What Is Functional Medicine?
Functional Medicine seeks to identify and tackle the root causes of disease. The twentieth century saw incredible advances in the ...
Whether you’re a practitioner or health aficionado, it can be hard to get your head around the taxonomy of bacteria. It can also be difficult to decipher what the figures mean, and what the research actually shows. It can be even more tricky to determine which recommendations are truly right for you (or your client).
Here we discuss both the value and limitations of in-depth and advanced gut health testing, and explain how to maximise their clinical relevance. This article is designed for practitioners and people who have already undertaken a gut health test. If you’d like a general introduction to gut health testing, head over to Gut Health Testing – All Your Questions Answered.
Yes, it’s real. One of the greatest shifts in modern medicine is the realisation that not all bacteria is bad. In fact, some bacteria are vital.
The microbiome has been studied for decades in the context of infectious diseases (a.k.a which nasty bug is infecting this person?). But as part of the metagenomic revolution that has taken place over the last 15 years, interest in the microbiome and its impact on host metabolism has gathered pace.
And this interest is intensifying: more than 13,000 studies on the microbiome have appeared since 2013. That means that of all microbiome studies ever conducted, a massive 80% have taken place in the last six years.1
It’s not surprising that thousands of studies show associations between the gut microbiome and gastrointestinal, immune, neurological and endocrine conditions. There are microbiomes in your mouth, lung, eyes, skin and urogenital tract. But when most people talk about the microbiome, they’re referring to the one in the gut.
To our current knowledge, the gut microbiome is by far the most diverse and complex. Depending on which study you read, there are between 39 and 100 trillion bacteria lurking in your intestines.2 This translates to 1,000 types of bacteria in every gram of stool!
Although we don’t yet know all the mechanisms, we do know these bacteria interact with all human cells. Established functions of gut the microbiome include:
But there’s also a lot we don’t know. When testing the gut microbiome, bear in mind that:
1. Most of the research focuses on bacteria, which means the influence of other microbes—including yeasts, parasites, protozoa, viruses and archaea—is likely underestimated.
2. The link between disease risk and bacteria is largely based on epidemiological and cohort studies. Correlation does not equal causation.
3. Testing is in its infancy, which means there’s a lack of standardisation. We’ll discuss this in more detail below.
The terms ‘microbiome’ and ‘microbiota’ are used interchangeably—especially in the media—but their meanings are subtly different:4
Microbiota is the collection of all microbial taxa in a specific community. This can include bacteria, archaea, fungi and protozoa and more. The community is linked to its environment i.e. ‘gut microbiota’ or ‘oral microbiota’.
Microbiome indicates the genes harboured by all the microbes in a specific environment.
So, microbiota refers to the microbes, while microbiome refers to their genes. To understand this, picture a group of humans. The collection of humans would be the microbiota, while the total DNA of all the humans would be the microbiome.
Because we discover new microbes by looking at their genes, ‘microbiome’ is the buzzword that’s stuck. And what we’ve found so far has been staggering:
Clearly, these microbes matter.
Microbiome testing can be a useful tool to find out if dysbiosis is contributing to digestive symptoms. Common indications for a gut health test include:
But, as you know, gut health and the gut microbiome have a far-reaching impact on the body. This means that a gut health test is a useful part of root-cause analysis for symptoms manifesting outside the digestive system too.
So far, studies have found associations between reduced bacteria diversity and the following conditions:
But that’s not all. Research is also investigating links between gut microbiome disruption and:
The research is far from conclusive, and we don’t know whether an aberrant gut microbiome is contributing to these conditions or the other way around. But at this point, it’s fair to say that gut microbiome investigation is relevant for most chronic conditions.
Says Functional Medicine Practitioner, Alex Manos, “Being able to assess an individual’s microbiome and digestive capacity—and then making personalised recommendations based on these findings—is a great tool for practitioners. It is one of the most powerful interventions we have to help shift someone back to health.”
Science shifts all the time, and it can be hard to keep up with testing methods. Let’s take a brief look at the key microbial assays, and their advantages and disadvantages as of 2020:
This was the foundation of early comprehensive stool analysis tests. It involves placing a stool extract in a petri dish and seeing which bacteria grow.
Advantages: when bacteria grow, you can test to see which antimicrobials they’re most susceptible to—which can be helpful clinically. At Healthpath, our Gut Health Tests don’t culture bacteria: we use the more precise qPCR method, below.9
Disadvantages: you can’t count the number of bacteria, just their coverage of the petri dish (i.e. 2+, 3+ etc.), which is limited information by today’s standards. The main problem with this method is that not all bacteria can grow in oxygen, which means you may get a skewed interpretation of bacterial distribution.
