About the author : victoriafenton

I spend a lot of my life talking about people’s bowel movements and digestive distress.  It’s an occupational hazard, I guess.  I order many, many stool tests – everything from 3 day comprehensive gut analyses to complex DNA-PCR GI-MAP tests (you can read about those here) and also the expensive and very detailed Genova GI Effects.

Several times this week, other professionals’ opinions of various test preferences came across my desk. First, a patient asked me what I thought of a 2014 podcast in which Chris Kresser and Steve Wright chatted about what they deemed ‘essential’ tests. Second, a colleague asked me what I thought of a recent Functional Review article (a newsletter for clinicians and practitioners) by Dr Michael Ruscio about the ‘best’ stool tests and the ones that he routinely orders.

After being asked both of these questions I took a very deep breath before answering, because the reality is that evaluating testing – particularly stool testing – isn’t a simple, off-the-cuff choice. And it is one that I have spent many hours contemplating. It is also a decision I evaluate fresh with each client, depending on the case.

As a clinician there are many factors which influence my decision on the tests to order for my clients (stool and otherwise). I assess everything from validity of the testing to evidence-base for the results, test reliability to clinical utility, test cost to turnaround time. I have labs I trust and I’m picky about which tests I order from each one. The serious evaluation process that I went through to decide on my ‘favourite’ tests was lengthy.

The US podcasts and articles mentioned above covered and recommended a lot of the tests that I order. However, they are of limited use to the UK audience as some of the tests mentioned are not available here.

And yet, these offerings actually do what every popular media release does – spark a host of questions and often confusion for clients.

Sometimes I see a flurry of demand for a specific test that we cannot order in the UK and I know there’ll have been a recent influencer talking about it. At other times existing clients will email me demanding to know why I haven’t run certain tests when a certain practitioner insists they’re ‘mandatory’. But this ‘test happy’ only perpetuates the impression that Functional Medicine can be very costly.

In truth, it can – I could order thousands of pounds worth of tests for my clients … and, as I am always saying, a lot of the testing will find something. On top of bankrupting people, these tests can provide the clinician and patient with an enormous amount of data

And yet, little of this data actually provides useful information.


Patient vs. Clinician Diagnostics


The beauty and the curse of all this data acquisition and testing availability is that a patient, empowered with their own results, can find every answer possible on the internet for what to do to treat what they find on their test. Googling each marker will lead them down pathways of conclusions, sometimes filling people with fear and paranoia that they’re doomed, often causing them to purchase (expensive) supplements with the promise that ‘correcting’ the markers deemed ‘out of balance’ they will resolve whatever their health crisis may be.

What’s missing with the overload of test results and the plethora of markers on each test result is true understanding – and viewing the results within the right context. Never is this more true than in the realm of stool testing – where selecting the right test to begin with is a nightmare and the litany of markers that come on the results are almost impossible to understand for someone unfamiliar with what the stool testing is trying to show.

It is this last part that is key – and what I want to cover in the rest of today’s article. As a clinician, I need to know ALL of this stuff… the long words, the weird bacteria and what they’re clinically linked to, the interplay between certain blood markers, the suggestive results on certain tests and what they allude to, even if they don’t ‘prove’ it conclusively.

But I also need to know what the testing cannot show, what it does not mean and the conclusions that we cannot draw from the data these tests provide. This is what I mean by understanding what stool testing is trying to show.

Stool testing is not a sequencing of your entire microbiome – it is a map of the things we know to be good/bad/pathogenic/parasitic. It is also not an ironclad, confirmed test with no margin of error – and each different ‘method’ of analysis has its own flaws and drawbacks. There are false negatives and false positives (more rare), there are definitely markers that are more useful than others – and when it comes to the world of the microbiome there really is so much that we don’t yet know.

You could be forgiven for thinking, after a cursory google of the markers in your own stool test that you know exactly what to do to rectify things (usually something like take a probiotic or go on a high-dose antimicrobial). But when it comes to stool testing, simple “find this – do that” recommendations are not that linear and straight forward. This is because every patient has a different microbiome – because every patient needs a different microbiome.


Microbiome Myths


My basic belief when it comes to the microbiome is that we don’t categorically know for sure precisely what ‘healthy’ means. We have general ideas, yes. But most studies conducted on the microbiome with respect to symptom and disease manifestation are retrospective in nature. By this I mean that we have a patient with a known health condition (let’s say Irritable Bowel Syndrome, or IBS) and we check their microbiome. Comparing this sample to that of a ‘healthy control’ (i.e. someone who reports no gastrointestinal symptoms) we note the differences between the two ecosystems – and estimate what in the microbiome of the unhealthy patient may be responsible for symptoms.

