite, sugar cravings, mouth ulcers, irritability etc. etc..

Rebuild your gut – give yourself a HUG!

All over the Web you will see people making claims about healing your gut. Many just tell you to take a big Probiotic pill, or eat Probiotic foods, and/or Prebiotic foods. It’s not that easy. It needs discipline. 

The Four things you need to really heal your gut:

i) Kill the bad 

ii) Heal the gut wall

iii) Replenish 

  • Heal the gut lining
  • Add back the lost commensal bacteria

The HUG PROTOCOL – Heal Ur Gut


During the first 12 weeks of the ‘Kill’ please consume no glucose, high fructose corn syrup, no lactose, no alcohol, no fruit immediately after a meal, and, ideally, avoid gluten. So, no Kefir, no dairy, no fizzy soft drinks, no wine.

i) Prepare yourself and your gut microbiome:

1. Take a good probiotic. It needs to contain strains of Lactic Acid families:

Lactic Acid Bacteria (LABs) were 95 per cent of the total when you had your natural birth and were breastfed. They are crucial to your health, but many people have lost almost all by the age of 50.  Research has shown you need a probiotic pill combining both main Lactic Acid Bacteriafamilies’ for the best results, as these two families are synergistic:

a. Lactobacillus, are known to be regulators of inflammation and immune responses. They are found in the gut, urinary tract, breasts and lung. After the age of 50 we have low levels in our gut, and few known strains.  They are recommended with gastric inflammation, diarrhoea, and with enteric infections.

b. Bifidobacterium, which also boost the immune system and promote IgA , is found as up to 8 per cent a healthy adult microbiome. It is known to produce vitamins, enzymes, lactic and acetic acid making the gut more acidic and controlling pathogens.

Your Bifidobacteria and butyrate-producers also cross talk and improve the coexistence of both groups (14). 

Most importantly in your probiotic, you need Lactobacillus rhamnosus – it has powerful benefits. It can adhere toi and colonise the gut walls, healing any problems in your gut wall. It prevents bacterial growth and helps increase the production of SCFAs. 

And you need Bifidobacterium infantis – another very powerful bacterium, which has even been shown in research  to help tackle IBS, ulcerative colitis, psoriasis and chronic fatigue syndrome..

You don’t need 45 strains and 300 zillion in your probiotic. You need these two families and about 3 to 4 strains of each including those above and 20 billion in volume per day. Don’t keep your probiotic in the ‘fridge, don’t take it with cold liquids or hot liquids. Don’t buy one containing sugar or glutamate if you have cancer. See the Practitioners’ strength probiotic Probio8 Max we recommend (below).

2. Take a tablespoon of Apple Cider vinegar – it contains lactic acid bacteria. And/or Kimchi, and/or a little fresh Sauerkraut, and/or Tempeh, and/or low sugar Kombucha.

3. Feed the new probiotic bacteria properly – eat and they shall multiply! We have an article on the best foods to feed your gut bacteria for gut health. And there is research from Holland showing exactly which foods and food groups increase the bacteria that make anti-inflammatory molecules, and which promote inflammation-producing pathogens (9). The good foods? They are the key foods in the Rainbow Diet.

Strains of Lactobacillus above all love pectin – carrots, raw vegetables, apples, pears. Strains of Bifidobacterium love inulin – chicory, artichoke, onions – and mother’s milk. They also love very dark chocolate (85 per cent plus) and cocoa, and according to three research studies, they like a glass of merlot. Both families love ellagitannin – from berries, pomegranate, walnuts. The correct foods to feed your gut bacteria – their favourite foods – are called ‘Prebiotics‘.

4. In particular, your good bacteria making anti-inflammatory compounds love soluble fibre – oats, vegetables, nuts and seeds and pulses (legumes), and fish oils, avocado and extra virgin olive oil. 

5. They have real problems with saturated fat, seed oils, alcohol (except red wine) and processed, refined and packaged foods and synthetic sweeteners.

6. Other supplements you should consider for your health:

  • Vitamin D3/K2 – 2500 IUs, or 5,000 IUs if you have cancer. Vitamin D has been shown to make significant changes to the gut microbiota, increasing commensal bacteria Bacteroides while reducing pathogenic Prevotella (9). Supplementation also appears to increase the immune properties on the gut lining, and also reduce hydrogen producing bacteria (10).
  • Fish oils (1000 mg), Krill oil (but not for men with prostate cancer), or Cytoplan Algae oil (for Vegans). Taking fish oils has been shown to increase anti-inflammatory compounds in the body.
  • Take a B complex – As an insurance policy you should also take a good vitamin B complex (but not if you have choline-avid prostate cancer), as you may not be producing much if your commensal bacteria are depleted. You don’t need to do this for more than 8 weeks – fermented foods have high levels of B vitamins due to LABs..
  • Take Turmeric – a double blind, randomised, placebo controlled study from UC San Diego researchers using 3 gm of turmeric, or curcumin along with 3.75 mg of piperine (black pepper) showed that both drove an increase in the number of bacterial families. A few people did not respond, but from the majority who did, the researchers concluded that the overall health benefits were coming from the positive changes caused by the herb in the microbiome (11).   

