16th May 2018

After all of my articles about #MeToo and how it relates to chronic illness, abuse, trauma, deeply ingrained response patterning etc., you may welcome today’s article which heralds a return to the absolutely practical. It wouldn’t be me if it wasn’t peppered with a heavy dose of pragmatism and down-to-earth common sense… but, for this week at least, I’m sticking to science as much as I can.

There’s just one issue with that… I’m writing about probiotics. And whilst the science is positively burgeoning in this area, what we know for sure pales in comparison to the vastness of what we don’t know.

I have written in the past about the perils of using microbiome mapping tests such as Ubiome or the American Gut Project to identify the way to ‘fix’ a problem that you think you are experiencing with your gut bacteria. These tests are simply mass-spectrum snapshots of an individual’s intestinal environment and, as such, have almost no clinical utility. Fascinating, certainly. But not diagnostic.

Then there’s the new test on the block: Viome. I am watching this company closely because they offer a slightly different approach to gut testing. Instead of one-off snapshots, Viome offer a subscription service where (for a subscription fee) stool tests are completed once per year. This allows you to make behavioural, diet, supplement, sleep or treatment changes and then track the precise impact the changes make to your microbiome.

This technology is advancing such that as an additional service, Viome make dietary recommendations using algorithmically calculated prescriptions based on the spread of the gathered microbiome data. I have heard anecdotal reports (from Integrative Doctors that I respect) that the Viome suggestions have proved not only incredibly beneficial, and they also mirror what would be recommended according to an individual’s’ genetics:

i.e. the Viome tech has recommended lowering the fat content of one person’s diet in preference of more carbohydrates. This person was indeed attempting ketogenic dieting, and had genetics (to do with lipid metabolism) which suggested she was poorly suited to high fat lifestyle. This suggests that the gut bacteria were reacting as negatively to the high fat diet as their metabolism was. This is interesting, certainly… do our bugs match our DNA such that if we are metabolically unsuited to high fat diets our gut bugs are also poorly suited to fat digestion? It seems… well in honesty it seems quite far-fetched, but I am intrigued…

AND YET – back to the topic of this article. If Viome is recommending things based on microbial pictures, how come they do NOT recommend probiotics……. AT ALL…? Is it because they’re not testing enough to know what to suggest?

In Functional Medicine we use more highly specific, and therefore supposedly clinically useful, gut tests – referred to as comprehensive stool analyses. These give us a ‘better’ map of the microbiome: not in depth and breadth, but by virtue of the fact that they report only on bacteria that have been studied in the literature as ‘good’, ‘bad’, ‘dysbiotic’, ‘healthy’, ‘pathogenic’, ‘parasitic’ etc. These test show the levels and the diversity of ‘healthy’ bacteria and ‘potentially unhealthy’ bacteria. Some of these tests offer quantification, but here controversy lies as some tests utilise ‘culture’ methods which can be inaccurate – particularly when it comes to quantification (extensively discussed here).

Nevertheless, discussions of test accuracy aside, patients come to me who have completed these tests and, as a result, have started taking a specific probiotic which contains the strains that their functional gut test showed that they were ‘lacking’.


This is despite the fact that no matter how fancy (or expensive) the stool test – no matter whether it’s commercial, Functional, culture, DNA-PCR, Integrative or Viome – you simply CANNOT use any of these tests to identify what probiotic you ‘should be’ taking.





But we should all be taking SOME FORM of probiotic, right? Just because we can’t tell which one from a stool test, we should still be taking something, right?

Well – not so fast.

Probiotics are supplements. As such, they suffer from the same lack of scientific rigour in their development as almost every other supplement. Do they contain what’s on the label? Do they contain other junk (excipients)? Do they contain enough of the suggested ingredients? Do they contain metals and other toxins? Do they do any good?

These questions are asked of pretty much every supplement – and probiotics are no different. And yet, somewhat differently to every other supplement, when the ingredients of probiotics are questioned, it’s always with the assumption that providing the product is safe and contains what it should contain, we should then take them. We’re in the age of microbiome diversity promotion – and probiotic supplementation is often seen as the solution to all microbiome, and therefore digestive, woes.

I don’t quite know where this thought process comes from – we don’t feel the same about other nutritional supplements (though some practitioners may argue that we should). The idea of supplementing for everything leaves us with the impression that our own diets and environments are inadequate for keeping us healthy and if we’re not supplementing with something, we’ll be lacking in it…

Now, this could get into a whole discussion on whether our current environment and diet is healthy enough in and of itself to keep US healthy. Which would take whole books, not single articles. And yet, when it comes to probiotics it actually doesn’t require such a high level discussion of the modern environment. This is because microbiomes, unlike nutrient levels, aren’t supposed to be ‘one thing’ that we all must supplement to the level of:


Gut ecosystems are built in relationship to an environment – the environment in which you are born, grow up and live.