Quantitative PCR is a technique that uses short strands of nucleic acid (‘primers’) to initiate DNA replication. Fluorescent probes then allow real-time quantification of target DNA during amplification.
Advantages: it’s quick and precise, and it immediately quantifies the bacteria. The bacteria also don’t have to be viable to be detected.10
Disadvantages: it’s species-specific, which means you have to know what you’re looking for. It would be prohibitively expensive to use this method to map all bacteria in a person’s stool sample.
16s rRNA sequencing
All bacteria and archaea carry the 16s rRNA gene. This method involves the detection of polymorphisms in the hypervariable regions of this gene, enabling us to determine all bacteria present.
Advantages: like qPCR, this can detect viable and non-viable bacteria. It also allows for species differentiation.
Disadvantages: samples can be vulnerable to contamination if not handled properly. It doesn’t quantify the bacteria (it only gives a percentage) and it’s also not possible to gather antimicrobial-susceptibility data.11 18s rRNA is being used in research settings to analyse fungal DNA—but this hasn’t yet trickled down to commercial tests.
Here at Healthpath, we use a combination of the above methods in our Ultimate Gut Health Test. We also use the gold-standard immunochemical assays and near-infrared spectroscopy to assess inflammation and digestive capacity.
The NHS offers limited gut testing (more on this below) so your best option is to use private microbiome testing. There are two main avenues for doing this :
These require an insured health practitioner to order a test for their patient. Although many labs innovate their products based on new research, there are some that still rely on old-fashioned culturing methods. From a patient point of view, the customer experience can be clunky because they need practitioner input to derive value from the results.
There are now many online providers who will ship a gut health test kit straight to the consumer. The process usually follows this pattern:
1) Order a test kit online, which is delivered to your home.
2) Perform the test according to the instructions, and ship the sample back to the designated address.
3) After a few weeks, receive your results via an online portal, alongside generic diet and lifestyle guidance.
The offerings from these online providers vary in quality and clinical relevance. Some only test for bacteria—and some test for metabolites too—but they rarely assess digestive function alongside bacterial metabolism.
Microbiome testing is a growing market and there are several tests to choose from. So, how do you know what test is right for you? It’s important to remember that not all tests are created equal, as we’ve mentioned above some tests use only basic biomarkers and technologies, leaving a lot of room for error. Below you’ll see how our tests compare to some others on the market:
Comprehensive mapping of a person’s microbiome is not currently available on the NHS.
Approximately 200 qPCR assays are used each week in NHS hospitals to investigate bacterial infections.12 If doctors suspect a particular condition, they can also order specific tests to investigate for blood, parasites and/or their ova. Some hospitals offer hydrogen breath tests too.
But for most patients, that’s the extent of the gut testing available. According to NICE guidelines, even a diagnosis of IBS does not require any form of gut health testing.13
And—as it is not yet accepted in primary care that gut health influences systemic conditions—it’s highly unlikely that a patient would be referred for gut microbiome investigation if they presented with depression, autoimmune disease, hypertension or any other chronic condition.
Not only is there a disparity between testing providers (which is described in more detail in Gut Health Testing – All Your Questions Answered), but there are also challenges with microbiome testing as a whole.
Let’s look at the three main issues:
Some straight-to-consumer tests distil complex research into sound bites, presumably to make it easy to understand. The problem with this is that it results in claims that can be misleading—or even unethical.
Be wary of tests that link the prevalence of certain bacteria to the likelihood of developing a disease. The research does not yet support causative claims.
2) Dubious clinical relevance
We haven’t identified all the bacteria that are present in the gut microbiome. Of those we have, we can’t definitively say whether they have an overall positive or negative effect on the gut microbiome (probably because it depends on the individual).14
Some providers include certain bacteria not because they’re research-backed or clinically relevant, but simply because they can test for it. Once again: data is useless without context.
Many providers also give percentage values for the bacteria found. Again, this isn’t helpful unless you know the total amount of bacteria found in the sample. The Healthpath Ultimate Gut Health Test converts percentage values into colony forming units, to give a more useful picture of microbiome richness and diversity.
3) Lack of standardisation
There is no established protocol for microbiome testing, which means that labs are free to choose their own methods. A lab with high standards will have good internal comparability, but its inter-lab comparability may still be low.