(ii) Kill the bad

This is a general plan for people with gut issues. People with Colitis or Diverticulitis might need a more specialised approach, similarly for people with cancer, depending on the cancer and whether they are taking drugs or not. 

Consider this general approach. Run both protocols, in parallel:

1. Protocol 1 – for 20 weeks:

   a. Kill any parasites – start here because research shows Parasites screw up the whole microbiome!  Take the all herbal Para Free Plus 25 days on, 5 days off, 25 days on – you and your partner. 3 pills with room temp water first thing; 3 pills last thing. Para Free Plus is all purpose. It contains yeast killers; and an antiviral Olive Leaf Extract. So, 8 weeks in total.

   b. Kill your viruses – Immediately after the Para Free Plus finishes, take Pau d’arco 1000 mg pill first thing, 1000 mg last thing. It attacks viruses. 12 weeks.

2. Protocol 2 – for 20 weeks alongside the Para Free Plus and then Pau d’arco – 

   a. Take Artemisinin (sweet wormwood); it attacks bacteria such as E coli, Fusobacterium – the dose is 300-400 mg before bed depending on weight. It also attacks yeasts and one third of all parasites.  Take for 7 days. Rotate with …

   b. Take Oregano oil pills – 180 mg first thing; 180 mg last thing. 7 days.

So, one week Artemisinin, then one week of Oregano oil. In all, repeat this 2 week protocol, 10 times, at the same time as using protocol 1. Why are we doing this rotation? Because some people we help have a compromised liver, especially after drugs and/or antibiotics, and the continuous use of high dose Artemisinin, may cause Jaundice. Artemisinin is also known to work better if pulsed (days on, days off).

iii) Heal the Gut wall

There are several things you can do:

  • Take Butyrate – sodium or potassium. Made from the fermentation of fibre by a group of some 90 bacteria, butyrate is a Short Chain Fatty Acid and is a strong component of a healthy gut. It is highly anti-inflammatory and known to heal your gut wall. It plays an important role in the epithelial cells of the wall where it alters cell cycle progression (12), and can block the formation of cancer cells and help to heal in cases of ulcerative colitis. Its effects seemed to be reduced by hydrogen sulphide producing bacteria or yeasts (13).
  • Consume Chicken bone broth? Rich in amino acids, collagen, analgesics and gelatin; bone broth is verty anti-inflammatory. However, chicken bone broth does contain high levels of glutamine and glutamate. While some people suggest this is healing for the gut wall, it can provide fuel for cancers, especially prostate cancer and brain cancer.
  • Marshmallow root, slippery elm and aloe vera – these are often recommended by herbalists and can definitely help.

iv) Replenish

Starting at week 12 of the programme – Eat more PROBIOTIC foods – You already take some of Apple Cider Vinegar, Kimchi, sauerkraut, low sugar Kombucha. But now, after killing off any sugar-loving yeasts, you can eat lactose – ‘go for it

* Re-establish greater diversity by consuming 

a. A tablespoon of raw, unpasteurised cheese (from cows’, sheep’s or goats’) – it gives you trillions of Bifidobacterium and Lactobacillus strains, plus immunoglobulins to rebuild your gut lining and strengthen your immune system. 

b. Four to five tablespoons of a specialist kefir – In the UK there is a strong Kefir product from a company called ‘Chuckling Goat’. It has 21 added strains of Lactobacillus and Bifidobacterium on top of the bacteria in the natural goats’ milk. 

In providing the unpasteurised milk, we are giving the gut trillions of Bifidobacteria and Lactobacillus family members.

The rebuild is over in three to four weeks. Of course you may not want to consume even this small amount of dairy – you could use Colostrum.

  • Rebuild the gut lining – Mother’s milk also provides a complete production kit, for a gut lining (baby is born without one). For many people who have taken drugs and antibiotics, it’s not just that the gut wall is damaged, so too is the gut lining.

So, we are taking you back to when you were two months old – to a time when your faeces had a pH of 5.5, and your emerging microbiome and the acidic gut kept the harmful pathogens at bay.. 

Mother’s milk also contains Immunoglobulin A, which will also stimulate the immune system.

