Ultimate Gut Health Resource – Probiotics, Prebiotics & More

Ultimate Gut Health Resource – Probiotics, Prebiotics & More


This post is a round up of all things related to Gut Health. I have researched Probiotics, Prebiotics, Books, Podcasts and list here a selection of the best resources.

What will you find in this article?

What is the Gut Microbiome?

There are over 1000 different types of bacteria that can colonise the human gut (the gut microbiota), containing more than 3 million bacterial genes (the gut microbiome).

Each of us has over 150 species of bacteria in our gut and we all have a very unique profile (almost like our unique fingerprints).

25060343441_ae73cce985_k (1)

The most significant relationship between the gut microbiome and health seems to be the diversity of the bacteria (and therefore their genes) – the greater the diversity the better.

Diet has the biggest influence on the type, abundance and diversity of your gut bacteria. We should all be aiming for a very wide and varied diet, high in fibre, and a diet that contains many different types of vegetables.


What do the Gut Bacteria do?

A landmark study, written by Martin Blaser and published in 2014 had this to say about the human microbiome:

“There is increasing evidence that the microbiome touches many, if not most, pathways that affect health, disease, and aging. It is reasonable to propose that the composition of the microbiome and its activities are involved in most, if not all, of the biological processes that constitute human health and disease, as we proceed through our own life cycle.”

Reference – The Microbiome Revolution 


The gut bacteria ferment indigestible fibres (fibres that our own enzymes cannot digest) from plants such as vegetables and turn them into short-chain fatty acids.

Certain vegetables such as potatoes contain resistant starch, which is food for gut bacteria. Resistant starch plays a huge part in health and weight loss. A large proportion of the trillions of bacteria that live in our large intestine favour resistant starch as a food source.

A very important short-chain fatty acid produced by the gut bacteria is butyrate.

Butyrate is fuel for the cells that line the intestine. When these intestinal cells are healthy our gut lining can function correctly and our overall health improves.

Butyrate is involved in the production of mucus. A healthy gut is lined with a thick layer of mucus, which protects the gut lining and prevents undigested food and pathogens from entering the bloodstream from the gut.


Less food for gut bacteria = less butyrate = less mucus = a less protected gut.



If the gut is less protected, a condition known as Intestinal Permeability or ‘Leaky Gut’ can develop and this can lead to a multitude of health problems.

Other Roles of the Gut Bacteria

  • They interact with our nervous system, and play a role in our mood and anxiety levels
  • They interact with our immune systems
  • They interact with our hormones and may play a role in appetite regulation
  • They manufacture vitamins for us such as some B vitamins and vitamin K
  • They affect how much energy we extract from food

Many people nowadays, as a result of our modern lives, suffer some sort of gut dysbiosis and increased intestinal permeability or ‘leaky gut’ as it is known.

Gut dysbiosis can involve low diversity of bacteria in the gut, too many pathogenic bacteria and too few ‘friendly’ bacteria, an overgrowth of yeast and low mucus levels.

A diverse gut microbiome has been linked with healthy weight, and obese individuals tend to have a lower number of different species living in their guts compared to non-obese individuals.

Increased intestinal permeability or ‘leaky gut’ is also a big contributor to ill health. If undigested food particles make it through the lining of the gut and into the bloodstream this can lead to food intolerances and an overactive immune system. In extreme cases, this can contribute to the development of autoimmune disease.

A healthy microbiome has been shown to help prevent leaky gut and to reverse it.


The gut microbiome plays a role in the body’s level of inflammation.

When the gut bacteria are in balance, they provide anti-inflammatory signalling to the immune system.

A gut dysbiosis can lead to systemic inflammation in the body, which has been linked to heart disease, and an overactive immune system linked to the development of autoimmune disease.

What Can We Do To Have a Healthy Gut?

Make Sure You Are Properly Digesting Your Food

To digest our food properly we need the right pH in the stomach. This should be between 1.5 and 3.5. If we have low stomach acid then we might not be digesting our food as well as we should be and this can lead to problems such as SIBO and gastroesophageal reflux disease (GERD).

We also need digestive enzymes and bile to properly digest food. For various reasons the production of digestive enzymes and of bile can be compromised.

If you think you may be incompletely digesting food there are supplements you can buy that contain HCl, digestive enzymes and bile, which are a temporary solution but may help if you are trying to heal your digestive system.

Thorne Research Bio Gest is a blend of hydrochloric acid (HCl), pepsin, pancreatin, and ox bile to aid in digestion of proteins, carbohydrates, and fats.