And it’s not just the testing protocols. Once they have the bacterial sequences from a sample, there are three main databases to choose from for aligning those sequences (a.k.a. checking which bacterium has which genetic sequence). One lab can rely on one database, while another lab uses another—and they don’t all include the same bacteria.
What this means is that the same stool sample could garner two different data sets from two different labs. This is a valid concern. Until standardisation is established, it’s best to choose a lab that is continually striving to maximise its own rate of comparability.
Here at Healthpath, we’re mindful of the above challenges. We also strive to offer the most reliable and useful gut health test on the UK market. We make sure that:
Here is a breakdown of our biomarkers:
In our reports, each out-of-range marker is highlighted with a concise summary of the research. This gives you an accurate, non-sensationalised view of the current state of knowledge—and encourages you (or your client) to think about how these findings might apply to your own symptoms and lifestyle.
Both tests use the same testing methods, and offer the same level of detail on reports. But the Advanced Gut Health includes even more bacteria and biomarkers, such as:
We also offer an Ultimate Gut Health Test, which includes everything in the Advanced Gut Health Test, plus a comprehensive range of helminths (worms).
uBiome was another company that offered gut health tests for order online. They were based in the US but shipped internationally.
At the time of writing (December 2019), the company has ceased to trade. It filed for bankruptcy following an investigation for its billing practices.
As mentioned, there is still so much we don’t know about the microbiome—and that’s exciting. Research is focusing on the following questions, with hopes we’ll have answers soon:
What constitutes a ‘normal’ microbiome?
The Human Microbiome Project, which ran from 2007 until 2016, made headway with this—but we still don’t know what a normal microbiome looks like in the gut, in the genitourinary tract, in the mouth and on the skin. Based on what we’ve discovered so far, it’s likely that the standard of ‘normal’ will vary by age, geographical location, ethnicity and even time of day.15
As part of this, we need to explore not only bacteria but also the virome, the phageome and the mycobiome. We also need to investigate the metabolome to uncover how these microbes (and their byproducts) affect physiological function.
How can we personalise our diet for our microbiome?
Some characteristics of your microbiome are fixed, but you can shift others through long-term change in diet. Huge-scale studies, conducted by The American Gut Project in the US and by Tim Spector/PREDICT in the UK, are monitoring ordinary people and their food intake to decipher patterns.
Other lifestyle factors, such as stress, sleep and exercise, play a role too—but we still need to quantify just how much of a role that is. Imagine a world in which you know how much sleep your microbes prefer!
How does the microbiome affect disease risk?
We know about casual associations between the gut microbiome and obesity, diabetes, IBD etc., but we need to find out more about the exact nature of these associations—which is driving the other?
Once we have a handle on this, we can create novel therapeutics that minimise disease risk or pathology through working with the gut microbiome.16
Immunologist Dr Jenna Macciochi suggests this will fundamentally change the practice of medicine. Says Dr Macciochi, “We now have some appreciation of the profound impact of the microbiome on our health, both in understanding and treating disease. This will change the face of clinical practice. In the future, it will be routine for practitioners and doctors to keep an eye on the make-up of patients’ microbiomes. Personally, I think microbiota-derived treatments are the future of precision medicine.”
The human microbiome is an enormous area of study that has gathered pace in the last 15 years. It has redefined our notion of ‘good bacteria’ and ‘bad bacteria’ and opened our eyes to the possibility that microbial balance is essential for good health.
Although we can’t yet describe the mechanisms behind this, we know that a disrupted gut microbiome is associated with several disease states. This makes gut health testing a valuable tool for investigating both digestive and systemic conditions.
But there’s still a lot we don’t know. We can recommend eating patterns and behaviours to influence the gut microbiome, but we can’t yet give someone a definitive list of their ‘best’ foods based on their bacterial data. That will come in time. For now, practitioners and consumers should be mindful of this—and seek testing companies that are upfront about the limitations and committed to learning more.
The compelling part is that we do learn more with every gut health test. The deeper our understanding of our microbes, the more we can work with them to optimise our diets and transform our health. Together, we’re at the beginning of a health revolution.
Fiona Lawson BA (Hons) DipCNM mBANT is a Registered Nutritional Therapist and health writer. She is a member of the Complementary and Natural Healthcare Council (CNHC) and the Institute for Functional Medicine (IFM). As Content Director of Healthpath, Fiona is on a mission to help people take charge of their own health. Read more about Fiona on her practitioner page.
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