Over the last five posts, we’ve covered the importance of the microbiome to health through its role in digestion and immunity, and how a dysbiosis (imbalance of good to bad bacteria), can result in a number of serious health problems, including obesity, diabetes, heart disease, cancer, allergies and autoimmune conditions!

In this final instalment, we are going to look at how and why dysbiosis may occur, and the best strategies to both avoid it in the first place, and to treat it if you are already affected.

Causes of Dysbiosis:

In early infancy:

“Some people are just born with it” – Good gut flora that is. In fact, everybody should be born with it. Within the womb, the unborn foetus is sterile, free from any bacteria, either good or bad. Under normal circumstances, we should get our first dose of beneficial microbiota from our mothers as we pass through the birthing canal. This should then be topped up through breast milk, which should also be high in beneficial bacteria, as well as being a good food source for the bacteria as well as the baby itself.

Unfortunately, more and more babies are being born by cesarean section. As the birthing canal is bypassed, the baby misses its first inoculation of good gut flora. To make matters worse, many babies are then bottle fed, missing out yet again on receiving their first dose of good bacteria.

Even a natural birth and breast feeding does not guarantee a good start however – If a pregnant or breast feeding mother has dysbiosis, the bad bacteria she is carrying will be passed to her child in place of the good bacteria. Equally, if she is treated with antibiotics during pregnancy of lactation, all microbes, good or bad will be killed in both her and her child. All these circumstances are made worse due to the proliferation of pathogenic antibiotic resistant superbugs in hospitals!

The most important determinants of the gut microbiotic composition in infants were the mode of delivery, type of infant feeding, gestational age, infant hospitalization, and antibiotic use by the infant. Term infants who were born vaginally at home and were breastfed exclusively seemed to have the most “beneficial” gut microbiota (highest numbers of bifidobacteria and lowest numbers of C difficile and E coli).1

In adulthood:

While all the above is important to bare in mind for prospective parents, what does it mean for adults that were born under less than ideal conditions?

The good news if you had a less than ideal start in life (and perhaps bad news if you did), is that the gut flora is not fixed for life, but can be influenced by many factors of diet and lifestyle.

Think of your microbiome as like a garden passed to you by your parents. Perhaps your parents left you a garden that was constituted of barren soil, and overgrown with weeds. Though it may be difficult, with time and effort it is possible to restore the garden by killing the weeds, fertilising the soil and planting the necessary seeds. Conversely, if an individual neglects to look after even the most pristine garden that they are left, and creates instead an environment more favourable to weeds and pests, they can actually end up in a worse situation in the long-term.

The following are all factors which can contribute to dysbiosis:


You are what eats what you eat – That is to say, that the food you choose to put down your throat, ends up being the food available for the microbes in your intestines. Beneficial bacteria tend to do well on indigestible (to humans) plant fibre, particularly that found in fibrous vegetables. Bad bacteria on the other hand tend to thrive on the simple sugars found in processed foods. By eating a diet that is low in fibrous vegetables, and high in processed sugars (i.e. the standard modern diet), you are effectively starving your beneficial bacteria, and feeding the bad ones!

Antibiotic Use

This was pretty much covered in last week’s post, but it’s worth mentioning again – Although taking a course of antibiotics may (though not always) kill unwanted pathogenic bacteria which are causing an illness, they will also almost certainly kill of all of your beneficial bacteria too.


The relationship between gut flora and stress is a complex one, which warrants a post of its own in the future (though I’m sure you’ve all had quite enough for the time being). In short, however, chronic stress can have a seriously negative impact on your digestion, and therefore your gut flora.

Prevention and Treatment of Dysbiosis:

“Prevention is always better than a cure” – This is one of the mantras of Primal Living, and highly applicable to the condition of dysbiosis.

Following these dietary guidelines should be your first step in achieving optimal intestinal symbiosis. A diet comprised predominantly from unprocessed, whole foods, and low in processed fake foods and sugars, should be sufficient to maintain healthy gut flora in most cases.

To be on the safe side, however, it could well be advisable to focus on including plenty of prebiotic foods, and perhaps even taking a probiotic.

Prebiotics vs Probiotics

A prebiotic is defined as:

…a selectively fermented ingredient that allows specific changes, both in the composition and/or activity in the gastrointestinal microflora that confers benefits upon host well-being and health.2

The most common (and researched) forms of prebiotic are non digestible carbohydrates, such as oligofructose and inulin. Though it is possible to buy prebiotic supplements, eating real food generally always works out as the best option. The best dietary sources of prebiotic fibre are:

Image: vudhikrai / FreeDigitalPhotos.net

    Chicory Root
    Jerusalem Artichoke
    Dandelion Greens

Think of these foods as like fertiliser or plant food for your good bacteria.

Probiotics are defined as:

…viable microorganisms, sufficient amounts of which reach the intestine in an active state and thus exert positive health effects4

Probiotics are good bacteria which are ingested orally, in an attempt to repopulate the gut. Probiotics come in two main forms – Either unpasteurised fermented foods such as live yoghurts, kefir and cheeses, and sauerkraut, kimchee and miso, or as a supplement in the form of encapsulated tablets.

Probiotics have been shown to have many positive effects, ranging from improved digestion, through to reduced risk of disease and fat loss. Quality is key however – Many commercially available probiotics, either capsules or “probiotic yoghurt drinks”, contain relatively little beneficial bacteria in the first place (in terms of number and variety), are not robust enough to survive the highly acidic environment of the stomach, and in the case of the yoghurt drinks are often full of sugar – Food for the bad bacteria!