These studies in IBS have been done – and they show a pronounced difference between the two patients’ microbiome. In people with IBS the diversity of microbial populations is lower, and research studies show decreased levels of Lactobacilli and Bifidobacteria in the IBS sufferers, coupled with increases in pathogenic anaerobic organisms such as E. coli and Clostridia. Additionally, the one ratio you will hear discussed often when it comes to microbiome analysis is the Firmicutes-to-Bacteroidetes ratio. In IBS patients this ratio appears to be increased (in favour of Firmicutes). This has come to be associated with poorer health outcomes.


The general ‘rules’ of  optimal microbiome, therefore, seem to be balance and diversity.


So if balance and diversity are the aims, you would be forgiven for thinking that tweaking the microbial balance using a high potency probiotic with high levels of the missing bacteria (lactobacillus and bifidobacteria) and killing any pathogens with some powerful antimicrobial drugs or herbs would rebalance and diversify, thereby equalling a ‘cure’.

As a practitioner, however, I’m always, always asking “why”? Why did this person’s microbiome shift in the unbalanced, lower diversity direction? Because to my mind there really must be a reason – and a large part of my practice is all about helping my clients to understand the why behind their illnesses. Sometimes it’s chance, bad luck, genetics and/or quirks of fate. Often it’s all of those things combined with a host of other factors which come under the umbrella ‘stressors’. Usually there’s dietary issues, often ‘adverse childhood experiences’, occasionally poor lifestyle habits such as late nights and overexercise. But one thing appears to be true, over and over again.


If we wade in with ‘treatment’ to put the microbiome where we think it should be, without addressing the reasons behind how it got to being problematic in the first place, any success in relieving symptoms will be temporary and the patient will regress.


There are studies where transplants of microbiome samples from one person into another do result in changes in illness presentation. But as far as I’m aware these studies haven’t been followed up years and decades later. I would be very intrigued to examine the way the transplanted microbiome shifted once in the body of the new host. As microbiome populations are symbiotic with their host, will the new host, and their lifestyle and behaviour habits, eventually shift the microbiome back to something resembling the original, symptom-causing microbiome?


When Functional Becomes Conventional


Any patient with gastrointestinal symptoms and ‘dysbiotic’ stool test results are never ‘ill’ due to a lack of probiotic supplementation. If we resort to shovelling in probiotics and antimicrobials as the ‘solution’ for every gut dilemma this renders the Functional Medicine world no different to that of conventional medicine – a pill for an ill. This is not how Functional Medicine was designed to interpret patient symptoms and data. This is why the test proliferation can sometimes do patients and practitioners a disservice.


You end up chasing test markers and treating every anomaly, rather than analysing the patient as a whole and really understanding the origin of any health condition. And sometimes, the ‘anomalies’ are actually evidence of the body’s own intelligence rather than signals of a specific problem in that area.


Taking, for example, the microbiome of autoimmunity patients and those with Intestinal Permeability. Some theories suggest that the host’s (i.e. the patient’s) own immune system has elected to ‘prune’ their microbial diversity in an attempt to minimise the bacteria to which the body is being exposed (via transfer across the gut wall). Whilst this is speculation, clinically discussed rather than scientifically verified, it is very interesting to contemplate whether the lowered diversity of microbiome is a defence mechanism instead of an illness. In this situation, wading in with high dose probiotics could be precisely the wrong thing to do.

What we do know for sure is that many inputs affect the bacterial population in the gut – everything from a missed nights’ sleep to emotional stress, eating a rich, fatty meal to having a sugar binge. Stress and anxiety can affect the gut – and it is highly probable that this, in part, occurs through a mechanism which in some way alters the microbiome.

We are learning more each day about what truly affects the gastrointestinal system and the bacteria within it. And it’s not straightforward. If we just supplement with pills in an attempt to return the microbiome to what we think might be ‘normal’ we end up no better than conventional medicine’s efforts of treating symptoms. Because the microbial shifts are, in effect, just another symptom.

And yes, Functional Medicine stresses that the gut is at the heart of many modern, chronic illnesses – and it is. But to my mind simply analysing the gut through fancy testing might not be enough to really identify a ‘root cause’ because we are instead just mapping the symptoms.


Paperwork Prescriptions


What lies at the heart of microbiome alterations is that, though we can do scientific research and microbial analysis to a high standard , we really don’t yet understand the bio-individuality of the ‘perfect’ microbiome for each individual patient. We don’t know how to know what this is – and we wouldn’t have reliable and consistent methods of creating it even if we did.

