Lifestyle | Health & Wellness

5 Reasons to Skip Gut Microbiome Testing – For Now

Editors Note: We are welcoming Tamara Duker Freuman MS, RD, CDN as a regular contributer to FODMAP Everyday. She will be contributing an article every quarter about topics related to managing your gut health. Tamara has a regular column on US News & World Report and is the author of the newly published The Bloated Belly Whisperer: See Results Within a Week and Tame Digestive Distress Once and for All .  


A New Type Of Lab Test Showing Up In My Office

Recently, patients have been arriving at my office with thick reports of a new type of lab test: clinical  microbiome tests. These are stool tests ordered by a doctor and sent off to private labs, which then sequence DNA in your poop in order to identify and report on which organisms inhabit your colon. The ecosystem of microorganisms that inhabit your digestive tract is collectively called the gut microbiota, and their genes are referred to as the gut microbiome. (Want to learn more about the microbiome? Read our article “The Microbiome Explained” here.)

“Good Bacteria” vs “Bad Bacteria”

In the last month alone, patients have presented me with such reports from three different companies, ordered by either integrative doctors or naturopaths. On their websites, marketers of these tests promise to tell you whether you harbor “good bacteria or bad bacteria,” advise you of “bacterial imbalances” you may have, and offer “actionable insights” to modify your inner ecosystem toward improving your health.

Some recommend specific diets or foods to help rebalance your microbiota, while others warn you of specific disease risks based on the test results. All of them suggest the purchase of numerous, specific and (costly) dietary supplements, sometimes sold by the testing company themselves, other times not.

Some of the more well known microbiome test kit companies in the United States.
Some of the more well known microbiome test kit companies in the United States.

What These Tests Can Really Tell You

If you’ve considered spending $100-$400 on one of these tests (some insurance companies may actually cover part or all of these tests’ costs), you should be aware what these tests can credibly tell you about your health and what claims made by marketers of these tests may be over-reaching.

# 1. There is no single reference range for what constitutes a healthy, normal gut microbiota.

Unlike blood tests that measure levels of electrolytes, blood cells, vitamins and minerals against a known ‘normal’ and healthy reference range, no such standard of ‘normal and healthy’ exists for the gut microbiota.

The diversity of our respective inner ecosystems is astounding – as different from one another as the ecology of deciduous forests of America’s East Coast are to the tropical rainforests of Central America. Can one of these forests be said to be a healthier ecosystem than the other?

Of course not. Whether a given ecosystem is healthy depends on context. Using the example of the forests, a Central American tropical rainforest ecosystem may be very healthy if you’re a red-eyed tree frog, but a health disaster if you’re an Eastern gray squirrel that accidentally found itself delivered there one day.

The American Gut Project

This analogy applies to our inner gut ecosystems as well.  I reached out to Daniel McDonald, PhD, Scientific Director of the American Gut Project at the University of California San Diego’s (UC San Diego) School of Medicine, to understand more about where the research stands on defining what is considered healthy in terms of a gut microbiota.

American Gut is a crowd-sourced non-profit research project in which17,000 people – and counting – have paid a small fee to submit a stool sample to the Knight Lab at UC San Diego for analysis. Using gene sequencing technology of the stool sample, researchers can identify the types of bacterial and archaeal organisms residing in a participant’s gut microbiota and correlate the results to self-reported data on the participant’s diet and other lifestyle factors.

The enormous combined data set of all participants enables researchers to identify relationships between basic dietary, demographic, and geographic factors and the pattern of microbial species that reside and predominate in a person’s gut ecosystem. It also enables comparison among people in similar age groups, geographies and diet types.

McDonald explained to me that our individual microbiotas are likely reflective of and adapted to the environments in which we live, such that “a healthy microbiome for someone living in the U.S. may not be healthy for people living in China.” 

There Is No Standard Reference Range

He also pointed me to a recent paper by Celeste Allaband, which he and a team of other UC San Diego colleagues co-authored, that was published in the American Gastroenterological Association’s peer-reviewed journal Clinical Gastroenterology & Hepatology. In it, the authors explain that “there is no standard microbiome ecology that all healthy people share.”

