How To Repair Your Gut Microbiome

Is It Really "Broken"

The first step in understanding how to 'fix' your gut microbiome is to understand whether it is truly 'broken' - and also to grasp that the microbiome will change literally with every meal that you eat and every missed night's sleep you experience - and so much else besides. It's really important to understand that the microbiome is alive - the bacteria inside you are a living entity. As such they are subject to change in different environmental circumstances and different situations. Everything that affects you, as a human being, will affect the bacteria that live within you.

And whilst studying and manipulating microbiome may be all the rage, the reality is that, as I have written before, we don't know what is an optimal microbiome. The likelihood is that each person's 'optimal' will be different from the next person's. More than that, over the course of a lifetime the microbiome that is living inside (and on) you will change and shift according to what is appropriate for you at that time.

This is because our gut bacteria are a symbiotic population - i.e they live in synergy with their host (us). The relationship is supposed to work both ways and we help each other out. They're not there by accident - they work for us and with us, and in return we are their home. 

Recognising the true nature of how this relationship is supposed to work, we can perhaps understand how best to answer the question of whether your microbiome is really 'broken'.

The most common term used for a 'broken' gut biome is 'dysbiotic'. This gives a good indication of what has happened. It is a state in which the biome living inside your gut has become somewhat disrupted and is no longer helping you out like it once did, or like it should. Symptoms of gastrointestinal (and systemic) distress are the result - but these are symptoms meaning that they are a consequence of something off-kilter. That something is typically the balance of (or the nature of) the bacteria.

Knowing whether your gut biome is 'broken', however requires far more than observing a few gastrointestinal symptoms. Most of the time, for healthy people, the gut bacteria will go through moments of being slightly in uproar, or giving slight symptoms of gas, distention, bloating, discomfort. "Normal" gut function is not always going to be entirely asymptomatic, and sometimes, typically depending on food and drink consumed, there will be hiccups in the gastrointestinal flow. I see this regularly in my practice - particularly for those who are actually getting 'over' or 'beyond' a real gut issue (like SIBO, for example). It's easy to believe a perfectly benign normal reaction is a pathology indicating 'illness'. However, if the odd hiccup occurs, especially after a perfectly obvious cause such as a lot of beans, a curry, a lot of alcohol, too much stress etc, this is just called normal. After these 'insults' or the ingestion of a lot of fermented stuff it is perfectly natural that your gut bugs are going to a) give off a bit more 'stuff' than usual and b) require a little time to re-settle.

It is when the symptoms of bloating, distention, pain, griping, swelling, indigestion or bowel irregularity become more permanent, lasting or continuing for a lengthy period of time, that the likelihood that there is something actually 'wrong' increases. It is at this point where you might benefit from further investigation. However, it must be remembered that in most cases there is nothing actually 'wrong', just something that's gone a little out of balance.

Working Out Where Your Microbiome Has Gone Awry

Testing for gut health is one of the more controversial areas of Functional Medicine. Even within our own discipline we have internal wrangling and clinical debates, all professionals do not agree and different labs offer different tests - each claiming relevance, accuracy and clinical utility. I have written about this before, so I won't go over old ground, but the microbiome can be sequenced using full, complicated 'gut analysis' testing (though you end up with fairly unusable data) or it can be tested using Functional Medicine diagnostics which are looking for and at very specific things.

The latter is typically referred to as a comprehensive stool analysis - and depending upon which test is used, this provides a relatively good idea of the presence of certain strains of bacteria within the gut. It's not full sequencing by any means, but it's clinically relevant sequencing - i.e. we examine what we know to be good, we check for what we know to be bad, and we assess the digestion and relative functioning of everything else.

You do have to pay a lot for the extremely comprehensive testing which analyses the bacteria in a much more specific way, but more markers is not always better. And yet, some of the more 'economical' tests have been criticised for quality, accuracy and for their reliability/repeatability. False positives are perhaps not too dangerous, but false negatives can risk having patients suffering for months, if not years, believing that their digestive system has been tested and they're "fine", so there must be something else wrong with them. So testing seems appropriate, and even necessary in order to establish treatment.