Thorne Bio Gest Gut Health

Designs for Health Digestzymes is another similar formulation containing HCl, ox bile and digestive enzymes.

Digestzymes Gut Health

Take Probiotics

Probiotics have been shown in a recent meta-analysis of 20 different studies to reduce inflammation:

2017 – Impact of Probiotic Administration on Serum C-Reactive Protein Concentrations: Systematic Review and Meta-Analysis of Randomized Control Trials.

Another meta-analysis showed they help with depression:

2016 – Effect of Probiotics on Depression: A Systematic Review and Meta-Analysis of Randomized Controlled Trials.

There are three main classes of probiotics. These are:

  1. Lactobacillus/Bifidobacterium mixtures
  2. Healthy fungus probiotics – the predominant one is Saccharomyces boulardii
  3. Soil-based probiotics, also known as spore-forming. You’ll oftentimes see the name bacillus included in these types of probiotics. These are the least well studied probiotics, but definitely seem to be effective also.

Recommended Probiotics

  • Elixa Probiotic – a new UK manufactured high-strength, short-course probiotic. Elixa is my personal favourite probiotic as I have had great results using it and it is the highest strength probiotic on the market with 500 billion CFU per dose! Elixa contains 11-strains (Lactobacillus Plantarum, Lactobacillus Rhamnosus, Lactobacillus Reuteri, Lactobacillus Acidophilus, Lactobacillus Casei, Lactobacillus Helveticus, Lactobacillus Salivarius, Bifidobacterium Bifidum, Bifidobacterium Lactis, Bifidobacterium Longum, Bifidobacterium Breve) plus Potato Starch (For the benefits of Resistant Starch for probiotic adhesion)
    Elixa-Probiotic Gut HealthI think Elixa has the edge over other probiotic products for several reasons. Firstly it is the lacto/bifido blends that have the most robust research supporting their positive effects. Secondly it’s the highest strength probiotic on the market. Third, it has an unrivalled delivery system in the form of it’s Fortress-5 encapsulation technology. It’s also reasonably priced considering it’s potency.
  • Another interesting product is by Garden of Life and is called Raw Probiotics 5 Day Max Care. This product is 400 billion CFUs and contains 34 probiotic strains. It also contains digestive enzymes.
    Raw Probiotics Max Care
  • VSL#3 is another strong probiotic at 450 billion CFUs and 8 different strains.
    VSL 3 Gut HealthYou can read more about VSL#3 and the science supporting it here. 
  • I also like Renew Life Ultimate Flora Extra Care – this is a 7 Day Intensive Course of Probiotics AND Prebiotics (in the form of fructo-oligosaccharides/FOS)
    Renew Life Ultimate Gut Health
    As you can see from the back of the pack this is a Lactobacillus/Bifidobacterium mixture containing 10 probiotic strains and 200 billion CFU per dose.
    Renew Life Ultimate Back
  • Garden of Life also produce a similar product that is designed to be taken on an ongoing basis called Raw Probiotics Ultimate Care. Its 100 billion CFU and contains the same 34 strains as the stronger product.
    Raw Probiotics Gut Health
  • Grace Liu of The Gut Institute sells a strong lacto/bifido blend called BIFIDO|MAXIMUS – it’s an Histamine-Free and D-Lactate Free Probiotic Blend with 200 billion CFU per dose. This could be good for anyone suffering from histamine intolerance as most probiotics release histamine. I can’t find this probiotic in the UK and it’s not cheap!
  • Prescript Assist is a soil-based probiotic blend backed by sound science: supported by peer-reviewed, published clinical studies. They claim “Inherent viability: a matrix of superior, highly-resilient microflora whose organic, seed-like structures survive the early GI tract to thrive in the intestines.” 