I have asymptomatic patients with what looks to be appalling stool test results and, conversely, Small Intestinal Bacteria Overgrowth (SIBO) sufferers who are desperately symptomatic and yet their gas levels (how we measure the bacteria in the small intestine) are really low. I also have patients who achieve complete remission of SIBO symptoms – and yet their test results still show the presence of gases that are deemed diagnostic for a ‘problem’.

If we treat paperwork and markers on tests, we are treating our patients based on what we believe to be ‘optimal’. And yet there really is no such thing – especially when it comes to microbiome manipulations. We do not know why each patient has ‘pruned’ their own microbiome (if that’s what’s happened). We do not know what levels of bacteria are ‘normal’ in each person.

Moreover, the modern stool tests contain many, many markers. Most Functional Medicine practitioners have ‘favourite’ tests, but from my discussions with colleagues I would go out on a limb and say that most of us think that almost all Functional stool tests contain at least some unusable or irrelevant markers or data points. The more expensive the test, the more markers given – and yet sometimes more is not better.

Getting hung up on the quantity of each individual strain of bacteria in a stool sample is a surefire way to waste both time and money with Functional Medicine. Whilst understanding the situation in the gut is necessary, clinically these results are a backdrop which must be analysed in conjunction with many other things (other tests, client history, symptom reporting, awareness of mitigating circumstances or other factors which may influence health).


Finding  the Root Cause… And How “Root Cause” Can Be Misleading


Stool tests attempt to diagnose what is happening in the colon – but they are not at all useful for understanding why. Whilst treating the ‘what’ is regularly necessary – it is understanding the ‘why’ that can truly transform the health of the patient.


Functional tests are alluring to patients (with some practitioners building whole careers on making money out of marketing Functional tests to the public) because when we’re desperate for answers to explain the way we feel, utilising Functional Medicine tests can actually provide them.

Abnormal markers vindicate our sense that we are unwell and gives us what we believe are solutions – which we follow in an attempt to heal.


Diagnostic testing does what the name suggests – provides diagnoses. Once labelled with diagnoses we feel empowered to treat. Finding evidence of something awry suggests potential treatments.

But as practitioners we MUST look to the reason why our stock interventions of dietary tweaking, antimicrobials, antifungals, probiotics etc. were necessary in the first place. This is why the crux of the Functional Medicine approach is the oft-repeated-mantra of ‘root cause resolution’. We aim not just to treat the symptom (gut dysbiosis is still just a symptom), but also address what contributed to its development.

And yet the phrase ‘root cause’ suggests that there is one single element – one thing to ‘blame’ for the current predicament. This is corroborated by the testing mentality. If we find an abnormal marker we can ‘blame’ the bacteria and attack it with some treatment, without ever really asking the question of why it’s out of kilter in there first place. This fuels the mentality of ‘a pill for an ill’.


In practice, however, there is rarely one solution – it is often, if not always, multifactorial. Root cause is typically ‘Root Causes’ – plural.


Solutions – regardless of the test results – commonly require many interventions and changing many things. This is why Functional approaches are difficult to prove in scientific literature: because science is built to analyse the merits of chaining isolated variables and interventions. A true Functional model approaches health from all angles – so when it comes to treating the markers on a stool test I can find myself having conversations with patients about diet, supplements, antimicrobials… and also exercise, meditation and mindfulness – and then childhood traumas, where they hold tension in their body, how they feel about their body and food, how much they trust themselves, how they feel about money, prospects, their self-esteem.

I can’t test any of these things on a Functional diagnostic test – and yet each element will affect gastrointestinal motility and the bugs that live inside us. In practice what’s in our gut is heavily (if not entirely) influenced by what we put into our bodies – and that doesn’t just mean food, probiotics or L-glutamine. It includes the tensions, stresses, fears, hopes and emotions that we carry and it includes the way we feel inside ourselves.

So yes – I regularly run stool testing. Yes, I am treating clients’ intestinal conditions almost every day. But I’m not doing this by tweaking the microbiome based on arbitrary numbers on my clients’ paperwork. I am doing this holistically, truly comprehending the wealth of inputs that can influence the GI tract, the microbiome – and our overall digestive wellbeing and health. There isn’t just one root cause, often there are many. I would say that the resolution of gut dysbiosis is NOT probiotics and antimicrobials alone, simply targeting specific test markers. Instead, it’s the approach which puts testing into context, appreciates the entire scope of the patients wellbeing and designs a bespoke and nuanced treatment protocol from there, covering all elements of healthcare (not just the bugs in the gut that the stool test said were “bad”).

If you have some test results that you’ve tried to understand – maybe even treat – and you’re still no better, do get in touch with me as I’d be delighted to help you – not just to treat your symptoms but also to establish your ‘why’ and work on your unique ‘root cause(s!) resolution’.

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