However, after many reviews of the literature, the white papers released from the labs themselves, discussing and listening to the opinions of other practitioners and professionals, I have come to realise that whilst these more complex gut panels *sound* fancy, the minute analysis of each strain of bacteria in your gut has little clinical relevance. Nor does it highlight the genesis of any dysbiosis. Basically, these gut-centric snapshots are useful to eliminate pathogens and identify digestive functions - but they are not to be used as treatment plans, supplementing with the strains of bacteria that are deemed 'missing' or 'low'. Contrary to some practitioners' recommendations, specific probiotic supplementation based on the results of a complex microbiome evaluation is NOT where the evidence lies when it comes to the benefits of probiotics on health outcomes.

We do believe that we know there needs to be a certain level of diversity and quantity of bacteria in the gut in order to classify it as 'healthy'. We also know that probiotic supplementation (note: multi-strain, broad-spectrum probiotics, not single-strain, targeted probiotic therapy) has shown positive effects in trials and clinical studies.

And yet, I have seen clients who thrive even though they have a lower quantity, lower diversity microbiome. I have also seen probiotics do nothing and even aggravate patients' symptoms, regardless of the classification of probiotic used.

I have hypothesised with colleagues that the symbiosis between the host's immune system and their microbiome may be in play when there is a seeming lack of microbial diversity in the gut. Perhaps the immune system is hyper-reactive and so is keeping the microbial population low in order to avoid being triggered. It could also be that the immune system has very specifically developed antibodies to a certain bacterial strain or subtype. Supplementing with the 'missing' bacteria using a probiotic would, in this case, create a flare in immune symptoms instead of 'benefiting' the gut, as would have been the intention.

It's just complicated - and this is one of those instances where I see that the testing (now accessible by patients without practitioner approval, recommendation or review) can really lead patients in the wrong direction. These tests come into their own in the identification of true pathogens, and also in identifying digestive function as they can identify remnants of undigested (or improperly digested) carbohydrates and fats in the stool, along with giving an idea of the level of digestive enzymes.

Probiotics - Wonder Supplement or Sham Science?

The whole probiotic industry was founded on the understanding that intestinal bacteria matter... But it was also founded on the fairly common yet completely inaccurate concept that "More is Better", so we'll just add some more in. Very little attention is given to whether this method actually works, and even less effort has been put in to identifying whether 'working' means that the bacteria colonises, or whether 'working' means that the patient taking the probiotic actually gets any better... because even if (and it's a big if) the former occurs, there is precious little evidence that the latter actually occurs.

The thing is that there is no clinical evidence to suggest that lack of a specific strain of bacteria, as demonstrated on tests, is creating the symptoms that a patient presents with. Therefore, there is similarly no evidence that supplementing to boost that specific strain will have any effect whatsoever.

Now, that's not to say that probiotics do not help. There is a wealth of evidence to suggest that in many patient populations (elderly, children with autism or behavioural difficulties, those with IBS), supplementing with probiotics can prove beneficial overall. But as studies like this suggest - the most clinical relevance can be with so-called 'multi-strain' probiotics. i.e. we're not trying to replace what we think is missing, we're just boosting microbial diversity and populations overall.

Moreover - the benefit of probiotics is during the time when they are being taken. There is relatively little evidence to show us how impactful the probiotics are longterm. In fact the bulk of evidence suggest that much like prescription drugs - stop taking the probiotics and the gut does not 'retain' the strains or diversity.

All of these probiotic effects are reflected by all the instructions given to anyone taking a comprehensive stool test, as mentioned above. Our instructions guide patients to stop taking probiotics for 14 days prior. Basically because we want to see the patients' "natural", not the probiotics. This implies that after 14 days all probiotics have gone... which is slightly useless, surely?

Beyond the Limitation of Probiotics - How Can You Help Yourself?

Probiotics are a minefield. There are live versions, dried versions, freeze-dried, soil-based, spore-forming, even phages. There are many ways to put probiotics into your system, even probiotic enemas. And the tablets you may have heard of are Prescript Assist, MegaSpore Biotic perhaps, Restore for Life (not actually a probiotic, but often marekted as one), Symprove comes highly regarded by some, with D-Lactate Free Probiotics being an expensive version often recommended, and Saccharomyces Boulardii is very popular, again despite it not strictly being a probiotic (it's a yeast).