    Prescript Assist Gut HealthIt contains bacillus subtilis: a proven probiotic species found in traditional foods and overall has 29 symbiotic strains as well as prebiotics.
    Prescript Assist Back Gut Health
  • Equilbrium by General Biotics
    Equilibrium Gut Health
  • Primal Defense Ultra by Garden of Life – this is a great formulation which contains a Lactobacillus/Bifidobacterium mixture plus Saccharomyces boulardii and Bacillus species. It’s 15 billion CFUs per dose (so nowhere near as strong as Elixa) and contains 13 different strains. 
    Primal Defense Ultra Gut Health
  • AOR Probiotic 3 – The enterobacteria contained in ProBiotic 3 act in symbiosis and promote a healthy intestinal flora. Lactic acid and butyric acid-producing probiotics inhibit the growth of pathogenic bacteria while promoting the growth of the beneficial Bifidobacterium strain.
    AOR Probiotic 3 Gut Health
  • Symbioflor – contains the natural intestinal bacteria Enterococcus faecalis and Escherichia coli, in inactive form. Grace Liu of The Gut Institute recommends this one.
  • I have heard Chris Kresser recommend Mega Spore Biotic as a probiotic but it’s only available through a health care practitioner.
    MegaSporeBiotic Gut HealthMegaSporeBiotic contains 5 strains: Bacillus Indicus HU36, Bacillus Clausii, Bacillus Subtilis HU58, Bacillus Licheniformis and Bacillus Coagulans. There are some interesting pdfs where you can read a lot more about MegaSporeBiotic here and here.
  • There is another probiotic called Just Thrive that I believe is made by the same people as MegaSporeBiotic. It is a very similar product, containing 4 of the 5 strains found in MegaSpore.
    Just Thrive Probiotic Gut HealthIt contains 3 billion CFUs per serving (whereas MegaSpore contains 4 billion). I am not sure why they would make a similar product but with one less strain…? Maybe someone in the know can explain in the comments below! MegaSporeBiotic does seem to be well reviewed online so I am guessing this JustThrive probiotic would be effective as well.
    Just Thrive Back of Pack
  • Probiogen looks like a great brand of probiotics, their Daily Digestive Balance contains 8 Billion CFU Saccharomyces boulardii, Bacillus clausii, Bacillus subtilis HU58™, Bacillus coagulans HC™.
    Probiogen Probiotics Gut Health
  • You could also try Bacillus Coagulans from Thorne.
    Bacillus Coagulans Gut Health
  • There is one more probiotic I came across with these Bacillus strains and it is targeted at Crohn’s sufferers. It’s called Perfect Pass and it contains: *One billion CFUs of each strain,*3 billion cells per capsule, Bacillus subtilis HU58, Bacillus clausii, Bacillus coagulans.
    Perfect Pass Probiotic Gut Health
  • Jarrow Formulas produce a Saccharomyces boulardii probiotic which also contains a specific prebiotic that is said to not feed candida.
    Saccharomyces Boulardii Gut Health
  • Another interesting probiotic I came across is one that might be good for anyone suffering from histamine intolerance. Many strains of probiotics produce histamines, and therefore are sometimes poorly tolerated by people with histamine issues. Phage Complete contains Lactobacillus plantarum, Lactobacillus rhamnosus, Bifidobacterium bifidum, Bifidobacterium longum and Bacillus subtilis – DE111® which are all non-histamine producing.
    Phage CompleteIt also contains a Phage Complex called PreforPro which is said to selectively kill pathogenic bacteria while promoting the growth of beneficial strains. I haven’t done a lot of research into phage therapy but it does sound interesting so could be worth looking into further.

Dr Ruscio, a functional medicine practitioner who specialises in gut health recommends the following probiotic protcocol:

Screen Shot 2017-07-29 at 10.47.56

I try and rotate the probiotics I take. If I could afford it I would do as Dr Ruscio suggests and take a combination of a lacto/bifido blend, S. boulardii and a soil-based formula.

It’s probably a good idea to try and get probiotics from food in addition to (or instead of) taking supplements.

Good probiotic foods are:

  • Kefir – Water kefir or dairy kefir. I have written about the benefits of kefir here and here.
  • Kombucha
  • Yogurt (homemade is best) – coconut or dairy
  • Sauerkraut
  • Miso
  • Kimchi


Take Prebiotics

I have written before about Probiotics and Fermented Foods to increase the levels of beneficial bacteria in your gut. Another important step towards good gut health is ensuring that you feed the beneficial bacteria with prebiotics.

Prebiotics are special fibres found in complex plants and roots that feed beneficial strains of bacteria, helping them to grow and crowd out pathogenic bacteria.

Just as with Probiotics, it’s probably a good idea to try and get Prebiotics from food before trying supplements.

Prebiotics in Food – Inulin-Oligosaccharides & Beta-Glucan

A special group of fibres called inulin and oligosaccharides tighten the gut and prevent leakage and inflammation. Foods that contain these fibres include:

  • Raw onion (4g/100g)
  • Raw garlic (3g/25g)
  • Raw leek (6.5g/100g)
  • Chicory root (41g/100g)
  • Jerusalem artichoke (18g/100g)
  • Dandelion greens (13g/100g)
  • Yacon Syrup & Dried Yacon Flakes – these contain fructo-oligosaccharides (FOS) which is similar to inulin
  • Soaked raw oats contain beta-glucan that is another prebiotic. Look for gluten-free, steel-cut oats and soak for 24-48 hours before eating.