Did I mention acidic gut? Yes. that’s exactly what you need. An alkaline body with alkaline power stations (mitochondria). You will get one of those be eating a magnesium- and potassium-rich, low sodium diet. But please understand, having an acidic gut is crucial to your wellbeing. Try a glass of water with a squeezed lemon and a tablespoon of Braggs Apple Cider Vinegar in it, to start your day. Never drink a high alkaline water from some specialist water filter company (or sodium bicarbonate). It’s the worst thing possible for your gut.

A tablespoon of unpasteurised cheese on day 1, plus 4-5 tablespoons of a specialist Kefir, rotated on alternate days, should see a major improvement in your gut in three to four weeks. 

Now be healthy!

Make prebiotic and probiotic foods part of your daily diet – Extra Virgin Olive oil, fish oils, avocado, walnuts, berries, pomegranate, fruits and vegetables, nuts and seeds, People who eat high levels of soluble fibre (oats, pulses, vegetables, nuts and seeds) have the best immune systems.

We can thoroughly recommend triple action Para-Free Plus, which is a Parasite killer AND a yeast killer AND a colon cleanse. CLICK HERE to buy.

“If you are in the UK and looking for any of these products, why not see what the Our Natural Selection shop has to offer? HERE.


There’s far more in our book ‘Heal your Gut – Heal your Body’. CLICK HERE to buy.



    1. The role of the adaptive immune system in regulation of gut microbiota; Lucia M Kato, Shimpei Kawamoto, Mikako Maruya, Sidonia Fagarasan; Immunol Review;  2014 Jul;260(1):67-75.
    2. Antibiotics and the Gut microbiota – Sheetal R Modi, James J Collins, David A Relman; J Clin Invest; 2014 Oct;124(10):4212-8. Epub 2014 Oct 1 
    3. High Fibre Diet –  soluble and insoluble fibre – https://the-rainbow-diet.com/the-colourful-mediterranean-diet/the-high-fibre-rainbow-diet/ 
    4. Stress & the gut-brain axis: Regulation by the microbiome; Jane A Foster, Linda Rinaman, John F Cryan; Neurobiol Stress;  2017 Mar 19;7:124-136
    5. Research –  A parasite can change and control your microbiome
    6. The intestinal microbiota dysbiosis and Clostridium difficile infection: is there a relationship with inflammatory bowel disease? Therap Adv Gastroenterol; 2013 Jan;6(1):53-68.
    7. Short chain fatty acids in human gut and metabolic health; EE Blaak et al. Benef Microbes; 2020 Sep 1;11(5):411-455.
    8. The interplay between gut bacteria and the yeast Candida albicans; J. Christian Pérez; Gut Microbes; 2021; 13(1): 1979877.
    9. Wu GD, Chen J, Hoffmann C, Bittinger K, Chen Y-Y, Keilbaugh SA, et al. . Linking long-term dietary patterns with gut microbial enterotypes. Science. (2011) 334:105–8. 10.1126/science.1208344
    10. Relationships Between Vitamin D, Gut Microbiome, and Systemic Autoimmunity; Erin A. Yamamoto, Trine N. Jørgensen;  Front Immunol; 2019; 10: 3141
    11. Effects of Turmeric and Curcumin Dietary Supplementation on Human Gut Microbiota; Christin T Peterson et al;  J Evid Based Int Med;  Jan-Dec 2018;23:2515690X18790725 
    12. Butyrate and the Intestinal Epithelium: Modulation of Proliferation and Inflammation in Homeostasis and Disease; Pooja S. Salvi, Robert A. Cowles: Cells, 2021, Jul; 10(7): 1775.
    13. Hydrogen sulfide and colonic epithelial metabolism: implications for ulcerative colitis; Dig Dis Sci  2001 Aug;46(8):1722-32
    14. Bifidobacteria and Butyrate-Producing Colon Bacteria: Importance and Strategies for Their Stimulation in the Human Gut;  Audrey Rivière, Marija Selak et al Front Microbiol; 2016; 7: 979.
    15. Dutch researchers review foods, food groups, inflammation and good health Gut microbiome study links foods to good health, or bad health
    16. How antibiotics scar the microbiome – https://www.canceractive.com/article/how-antibiotics%20can%20scar%20your%20gut%20microbiome


Some Helpful Links:

Go to: Key probiotic effective against IBS

Go to: Sugar increases risk of colitis

Go to: The cause of Crohn’s

Go to: All cancer begins in the gut

Go to: Chronic Fatigue Syndrome

Go to: Growing evidence Rheumatoid Arthritis starts in the gut

Go to: Fibromyalgia

Go to: Hashimoto’s