Which begs the question: what is the reference range these microbiome stool tests are comparing your stool sample against, and who’s to say it’s a relevant standard for a person with your lifestyle and genetic background? On what basis did they decide it was definitely healthier than yours?

A woman lying on the couch curled up with abdominal pain.


#2. Clinical microbiome test data often aren’t specific enough to be meaningful.

The results of one of my patient’s stool microbiome tests warned her (with an alarming red font) that she had a high relative abundance of bacteria in the genus/species Escherichia coli, claiming that it placed her at high risk for developing Irritable Bowel Syndrome (IBS). Many of us are familiar with E. colifrom media reports of life-threatening outbreaks of food poisoning and would be understandably scared to think we harbored a lot of these critters in our guts.

But The Devil Is In The Details. 

As McDonald explained to me: “Simply knowing the genus [a grouping used to classify bacteria with common traits] of a bacteria and its relative abundance is not useful for clinical analysis. This is because each genus can have a wide range of strains, which are genomically distinct. For example, there are thousands of E. coli genomes that have been sequenced …with at least one strain considered a probiotic and others that can cause debilitating illness.”

e.coli grown in a petri dish

You say E.coli, I say E.coli

On the probiotic side, he’s referring to E. coli Nissile1917, one of the first known probiotics that has demonstrated benefit in helping to prevent flares of Inflammatory Bowel Disease.

On the illness side, he could be referring to E. coli O157:H7, a strain responsible for potentially lethal food poisoning from undercooked ground beef and raw milk.

In other words, within the E. coli umbrella, there are beneficial probiotic strains, “commensal” strains that neither help nor hurt us, and pathogenic – or disease-causing – strains.

Which strains did my patient harbor? Her stool test didn’t say. So is the fact that she harbors a higher amount of unspecified E. coli relative to an arbitrary reference microbiota actually as problematic as the screaming red font would imply? Who the heck knows? Even if these tests were to offer the granular level of genomic detail required to understand precisely which critters we were harboring, there’s still way more research that needs to happen for us to know what to do with that information.

Which leads us to the next point…


#3. The claim that harboring certain gut bacteria increase certain disease risk – and that modifying the microbiota can prevent disease – is not established scientific fact.

A common theme in clinical microbiome tests is the identification of specific gut bugs that are supposedly indicative of increased disease risk. This forms the basis of recommendations to take certain probiotics to “rebalance” the inner ecosystem and reduce disease risk.

If simply taking a probiotic supplement is an established way to prevent scary diseases ranging from Inflammatory Bowel Disease (IBD), Irritable Bowel Syndrome (IBS) and Celiac Disease to atherosclerosis, Type II diabetes and psoriasis, then who wouldn’t want to do that?

If Only It Were So Easy

In reality, there’s a huge chicken-and-egg question involved with singling out specific gut bugs as a sign of disease risk, and a whole lot of putting-the-cart-before-the-horse involved with trying to modify such risks even if they were to be established.

Which Gut Bacteria Are A Sign of Disease Risk?

Let’s start with the assumption that specific species/strains of gut bacteria are necessarily a sign of disease risk. I road-tested this idea with Ari Grinspan, MD, Assistant Professor in the Department of Medicine, Division of Gastroenterology and the Director of GI Microbial Therapeutics at Mount Sinai Medical Center in New York City.

He explained to me that small studies of patients with certain diseases – including Crohn’s disease (a form of inflammatory bowel disease) do commonly share some signature gut bugs. But researchers do not yet know whether these organisms actually cause the disease, or whether their presence is caused by the disease.

To answer that question, he explains, we’d need to see large studies that look at the gut microbiotas of a healthy general population at some starting point, then follow these people over time to see who develops Crohn’s disease, and whether there is indeed a link to the gut bugs they harbored before developing it.