I find raw leeks easier to eat than raw onions, they are milder and they are also higher in inulin. I chop raw leeks finely, add a crushed garlic clove and marinate in some raw apple cider vinegar, extra virgin olive oil, salt and pepper. I then have this mix with eggs, on top of baked potatoes or mixed into salads.

Prebiotics in Food – Resistant Starch Types 2 and 3

Some foods contain a type of indigestible starch called resistant starch (since it is resistant to digestion). This starch is indigestible to us, but our gut bacteria love it. There are four types of resistant starch, but the important ones are types 2 and 3.

Type 2: This is found in certain foods when they are raw. The best sources include:

  • Raw green (unripe) plantains. You can add green plantains to smoothies, or thinly slice and dehydrate to make chips. You can also use green plantain flour in smoothies but I haven’t found a source in the UK
  • Raw green (unripe) bananas – use in the same way as raw green plantains
  • Raw potatoes (not recommended) & raw potato starch
  • Raw tigernuts and raw tigernut flour

Type 3: When certain foods are cooked and then cooled, a special type of resistant starch is formed. It has a dense, DNA-like configuration and our gut flora thrives on it. The best sources are:

  • Roasted and cooled heirloom potatoes such as purple potatoes (15-19g/100g)
  • Cooked and cooled beans such as pinto beans (10g/100g)
  • Cooked and cooled yams (6-8g/100g)
  • Boiled and cooled white potatoes (3-7g/100g)
  • Cooked and cooled sushi rice (3-4g/100g)
  • Cooked and cooled lentils, chickpeas, hummus (2-4g/100g)
  • Cooked and cooled rice (1-3g/100g)

Prebiotic Supplements

There are several supplements that can be added to the diet to provide fibre for the gut bacteria:

  • Bimuno – a second generation prebiotic – a source of a special prebiotic called B-GOS
  • Tribal Prebiotic is coming soon from Elixa Probiotic and I am really excited for the launch of this product
  • Inulin-Fructo-Oligosaccharides (Inulin-FOS)
  • Psyllium
  • Acacia Gum/Fibre – I buy Heather’s Tummy Fibre made from Acacia Senegal
  • Pectin
  • Chorella
  • Arabinogalactan
  • Glucomannan/konjac root
  • Oat Bran/Beta-Glucan
  • Galacto-Oligosaccharide (GOS)
  • FOS-rich Yacon Syrup/Yacon Root Powder/Yacon Flakes – a source of FOS – I buy mine from Of The Earth Superfoods
  • Ground flaxseed
  • Baobab Hadza Fruit Fibre
  • Green Banana Flour – a source of resistant starch in the RS2 form
  • Green Plantain Flour – a source of resistant starch in the RS2 form
  • Raw Unmodified Potato Starch (RUMPS) – a source of resistant starch in the RS2 form
  • Chitosan
  • Hemp seed powder
  • Wheat grass
  • Guar gum
  • Amla Powder
  • Grass-fed gelatin and collagen
  • Ground chicory root – a source of inulin
  • Beetroot powder
    Beetroot Powder Paleo

For a while there was a big focus on Type-2 Resistant Starch (RS2) with a lot of people taking Bob’s Red Mill Raw Potato Starch. However, like with most things, it turns out to not be a good idea to focus only on one fibre source as RS2 feeds certain gut bacteria but not others. We want to aim for diversity and variety in gut bacteria. According to Dr Grace Liu of www.thegutinstitute.com RS3 is probably more beneficial than RS2, and we should be feeding our gut with the whole spectrum of ancestral fibres.

The best strategy is to include a whole range of the above wholefoods in your diet.

In terms of supplements you could try making a daily smoothie and adding Dr Grace’s BIONIC FIBRE or using Richard Nikoley’s (Free The Animal) smoothie recipe. Or simply rotate taking a few of the different fibre supplements for variety and diversity.

Heal a Damaged Gut Lining

Certain foods damage the gut lining and can lead to intestinal permeability. The one you hear the most about is gluten from wheat. So adopting a gluten-free diet is a sensible step to take if you think you need to heal your gut.

The following information comes from Dr Axe’s article 4 Steps to Heal Leaky Gut and Autoimmune Disease

“Top 5 Supplements for Healing Leaky Gut

There are many supplements that support your digestive health, but I believe the most beneficial leaky gut supplements are l-glutamine, probiotics, digestive enzymes, aloe vera juice, quercetin, NAG and licorice root.