Studying ancient tribes, or even foreign populations, in an attempt to identify what bacteria you should have inside you just isn’t the best way to understand what your gut bacteria ‘should’ look like. Your gut bugs are forged from your history and exposures… and they’re uniquely suited to the life that you have led and continue to lead.

Providing there is neither disease nor symptoms present … there really is no compelling evidence to suggest that your bacteria, unsupplemented, isn’t enough.


This last sentence is the key. We often assume that everyone should take probiotics. But in truth, the evidence we have for probiotic supplementation is to rectify and resolve issues of disease, symptoms, inflammation and gut dysbiosis. i.e. probiotics can be used to fix a problem but are not necessarily a safety-blanket to ensure good digestion or general health overall.

This isn’t to say that they don’t help with general health – just that the majority of studies into probiotics have been to assess their role in disease management, not in healthy individuals. Which basically means that we don’t know that probiotic supplementation is necessary. Your gut bugs might just be precisely suited to you and managing your diet and that’s all you need to worry about.




So, this said – remarkably few people are completely happy with their diet and their digestion. And the likelihood is that if you’ve done a comprehensive stool analysis and/or are reading a Functional Medicine blog then you are experiencing symptoms or some form of disease.

So for disease and symptoms, therefore, is the addition of probiotics curative? And if ‘more’ and ‘diversity’ is ‘better’ (as so often thought) – can you supplement the ones that show up as ‘low’ or ‘no growth’ on your comprehensive stool analysis? Thereby aiming to complete the diversity spectrum based on what you show up as ‘missing’?

I would suggest that this is a very narrow-minded view of bacterial diversity. Functional Medicine promotes itself on the foundation of asking ‘why?’. To simply supplement a ‘missing’ bacteria, without asking ‘why is it missing?’ is incredibly lazy medicine. Many practitioners simply assume that a lack of certain bacteria is due to long-term, historic antibiotic exposure or some other antimicrobial interaction (with soaps, for example) and whilst this is plausible, it isn’t always the case.

To understand this, it is necessary to think of intestinal bacteria as something that exists in synergy with your immune system and overall wellbeing. The bacterial milieu is seeded at birth, fostered by breastfeeding and early exposures – and more importantly, it evolves by balancing against the immune system of the host.

Incidentally, this is why people believe that more dirt exposure in youth is good for you as it expands the bacteria encountered, builds a broader microbiome and, in so doing, trains the immune system to be stronger, more adaptive and more resilient (because it’s seen more bacteria it’s had to get used to).

When I see lower levels of certain bacteria In my clients, I always bear in mind that, in some instances, this may be that person’s natural state. A snapshot today cannot tell me how that client’s bacterial ecosystem evolved – nor can it tell me what their immune system has kept in check within their gut environment and chosen to keep low for some reason. When I see a microbial picture, I am seeing the bacteria that their body has evolved to live with – and this might be by intent, rather than simply by error.

For example:

Sometimes, lower levels of lactobacillus are pruned to that state by the immune system itself, simply because the production of lactic acid by these bacteria has proved problematic. Putting this patient on supplemental lactobacillus probiotics because they’re ‘low’ on a stool test is asking for immune and digestive trouble.

Similarly, lowered levels of ‘good’ bacteria may be due to higher levels of ‘bad’ bacteria or parasites. Whilst it is in no way true that probiotics feed parasites (a myth that perpetuates online), probiotics thrown into an environment to compete with parasitic growth can create more fermentation, symptoms and dysbiosis. It may be that treatment is needed before probiotics can begin – or perhaps a specific type of therapeutic probiotic is indicated (see below), rather than just throwing the supposedly ‘missing’ probiotic into the patient.




Which brings us onto the other interesting part about probiotics. We have very little evidence to suggest that a microbiome lacking in certain strains of probiotic will accept the strain added via probiotic supplementation and allow that strain to colonise.

This basically means that using probiotic supplementation is not like using vitamin and mineral supplementation, in which you take a supplement and you will then definitely have more of that vitamin or mineral available.

Even if the probiotic survives the acidic stomach environment and the small intestine, arrives as intended within the large intestine (and these are very big ‘ifs’) this still doesn’t guarantee that the probiotic strain that you intended to take hold does anything of the sort.