Such studies have simply not been done yet. Grinspan is also quick to point out that the risk of developing many diseases – including Crohn’s – are known to be associated with factors other than the gut microbiota, like genetics and environmental exposures.

the word "Disease" being highlighted with a pink marker on the page

If So , Then What?

Even if researchers were to eventually find that certain gut bugs actually do cause certain diseases, we still have no scientific understanding of what to do about it. “If a patient came to me with a stack of papers that showed they harbored certain bacteria associated with Crohn’s disease, there’s nothing I can currently advise them to do differently other than to avoid smoking cigarettes,” says Grinspan.

Do you see how many pesky scientific hurdles we have to jump over to get to a place where we can say with confidence that:

(1) having a particular species or strain of bacteria in our guts necessarily raises our disease risk;

(2) eradicating that particular bacteria would reduce our disease risk; and

(3) taking a particular probiotic pill is a known way of eradicating that particular bacteria?

When clinical microbiome tests make such claims, they are doing so based on speculation, not established science.


#4. It’s not even clear to what extent your gut microbiota can be micromanaged through any means.

As mentioned above, a hallmark characteristic of all the clinical microbiome test results I reviewed was a strong sales pitch for various species of supplemental probiotics – and in some cases, recommendations for specific branded products – targeted at modifying the state of a person’s inner ecosystem. This led me to wonder: to what extent is our gut microbiota even modifiable by any means?

How Diet Influences Your Microbiota

We know from both animal and human research that the gut microbiota can be modified to a notable degree by changing our diets. Going from a diet that’s heavily protein and fat based to one very high in fiber-rich plant foods can alter the relative predominance of certain bacteria in a person’s gut microbiota – and it can do so rapidly. However, we have less specific knowledge about which specific foods or types of fiber can produce specific alterations in a person’s gut microbiota down to the species/strain level.

a basket of fresh vegetables But barring a dramatic change in diet from very low fiber to extremely high fiber – like say from going from a typical Western-style diet to a full-on vegan diet – the typical adult’s gut microbiota appears to be remarkably stable and resistant to change.

For example, while antibiotic medications kill significant numbers of bacteria – changing both the relative abundance of certain bacteria and decreasing the total number of bacteria your colon harbors – your inner ecosystem will typically rebound to its usual baseline state within a few weeks to a few months of stopping antibiotic use.

Probiotics and Your Microbiota

Even when they provide some sort of health benefit, taking probiotic pills has not been shown to modify your microbiota to a notable extent, either. A significant number of people appear resistant to colonization by supplemental probiotics – and even those who can be colonized, the effect is short-lived. Studies repeatedly show that the supplemental strains disappear from the colon within a week of stopping supplementation.

Any health benefits you derive from a probiotic supplement, therefore, are likely occurring as the micro-organism is passing through your body on its way out – not as the result of an alteration in the composition of your microbiota.

(As an aside for those who follow a low FODMAP diet, it’s worth noting that Monash University does not recommend you take probiotics during the Elimination or Challenge Phases of the diet, as they can cloud your reactions to a lowered FODMAP diet.)

Stool Transplant & Your Microbiota

It’s not even clear to what extent having a full-on stool transplant truly modifies a person’s gut microbiota. Grinspan is particularly well positioned to address this, as he performs fecal microbial transplants (FMT) – also known as stool transplants – for very sick patients infected with Clostridium difficile bacteria, known as the dreaded “C. diff.”FMT involves transplanting stool from a screened, healthy donor via colonoscopy into the gut of a sick person.

In other words, it involves directly inserting an entire ecosystem easily comprised of a thousand different species of bacteria directly into another person’s gut. Compared to taking a typical probiotic pill, which contains one to ten different species and is delivered through the mouth, FMT should conceivably have a greater chance of modifying the composition of a person’s gut microbiota substantially and for good.

So does it actually?

According to Grinspan, every patient’s response to FMT is different, and it’s not well known to what extent stool transplants create significant or lasting changes to the microbiota. “Some recipients of FMT are more accepting of donor bacteria and will experience more ‘engraftment’ than others.