  1. Probiotics are the most important supplement to take because it helps replenish good bacteria and crowds out bad bacteria. I recommend getting probiotics in both food and supplement form. I see people all the time only follow part of the protocol in healing their leaky gut syndrome by removing the damaging irritants. But the part they often leave out is re-inoculating their gut with beneficial bacteria that will keep bad bacteria at bay. So load up on BOTH probiotic-rich foods and take AT LEAST 50 billion units of probiotics daily from a high-quality brand.
  2. Digestive enzymes (one or two capsules at the beginning of each meal) ensure that foods are fully digested, decreasing the chance that partially digested foods particles and proteins are damaging your gut wall.
  3. L-Glutamine is critical for any program designed to heal leaky gut. Glutamine powder is an essential amino acid supplement that is anti-inflammatory and necessary for the growth and repair of your intestinal lining. L-glutamine benefits include acting as a protector: coating your cell walls and acting as a repellent to irritants. Take 2–5 grams twice daily.
  4. Licorice Root (DGL) is an adaptogenic herb that helps balance cortisol levels and improves acid production in the stomach. DGL supports the body’s natural processes for maintaining the mucosal lining of the stomach and duodenum. This herb is especially beneficial if someone’s leaky gut is being caused by emotional stress. Take 500 milligrams twice daily.
  5. Quercetin has also been shown to improve gut barrier function by sealing the gut because it supports creation of tight junction proteins. It also stabilizes mast cells and reduces the release of histamine, which is common in food intolerance. New studies have also shown its effectiveness in healing ulcerative colitis. Take 500 milligrams three times daily with meals.”

A good supplement that contains these things to heal your gut is GI Renew. GI Renew contains a synergistic blend of nutrients to support the gut barrier. Patients with poor gut integrity easily develop food sensitivities and may have compromised nutrient assimilation. GI Renew capsules provide therapeutic levels of L-glutamine, N-acetyl-glucosamine, MSM, DGL, slippery elm, marshmallow, chamomile, okra, TOA-free cat’s claw, quercetin, and mucin for comprehensive support of optimal gastrointestinal health.

Drink Bone Broth

Bone broth contains the amino acid glycine as well as collagen to help heal your gut lining. You can also take gelatin for gut health if you don’t drink bone broth. This can be added to smoothies or tea and coffee as it dissolves easily and is flavourless.

Gelatin Gut Health

Additional Things to Research

Phage Therapy

There are a couple of things I have heard about that are interesting but I haven’t yet had chance to research. These are Phage Therapy and Restore. Restore claims that it can heal a damaged gut lining but I need to do more research into this product.

Restore for Gut Health



A great place to start to learn more about gut health is with any of these blogs:

www.humanfoodproject.com – website of Jeff Leach

www.drbganimalpharm.blogspot.com and www.thegutinstitute.com – the two websites of Dr Grace Liu

www.freetheanimal.com – website of Richard Nikoley

www.vegetablepharm.blogspot.co.uk – website of Tim Steele aka Tatertot

www.mrheisenbug.wordpress.com – website of Shant Mesrobian

www.restoretheflora.com – website of Matt Pepin






  • The Diet Myth by Professor Tim Spector (one of the scientists involved in the British Gut Project)
  • Follow Your Gut: The Enormous Impact of Tiny Microbes by Rob Knight
  • Bloom: Reconnecting With Your Primal Gut in a Modern World by Jeff Leach (forthcoming book by the folks at Human Food Project)
  • The Gut Makeover by Jeannette HydeGut Makeover
    Click here to read our full review of The Gut Makeover

Gut Testing 

If you would like to do some testing on your gut microbiome (for fun, not for diagnostic purposes) – visit Ubiome, The American Gut Project (AmGut) www.americangut.org or The British Gut Project www.britishgut.org. Read my blog post on my uBiome experience.

Gut Tests for Diagnostic Purposes

  • Comprehensive Stool Analysis with Parasitology from Biolab UK – www.biolab.co.uk
  • FloraPrint £300 from Cambridge Nutritional Sciences – www.camnutri.com
  • Candida Overgrowth £65 from Cambridge Nutritional Sciences – www.camnutri.com
  • BH #401H – GI Pathogen Screen with H. pylori Antigen from Bio Health – www.biohealthlab.com
  • Comprehensive Stool Analysis with Parasitology x3 from Doctors Data – www.doctorsdata.com
  • Comprehensive Digestive Stool Analysis / Parasitology ™(CDSA/P) from Genova Diagnostics (formerly Metametrix) – www.gdx.net
  • Comprehensive Stool Analysis from Great Plains Laboratory – www.greatplainslaboratory.com


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