Probiotic supplements have been proven to be transient: this means that most of the probiotics you take will go all the way through your body and out in your stool. They don’t stay around, they don’t colonise and they don’t suddenly show up in a stool test after a few months of taking them (unless you take them very close to the time you complete the test).

Which, you would think, makes them utterly useless, right?

Well – actually no.



This is where probiotic research is really expanding. We have research data and clinical evidence to suggest that different types of probiotics are incredibly beneficial in remedying gut compromise. Probiotics have been shown to assist with everything from treating parasites, disrupting the protective biofilms which allow ‘bad’ bacteria to dominate, relieve H. Pylori, remedy inflammatory and permeability issues – and generally improve the fermentation, bloating, constipation and diarrhoea symptoms associated with Irritable Bowel Syndrome. (See below for what strains have been shown to do what).

How can something that doesn’t take root and stay within our gut do all of this?

Well, it’s actually quite simple and revolves entirely around the fact that gut ecology is an ecosystem. It is a living set of organisms. This means that ANYTHING that interacts with that ecosystem will change it. We are learning that nights of missed sleep, slight changes in macronutrient or micronutrient composition of the diet, toxicity, stress and exercise can all affect the ecosystem of the gut.

Simply put, EVERYTHING that you ingest (including through breathing, drinking, eating and even through your pores) will lean up against the bacteria which form part of your unique ecosystem. Some interactions will make no difference at all, other things will have but minor impact.

But when it comes to probiotics we are starting to realise that the role they play is huge. Because they are bacteria talking to bacteria it’s like meeting like. As such, they can shift, nudge and shape the rest of the bacteria which are residing within the symptomatic gut.

They can allow for struggling colonies of ‘good’ bacteria to take a more assertive role, they can alter the short chain fatty acid production temporarily which can then alter the balance between aerobic and anaerobic bacteria which will change digestive function.

They can, as I have said, disturb biofilms enough to allow the normal immune processes to work to move dysbiotic or pathogenic flora out of the body. Probiotics can be the means by which the body’s own natural defense/repair/protect mechanisms are brought back online.

So just because they don’t stay inside you, whilst they ARE inside you, their effect can be dramatic and profound.




Dr Michael Ruscio has a very helpful way of breaking the world of probiotics down into manageable and discernible sections. This is useful because if you put ‘probiotic’ into somewhere like Amazon, you get over 2000 results and choosing between them is just difficult. And all of them do different things. Instead of analysing “what’s missing, let’s replace” you can use his broad categories to guess at what effect you want your probiotics to have.

Probiotics can, therefore, be loosely broken down into 4 groups:

Lactic Acid Producers – these you’ll have heard of. They’re the lactobacillus and bifidobacterium that you get in most common probiotics. In fact, you’ll most often get a lactobacillus-bifido blend. These are the types of bacteria we have most studies for and are shown to be of benefit in IBS-type conditions. We know that these types of bacteria do good things for food digestion, intestinal lining health and symptom-reduction in bloating conditions. These are the guys they put in those ‘probiotic yoghurts’ and, whilst some lactobacillus and bifidobacterium used in these products are native to human guts, many of the species included in probiotics (and probiotic yoghurts) are NOT native to the human gut. This doesn’t make them ‘bad’, it just highlights what I said above – probiotics are not always meant to take residence and are often used to shift the patient’s bacterial balance rather than to directly seed their ecosystem.

Non-Lactic Acid Producers – Bacillus, soil-based or spore-forming bacteria are non-lactic acid producing (contrary to the above) and are most often found in (surprise, surprise) soil or water. They are increasingly being seen as potentially beneficial given that within soil ecology certain bacteria are fundamental to keeping the balance of your ecosystem in check. The argument is that these species can perform similar roles in the human digestive system. When used in probiotics these are clinically shown to help with the rebalancing of microbiome populations. They are also interesting because our modern environment is very ‘clean’ – we are not exposed to dirt as much as we once were. In some circles this (known as the Hygiene Hypothesis) is thought to play a role in the rise in illnesses because our immune system isn’t forged in the context of dirt/bacterial exposure. The argument being that immune systems might benefit from such exposures.

Phages – becoming more common, these are actually ANCIENT treatments. We can buy phage-treatments in the UK and if you speak to someone who is a proponent of these then you will be quickly convinced of their utility. Phages are basically viruses which influence native bacterial populations. Studies show compelling evidence for their benefit – but the strains used in studies aren’t the ones that I can obtain for my patients. So… quite simply… I rarely use Phages but am keeping an eye on the emerging research in this area. If you work on the “like speaks to like” adage of manipulating ecosystems, it makes sense that introducing viral components may be a powerful way to alter bacterial and viral load.

