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.
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?
#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.”
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.
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.
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.
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 [bctt tweet=”“no scientific data exists to suggest that you can just take someone’s shit, sequence it, and tell them what to eat.”” username=”FODMAPeveryday”]
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 Proteobacteria – a 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.”
Read All Of Tamara’s Articles:
- What Conventional Wisdom Gets Wrong About Bloating
- Timing of Digestive Symptoms: What It Means
- What Is Leaky Gut Syndrome?
- Are You Full of Sh*t? Stool Burden and the Low FODMAP Diet
- Everything You Want to Know About Farting*
- 5 Reasons to Skip Gut Microbiome Testing – For Now
- Exclusive Interview with Dietitian Tamara Duker Freuman
- Q & A With The Author Of “Regular, The Ultimate Guide to Taming Unruly Bowels and Achieving Inner Peace”
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.
Thank you for this and the other info you send us!
This topic was covered on Canadian television
CBC Marketplace. You could look it up for episode on November 2, 2018.
They came to the same conclusion that the tests were all hype, trying to sell to searching people.
Thank you for the compliment and for letting us know. We will be sure to go check that out.
Nice review—thank you. I keep waiting for more clinically useful tests. I have to add: Exercise! Activity also alters our gut biome, interestingly.
I will also note that I personally find a certain probiotic helpful for preventing yeast infections and take it faithfully when I am swimming regularly— but that lines up well with the “helpful while taking it” rather than colonizing discussion.
Stephanie, sounds like you are well attuned to your own system – which is what we all need to be. Every one of us will have unique digestive experiences and need to be our own best monitors!
I agree that the science and clinical applications are in their infancy. Having said that, I have had good clinical success with the testing and subsequently recommended probiotics. I use a reputable company that does not sell products. I review the test results, utilize symptom data, food logs, medical history, family history etc. and recommend specific probiotics and sometimes prebiotics. The probiotics come from reputable companies with pharmaceutical grade quality control. I have had tremendous success with symptom relief. The thing that has been surprising however, is that colonization has not occurred. If the probiotics are discontinued, the symptoms return. I do not consider the tests (at least from the companies I use) to be a sham. Rather than depending on a company selling a product–perhaps what is needed is the guidance of a Registered Dietitian/Nutritionist that specializes in this area and has experience in using the data to make clinical recommendations.
Hi, Linda,
Well, there’s no arguing with success, so I’m glad to hear you are finding these tests clinically useful! I guess the trouble that many clinicians (myself included) run into with these tests, is how actionable is the data they provide into steering us toward an appropriate probiotic choice? Looking at a laundry list of species someone harbors, knowing it is a sliver of the 1,000 species that the typical person harbors and knowing that the results can change significantly over the course of a day or a week, makes it very challenging to say with any degree of certainty that taking X strain of probiotic will fill some perceived ecological niche that is off-kilter. I don’t know many RDNs who are qualified to make such recommendations in an evidence-based way–even those of us with specialized GI training– and I don’t know many (any?) MDs who are either. I think for now it may just boil down to clinical experience– if an RD or MD has had many patients with certain symptom patterns respond well to a certain probiotic, that can guide a reasonably informed recommendation…. and the risks of trying one or more products out are pretty low other than the cost. Your patients are lucky that you seem to have cultivated this clinical judgment and perhaps you can publish some case reports on your success stories to help guide the rest of us!
I’m on weight watchers. I need. To calculate point values. Do you have nutritional values. I used the Bella starter too and 2T pure maple syrup plus Lactaid lactose free nonfat milk.
Hi Hallie, Great to hear about the Belle & Bella; it has proven to be very popular. We do not provide nutritional values. Also, FYI in case you missed it, you might like our article on DIY Lactose-Free Dairy.
Is this company providing the tests that you speak of? The ones that are not all that helpful yet?
https://smartnutrition.co.uk/ibs-gut-disorder-clinics/digestive-testing/
The test in that particular link is not a stool microbiome test, though apparently the company does also offer a stool microbiome test. However, in my clinical opinion, the test you linked to is similarly problematic– it offers a lot of data that has no diagnostic value (and is not approved at least here in the US to diagnose any conditions) and tells you very little about your health. In my experience, I’ve found those stool tests are often used by alternative health practitioners to justify selling you supplements.
Very informative and well written .
I have received a “gift” from my daughter of two Gut Intelligence tests(stool) and one Food Sensitivity test (blood).
I have noticed contradictions in what foods my blood test show as highly sensitive, as compared to those very foods as being “Superfoods” or “Enjoy” as recommended by the Gut Intelligence microbiome test .
One diet which literally turned around a lengthy challenge with a Celiac issue was the AIP (Autoimmune protocol) diet.
I hope you are at a point of clarity of how to move forward. I wasn’t sure if you had a question or not. Thank you for writing and we wish you good health!
I was just listening to this https://www.youtube.com/watch?v=zv4OALmw5R4&list=PL321-bGRTfd9iXAvcOGt0DuJvKE0Q2P3t and landed on here.
I am really wondering whom I should follow? Your advise or this Dr. if there are tonnes of technolgies being developed to look into our differences biologically, each one of us unique and thus so many of us get “one size fits all” medicine. There is even a Tummy Clinic in Toronto, that just throws up this Fodmap in your face as a one stop solution whilst you pay them for their “services” each doctor seems to be afraid of stepping outside of the Box. I am frankly tired of it. I will look at what is missing in my own digestive system, and I do not have to be stupid and buy supplements, I can look up research on foods that help or beter yet, find a place that has the right fecal matter for re-introduction. Gross as it sounds…
We absolutely agree with you that it is Never one size fits all. That is Exactly why it is recommended that everyone following this diet work with a Registered Dietitian, or the equivalent in their country. Of course new technologies are being developed, and when they are proven in a clinical setting they are adopted by RDs and by us. On the other hand there are many “tests” out there that have already been proven not to be reliable. GIs and MDs are excellent for diagnosis, but it is the RDs who are trained in actual, practical advice and application of a program that will work for you, individually. Their 9am appt. might have IBS, be overweight, be diabetic and not know how to cook. At 10am they might see someone with IBS, who eats a plant-based diet and wants to steer clear of refined sugars. They can help each person follow the low FODMAP diet, get their GI tract in order and reduce their triggers and symptoms – but the approach will be unique to each. We each have to self-educate and make the best decisions for ourselves, but at the same time we should NOT be self-diagnosing, and we see time and time again, anecdotally as well as statistically, that there is a much higher chance of success with the low FODMAP diet if you work with a RD.
I would like to see an article investigating whether or not COVID causes any “long haul” digestive problems. It might be coincidental my gut issues ramped up after having covid, but it might not.
Hi Elaine, it is a great question, but since we are far from being “in” a long haul time frame – YET – there would be no data to be explored. We will certainly keep an eye out.
This was an interesting round-up of medical data as it relates to COVID and GI issues. https://www.medicalnewstoday.com/articles/gastrointestinal-symptoms-in-covid-19-what-do-we-know-so-far#GI-symptoms-associated-with-COVID-19-