The reason for this variety is that there isn't one universally well-regarded and 'optimal' way to take probiotics. Moreover, the probiotic 'industry' is completely unregulated. Originally, the way probiotics were certified as effective was to firstly test the capsule to see whether it actually contained the strains that were reported on the bottle (more failed this test than you'd imagine!) and then to test whether some of that strain 'came out' the other end (I'm not joking). As you can tell, this tells us nothing of whether the strains took up residence in the gut, and if so, for how long. It tells us nothing of the actual impact of the probiotic at all. It just tells us that probiotics did pass through the digestive tract - which is actually better than some old versions of probiotics which were mostly broken down in the stomach by the acidic environments.

But there is clearly merit to probiotic supplementation - and little harm, providing you find a version that suits you. In truth, however, there is no way to predict which strain or type of probiotic will suit you beforehand - you simply have to try them. You can try Spore Forming Probiotics, Saccharomyces Boulardii based Probiotics, Soil Based Organisms and blend which are more general. Each has a slightly different effect and so is likely to either be well or poorly tolerated, depending on your current microbiome health.

However, in my clinical opinion it is not enough to just think that for every gut issue throwing probiotics into you is the solution, particularly as the ability for these probiotics to 'take hold' is doubtful and impossible to verify without repeated testing (a costly and unnecessary process).

So instead, I revert back to the fact that a lower diversity microbiome is a response to something. If it occurs as a result of the immune system overreacting and pruning the bacterial population then adding in probiotics is not a solution, we must focus on the immune healing. And if the lower diversity has occurred due to a lack of prebiotic fibre to support a healthy gut population then realistically probiotics won't help either. This is supposed to be a symbiotic relationship. In order to get the benefit from the bugs, they must receive benefit from you... and that means feeding them!

Prebiotics: Food to Feed our Bacteria, Not Just Ourselves - For Some People

I started this article by explaining that the gut bacteria were a living collective of organisms. As such, they respond well to the typical things that feed organisms: the right light, the right air and the right food. Now the first two are guaranteed - the darkened internal environment and the presence of/lack of air in the right places means that the bacteria which thrive in these environments (whether aerobic or anaerobic) are content... but what we don't always provide enough of, or the right type of, is FOOD. Not just calories food, but FIBRE food.

This means vegetables rich in prebiotic fibres such as cruciferous veggies, Jerusalem artichokes, alliums (onions/garlic), fermented vegetables (which come part-digested and with a host of bacteria living in them as well as being made up of prebiotic fibres) and the single food known to feed the microbiome more than anything: leeks. Diets rich in these foods are perfect to fuel the large intestinal population of bacteria, meaning that the population that are there thrive and any probiotics that you add might also be lent a better chance to populate. Fibre and resistant starch (think cooked and cooled potatoes) have to be part of the diet if you want to nurture your microbiome.

But there's a problem. The problem is that approximately 75% of my clients would really struggle on this recommendation. They are the kinds of people with IBS and/or SIBO, where a so-called Low-FODMAP diet is recommended - quite literally the polar opposite of the fibre-rich, gut-friendly diet stated above. Or they are the patients with histamine intolerance and for whom eating fermented foods would give them huge reactions. What to do in this situation?

These are the clients whose microbiome has become problematic and/or whose digestive systems are struggling. The route to therapy in these situations seems NOT to be bacterial...

This would strongly suggest to me that whilst gut bugs are important, and the microbiome is indicated in many health issues, therapeutically speaking gut health is about far more than gut bugs. In fact, the changes in intestinal bacterial populations may be a consequence of upstream dysregulation, the symptoms that result merely a reflection of some larger issue, rather than simply down to microbiome irregularities. If this is true, which it certainly appears to be, then microbiome and probiotic treatments aren't the solution - they're another sticking plaster over deeper issues.

More Than Bugs

This last part is interesting, though it is much conjecture on my part. And yet more and more I'm confronted with clients who bring up memories of my own situation - a situation that could arguably have been pegged as one of gut dysbiosis, parasites, SIBO etc., but a situation that did not resolve because I tinkered with my microbiome, either to treat the bugs, to lower bacteria using a Low-FODMAP diet or to increase bacteria using probiotics.