Even the best probiotic encapsulation is little use if your diet is not right – It is akin to throwing seeds on fallow ground.


Synbiotics is the combined use of pre and probiotics in order to garner the best results.

So the optimal gut flora friendly eating plan would be:

  1. Follow the Eat Primal nutrition guidelines
  2. Include some prebiotic foods (NB don’t go overboard, start small and build up to avoid gas!)
  3. Take a High Quality Probiotic such as Protexin Bio-Kult
  4. Include some live fermented foods in your diet

Following these guidelines should both enable you to maintain healthy gut flora, thus reducing your risk for numerous diseases, obesity and infections, and given sufficient time can even rectify existing dysbiosis.

In some cases of severe dysbiosis, however, this treatment alone is not enough. Just as having a healthy population of good bacteria can prevent the growth of bad bacteria in the gut, so can a well established population of bad bacteria prevent the growth of good bacteria – It can be a simple case of whoever got there first. Also, though bad bacteria tend to thrive on sugars, this is not always the case, and many can also feed on the same prebiotic foods as good bacteria.

In these circumstances there are a few possible approaches, the good, the bad, and the ugly:

Following a vlcd/ketogenic diet/GAPS diet/Specific Carbohydrate style diet

Though all these diets differ in their specifics, the general principal is the same: By cutting out all the fermentable carbohydrates from the diet, the bad bacteria will eventually starve and die. Potential problems with this approach are that you are also starving your good bacteria, and there is always the chance that the bad bacteria may be more durable and/or may even be able to adapt to other energy sources such as protein and fat!

Strategic use of antibiotics

Having harped on about the dangers of indiscriminate antibiotic use repeatedly throughout this series of blog posts, this one may well come as a surprise, in some cases, however, it may well be the only course of action left.

When the bad bacteria have taken over, either in the case of dysbiosis, or a very serious infectious illness, antibiotics may well be the only option.

The key to the successful use of antibiotics, is the complementary use of pro and prebiotics before, during and after the course of medication. This should hopefully ensure that once the antibiotics have done their business, it is good bacteria that are able to re-establish themselves in the host.

Fecal Transplants?!

No, you did not misread that, and I am not pulling your leg. One of the newest areas of research into the treatment of dysbiosis and chronic infections of the gut by pathogenic bacteria is bacteriotherapy, A.K.A stool transplants.

The procedure has been common practice in animals by veterinarians for many years, but it has only started to be performed on people very recently. The condition for which it has been used to treat most commonly, and with great success, is clostridium dificile infection – a highly persistent, antibiotic resistant bacteria which causes recurrent diarrhoea and colitis.5 The pioneer, as it were, of fecal transplants, Thomas Borody, an Australian Gastroenterologist, however, claims to have successfully numerous conditions ranging from IBD and IBS, through to ACNE, Parkinsons and Multiple Sclerosis!6

The procedure involves cleaning out the patients intestines after a strong dose of antibiotics, taking the stool of an individual (ideally a relative) with a healthy microbiome, dissolving it in water, and then transferring the solution back into the patients intestines via a tube, like a reverse enema. Despite what appear to be very promising results so far, for some reason the procedure doesn’t seem to be catching on…

Though the “ick factor” may well be one impediment against more widespread study of this technique, along with doctors not being too keen on being associated with the technique for fear of losing credibility, there are also bigger obstacles in the way. Before a new medical technique can become mainstream, it needs backing up by well designed, randomised and controlled clinical trials.

Dr Coleen Kelly, a clinical faculty member at Brown’s University Medical School, who has also used the technique with success has proposed the plans for a randomised clinical trial to study the technique to the NIH, but has hit a roadblock as:

before the NIH approves any trial, the substance being studied must be granted “investigational” status by the Food and Drug Administration. The main categories under which the FDA considers things to be investigated are drugs, devices, and biological products such as vaccines and tissues. Feces simply do not fit into any of those categories.7

Those more cynical of us out there might read into this that there is no money to be made from s&%t, as it can’t be branded, copyrighted and sold! (It would also probably be hard to market on one of those bigpharma TV ads they have on TV in the US…)

The good news is that for the vast majority of people, the simple dietary changes highlighted above should be more than adequate to either prevent dydbiosis occurring, or even rebalance it.

If you are suffering from extreme digestive issues such as IBD/IBS or an autoimmune condition, then I would recommend checking out the GAPS Diet, or the Specific Carbohydrate Diet.

Of course if all else fails, and your GP won’t refer you for a fecal transplant, you could always try one yourself at home?

1. Factors influencing the composition of the intestinal microbiota in early infancy. Penders J (2006)

2. Prebiotics: The Concept Revisited Marcel Roberfroid (2007)

3. Presence of Inulin and Oligofructose in the Diets of Americans Alanna J. Moshfegh

4. Probiotics, prebiotics, and synbiotics. de Vrese M et al (2008)

5. Systematic Review of Intestinal Microbiota Transplantation (Fecal Bacteriotherapy) for Recurrent Clostridium difficile Infection. Ethan Gough (2011)

6. Same poop, different gut: For physicians and researchers alike, fecal transplants present an opportunity to gain insight into disease. Cristina Luiggi (2010)

7. Swapping Germs: Should Fecal Transplants Become Routine for Debilitating Diarrhea? Maryn McKenna (2011)

2 thoughts on “Why you should be Pro-Biotic: Part VI – You are what eats what you eat…Or someone else’s poo?”

  1. Pingback: Cutting through the B.S. on I.B.S – Part I

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