The Trouble with Microbiome Tests

First came DNA, then came the bodies of bacteria. Beyond the ancestry and genetic de-coding that favoured early genetic tests, this new wave of microbial mapping seems even more scientifically elusive. With countless companies offering their versions, one has to wonder: should we trust the hype?

It all started in 2012. uBiome, founded by Jessica Richman, Zachary Apte and Will Ludington, decided to pioneer citizen science in their company, focusing on swabbing various human regions for the chance to see what’s on there. At the same time, the non-profit American Gut Project created a valuable platform for continual data-collection, something to serve the necessary research needed for the field to thrive. Today, there are more and more companies offering microbiome testing, in one form or another – and the count continues.

Now, you may be wondering, you started GUTXY, a company offering microbiome testing, aren’t you biased? In actuality, being in this field, I believe, makes me even more open-minded – and skeptical – about it. Having the knowledge to notice the nuances of what’s actually going and what needs to happen for it to work, makes me even more of a reliable source of commentary (and critique.)

And yes, it’s true, there is a lot more that needs to be done, to get microbiome testing to where we want to be: here’s where the trouble lies.

Your health is your history

Many who come to microbiome testing either have a specific fascination with their fitness and optimizing their health, down to the most minor details; others, on the hand, arrive to the sampling tube following years of personal struggles. More often than not, it’s digestive distress: countless episodes of bloating, constipation and diarrhea that create a psychological burden and emotional toll. What we’ve learnt through microbiome research has affirmed what we’ve always wondered: your health is the accumulation of your lineage, daily habits and environment – all things you. The genetic component has often been overly emphasised, whilst recent trends have highlighted the importance of our diet and lifestyle in creating the level of wellness we desire. Knowing everything that adds up, it can seem rather far-fetched to expect a single test to summarise this, right?

Knowing everything that adds up, it can seem rather far-fetched to expect a single test to summarise this, right?

Your body is a jungle

Understanding the microbiome has allowed us to peer into this vast microbial world inside us all, seeing for the first time how vital they are. They sculpt our organs, break down our food, help us defend infections and even guide our behaviour. Non-human, microbial cells outnumber our human ones 3:1. So far, we have named only a fraction of these microbes, and even substantially less have noted functional information. We know they’re there, but we don’t know why or what purpose they’re actually serving. This – naturally – leads to confusion.

Non-human, microbial cells outnumber our human ones 3:1.

Once you have a microbiome test, you receive a list of the microbes present, as well as the relative abundance (percentages) of them. Next step, is figuring out whether your result is actually good? What could make it better? If most of the microbes are currently unknown, how can we decide?

Well, we can only account for what’s there. Certain microbes are well-documented: take Lactobacillus and Bifidobacteria, they have been researched to exhaustion (given how easy they are to cash in on as commercial probiotics.) So, the focus must turn to those we currently have a clasp on; even though, in the massive scheme of our microbiome, it’s only a small selection, they do still play a tremendous role, and are worth knowing. With a single microbiome test you can find out your levels of beneficial bacteria such as Akkermansia muciniphila, Fecalibacterium praustnii and Roseburia – all linked with good gut health. There’s no other way to know how you fare, unless you sequence your microbiome. It really is that simple: if you believe your gut microbes matter for your health, and want to know how healthy your gut really is, you need to test it.

Your microbiome is a maze

It’s difficult to capture all that encapsulates your inner essence: it’s not something to summarise. Looking for simplified certainty? Then microbiome testing is not for you. Testing opens up a vault of knowledge. Knowledge that, at this point in time, may be more like a secret puzzle than an actual solution. You will gather a long list of Latin names, a lot of numbers which, through a simple search, will show conflicting “ideal” numbers. What’s more, if you’re looking for your test to give you extreme dietary details, you will be mistaken. No microbiome test can tell you: the difference between a red and green apple, the exact amounts you should be eating, who – or what – all your microbes are, nor what all your microbes are actually doing. What microbiome testing can give you is:

  • The unique microbial composition of your gut at time of sampling
  • Information on whether these microbes are related to health or disease
  • Suggestions of how certain microbes can be increased or decreased based on specific lifestyle changes
  • Interpretations on your results based on the latest scientific literature

Nevertheless, the community inside you is too much of a maze, too vast, for the human mind to grasp – right now. As with most science, the more we learn, the more we realise what we don’t know. It’s as much a chicken-egg game, as it is a time-sensitive soup.

You today, is not you tomorrow

Sampling, and its current modalities, have many obstacles. Of course, the fresher a sample, the better the results. Since, from a consumer standpoint, that’s undesirable – and thus unlikely – most companies (including us) have selected stabilization solutions to preserve samples. This means you can simply collect and ship – at your own pace. Much better than having to freeze your faeces, right?

Still, different researchers use different tubes, different solutions and different lab protocols (for the most-part). This can be troublesome. If we’re to compare one set of results to another, reproducibility requires as similar a set of measures, so we actually know we’re comparing only a few selected differentiating factors.

Instead, with no “golden” lab standard, we’re left with a debate on what’s better. It also makes it really hard to find the true links, the missing pieces in the microbial puzzle.

This only gets more complicated. Your community is affected by almost everything. Travelling? Your microbes will change. Stressed? Your microbes will change. Growing older? Your microbes will change. Eating a donut? Your microbes will change. It can seem overwhelming when so much can cause shifts. It can even put you in a (literally) shitty situation.

Your bacterial blueprint

The research speaks for itself: numerous conditions – everything from depression, cancer to Irritable Bowel Syndrome – has been linked to the state of our poop. If your releases are sub-par, it’s likely your body isn’t functioning as good as it could be. With expansions in the microbiome field becoming a daily reality for  science institutions worldwide, it’s no wonder a very real need is emerging to keep track of our digestive outputs.

By testing your microbiome, what you’re truly getting is a snapshot – photographic memory of your microbial community at a given point in time. This affords you the opportunity, as research develops, to cross-reference and actually have your own personal bacterial blueprint. By testing now, you have the luxury of documenting your microbiome, so that you can be your own reference: a powerful tool as research continues to evolve and the underlying science grows deeper. It will take time to name and explain most of the microbes in our bodies, but if you have a record of your microbes now, and in future years to come, you will have an extremely valuable album of your microbiome at different timestamps, one you can use to track your health as you age – and optimize accordingly.

It will take time to name and explain most of the microbes in our bodies, but if you have a record of your microbes now, and in future years to come, you will have an extremely valuable album of your microbiome at different timestamps

Personally, by documenting my own microbiome, and trying different services, I saw there was something missing: testing needs to be a comparison of you – to you. Microbiome tests should not only be a comparison against a vast resource of unnamed, unknown samples – from people who have experienced completely different lives to you. We need to see how we change, and how we evolve, by using our own data as the centrepiece. It’s no wonder we developed RESET! This is the only way to get as close to an accurate picture as we can; one that includes your health history, lineage, and even everything you ever ate.

With my years of experience as a scientist in this field, what I can recommend is to invest in testing your microbiome. Do it with whoever you may, but make sure to collect those elusive parts of your puzzle – now. Mapping out your microbial blueprint from today, onwards, will afford you the luxury of having tangible insights and personal information that will continue to unravel as research ripens. This is something that will surely serve you, in the healthiest expression of your body (and bacteria), for years to come.


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