Some patients don’t have long- lasting changes in their microbiota; a month later, we can only identify a few bacteria in their stool that were also found in donor. Others look a lot more similar to their donor.”

Interestingly, Grinspan notes, regardless of how accepting a person is of their donor’s microbiota, FMT seems to cure C. diff infection almost universally – we’re just not quite sure yet exactly why.


#5. There is no scientific basis for deriving diet recommendations based on the gut microbiota

Some stool microbiome tests offer pretty generalized diet advice: “Consider a diet supplemented with fermented foods,” or “Consider working with a clinical dietitian to follow an anti-inflammatory diet.”

But others get pretty down and dirty into the dietary advice weeds. The results given to one of my patients by a popular clinical microbiome test provider advised her of a list of fifty (!) foods or ingredients she was supposed to avoid, under the premise that they were “unhealthy for your gut’s biodiversity.”

Among these foods were some of the most fiber rich, plant-based foods known to humankind including oatmeal, barley, five different types of beans, prunes, figs, and raisins.

barley and corn spilled over a surface

Similarly, this patient was advised to minimize intake of other high fiber, nutrient-rich plant based foods such as leeks, peppers, collard greens, green beans, spinach, pumpkin and zucchini. Because diets with a high degree of variety in plant foods have been associated with a high degree of biodiversity in the gut microbiota, I was somewhat baffled by a recommendation to limit the types of fiber-rich foods one ate in the supposed service of biodiversity.

What The Experts Say: The Bottom Line

To understand how a stool test’s results could credibly be used to derive any dietary recommendations – let alone recommendations with this degree of specificity – I turned to Dr. McDonald of UC San Diego again.

In no uncertain terms, he advised me that “no scientific data exists to suggest that you can just take someone’s shit, sequence it, and tell them what to eat.” Click To Tweet

I think that pretty much says it all, don’t you?


My Personal Experience and Final Take Away

Look, I get the appeal of these tests. Our bodies play host to tens of trillions of critters, and we have no idea who they are and what they’re actually doing in there. It’s fascinating to get a glimpse into their identities for curiosity’s sake alone, and tempting to entertain the notion that we can somehow tame them to enlist their help in our quest for good health and longevity.

Driven by this curiosity, I actually participated in the American Gut project about five years ago as a “citizen scientist” myself. After keeping a food diary for myself and my family for a week, I mailed off our stool samples and soon after received colorful poster-sized printouts that described the predominant genera inhabiting each of our guts, with comparisons to the guts of other demographic groups.

I was fascinated to see how completely different the gut microbiotas of my then toddler-aged twins were despite sharing a womb, a bedroom and pacifiers, and despite following the same diet (albeit with different food preferences.)  I was also super freaked out to learn that one of my kids harbored a predominant bacterial phylum called Proteobacteriaa grouping that includes a rogue’s gallery of nasty disease-causing critters. THIS is what I get for breastfeeding that kid for an entire year?!

Interesting (and frightening) as I found these results, there wasn’t much to do about them. Should I have rushed my extremely healthy toddler (and now-healthy eight-year-old) to the doctor to start looking for infectious diseases that a weirdo gut microbiota suggested might be lurking within? Feed my kids more yogurt?  Stop feeding them yogurt? Put everyone in the family on a probiotic?  And if so, which one? The same one for us all? A different one for each of us? At the end of the day, I didn’t do anything differently in terms of my children’s diet, lifestyle or otherwise.

Clinical microbiome tests provide a whole lot of interesting data. But they can’t yet offer any conclusions at this time about what these data mean and what – if anything – we can or should do about that data.

As Allaband and her colleagues concluded in their paper, “although there is great interest in the microbiome, there is still a long way to go before microbiome-based diagnostics become a routine part of clinical care.”


We always love to hear from you so let us know what you think about this article, and if you have a topic related to IBS or the low FODMAP diet you would like us to write about. Send us a note below in comments. 

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