Yeast-Based Probiotics – though you may not be able to pronounce it, if you’re at all interested in gut health you will have heard of Saccharomyces Boulardii. This is a yeast NOT native to human gut ecology. It is resistant to being destroyed by stomach acid and bile and so it can help to change gut ecology, breaking down any protective biofilms and actually treating parasites, Inflammatory Bowel conditions, H. Pylori, giardia and even yeasts themselves. It’s like a very tough yeast which clears the way for a healthier gut environment to form. It doesn’t colonise, it doesn’t stay within the gut – however, it has been shown to be an effective antifungal and antimicrobial treatment, demonstrating the intricate interrelationship between yeasts and bacteria. It seems that ‘killing’ (using conventional medicines) isn’t the only strategy to deal with dysbiosis and ‘re-balancing’ using competing species of yeast/bacteria works just as well.

None of the above “bacteria to treat bacteria” methods should be a surprise… This is how nature works, after all.




The reality about working out which is right for you is simple… TRY them. And just choose one from each “class” laid out above. You’ll work out relatively quickly which class suits you and can work from there.

Focus on really good quality probiotics and start slowly – taking just a small amount each time. What you are doing with ANY of the above probiotics is effectively monocropping… you are taking a miniscule fragment of gut ecology, sometimes even something that is not part of normal gut ecology, and attempting to create a more harmonious gut environment. If it doesn’t work, it doesn’t actually mean that there is something wrong with your gut. Just read back over this article – probiotics aren’t always going to work. But if you choose one from each class you will find what benefits your body most.

This is the Dr Ruscio approach.

However, I find that typically my clients either get on with all probiotics – feeling both immediate benefit and no negative side-effects. OR they really struggle with all probiotics, no matter the class. I am definitely in the latter camp. My gut doesn’t love taking probiotics – and I have extensively experimented with all classes.

And this doesn’t bother me at all. This is why the first paragraphs of this article are just as important as the later sections. Probiotics aren’t necessary or mandatory. Gut health can be achieved through many methods, and I have come up with my own version of what I need to do to help my gut – without supplementing.




If you have read through this whole article you will have realised that probiotics are treatment agents and they can’t make up for poor diets or serious immune issues. They work because they shift the existing microbial balance and immune system in a direction that is more beneficial to the host.

And they aren’t the ONLY things that can do this. As I said earlier, everything you ingest interacts with internal bacterial populations. This means that just because my immune and digestive environments don’t gel well with external bacteria, I can manipulate my own internal bacteria in a beneficial direction as follows:


  1. Keep nasty stuff which will negatively affect my microbiome OUT of my life
  2. Bring good stuff which will positively affect my microbiome INTO my life

To keep up with a) entails not ingesting processed foods, too many mouldy foods, toxin-laden foods etc. Maintaining b) involves all of the ‘eat real food’ recommendations and loading up on fibre, fermented foods such as sauerkraut and kimchi when I can manage it… and really focusing on the quality of the fats that I eat so as not to encourage inflammation or intestinal permeability.

This way, all of the fibre feeds all of the bacteria that I know my immune and digestive system get on with. The rest of the dietary measures mean that I’m getting billions of varied additional bacteria from my diet, rather than a pill – and should any bacterial issues occur the microbial milieu already within me are healthy enough to keep this in check. It’s taken me a while to get here – and I’ve got a lot wrong on the way. But I do not stay in this place with the help of probiotics at the moment. That’s not to say they didn’t play a role in getting me here, or that I won’t ever use them in future… but it is possible, probably even desirable to find the best health you can WITHOUT the addition of supplements such as probiotics.

If you would like help to work your way through the world of microbiome support, my first recommendation would be to purchase Dr Ruscio’s Healthy Gut, Healthy You book. My second recommendation would be to NOT assume that just because you have digestive issues, you automatically have series gut dysbiosis issues and start random supplementation.

And finally, if you’re really stuck, I would recommend consulting someone who can run a Functional stool panel BEFORE looking to complete stool mapping for a solution (even Viome). If you do have microbial issues it more than likely requires an holistic approach that isn’t just gut-centric but continues to ask the ‘why’ questions – even if gut bug issues are involved somewhere and require treatment and supplementation. If you would like my help to sort out your gut situation, please do reach out to me here.