It is clear to me that whilst the current zeitgeist is to focus on the impact that gut health has on the rest of our body, we regularly forget the impact that the rest of our body has on our gut. My first personal breakthrough, digestively, was a decade or more into my journey and revolved around structural and fascia issues. So distracted by the fact that my symptoms emanated from my gut, it seemed implausible if not impossible that my actual 'issue' might arise out of back injuries, my tension-filled body, historic head injuries, my jaw and neck alignment, and/or all of the above.

It is even more far-fetched to suggest that latent emotional tensions and traumas are being stored within the biochemically and neurologically-dense fascia, or within the connective tissue (which is already a hot-bed of complications for me). And, being a lapsed musician, I hadn't realised that I'd also forgotten how to breathe during the years of being 'ill', and it's only when you start to release the tensions around the diaphragm to enable yourself to breathe properly that you realise how interconnected the peristalsis of the gut and the comfort of the abdominal environment is to everything else that sits inside your abdomen - spine, nerves, female organs, liver, kidneys and all the nerves and fascia which interweave all of these organs and systems.

I am open to being proven wrong, but when I come across a gut bacterial situation that won't resolve itself by the usual methods (dietary tweaking, potentially a course of treatment for parasites or pathogenic bugs, maybe even trialling a course of SIBO treatment) then sometimes I return to the drawing board and realise that the bacterial dysbiosis we experience is a consequence of something else, not a root cause. If a low-FODMAP or low-histamine diet can help in the short-term, great. But I still care about the deeper 'why' behind the issues with fibre and histamine.

Whilst dysbiosis can always, theoretically, occur after infections, extensive antibiotic courses, travellers' diarrhoea, food poisoning, drinking contaminated water in an exotic location etc., dysbiosis can also be the necessary response to a gut being held in tension and not being allowed to function effectively. There are more reasons than we acknowledge for the gastrointestinal tract being affected - and with my Functional Medicine and Nutrition hat on it's convenient to make this all about food, nutrients and adrenal function or cortisol affecting the digestive motility and availability of stomach acid and digestive enzymes.

With my counselling, psychology and emotional therapy hat on, and my patient-experience in mind, however, it is clear to me that the gut is not just the nexus of the human body, it is also the mirror. It can show us where we are tense and hurting, it can show us when we have locked down and closed ourself off for protection.

In these instances it's not about food. It's also not about anti-microbial therapies or treatments to alter motility or microbial balance. Instead, it is about finding a way to work through the trauma, the experience, the memories (physical, not just mental) that have caused the body to lock down and for the motility and gastrointestinal milieu to be disrupted. This is where I refer out - to osteopaths and bodyworkers who can resolve the trauma locked in fascia and soft tissue. It's when I dig down and ask my clients about what their illness is protecting them from and what traumas they are holding onto.

And this bit - the bit where taking a probiotic pill doesn't work - is the really challenging part of how to 'fix a broken microbiome'. This is the part that hurts. It's the part where you have to challenge the way your body has locked down in response to your past experience. More importantly, putting the effort in to do this bit is the bit that actually makes the difference.

So if you want to Repair Your Gut Microbiome and all of the usual suspects haven't helped, this might be the piece that you're missing - and I would encourage you to contemplate the interconnectedness of your abdominal and spinal core and where you might be holding pain (physical and mental) throughout your body.

Then I'd encourage you to work through it - alone, with a bodywork expert or with someone like me whose expertise lies in understanding how physiology responds and contracts due to our life experiences and can help you comprehend all of the biochemical, systemic ripple effect throughout the body that happens as a response: from immune health to hormones, gut health to mental health and beyond. By focusing on core issues, rather than the gut dysbiosis that occurs as a result, someone like me can help you unlock the fears and patterns you have established in response to your history and, sometimes with the help of hands-on work, help you move through this.

Sure, the bacterial stuff is important and the food helps - but the biggest marker of how healthy your body will be is how you are living inside it. If you are resisting and holding onto tension then the best diet and the best probiotic in the world will make no difference. And, though it's often the harder way, if you have a gut situation that you just can't seem to fix, sometimes this is the only reliable way to truly heal.