Testing Isn’t Advanced Enough—Yet—to Give You an Accurate Picture of Your Gut Microbiome

• The Promise of Gut Microbiome Mapping|
• Don’t Rely on Tests—For Now|
• Bypass Microbiome Testing & Heal Your Gut|
• An Adaptable, Resilient Microbiome|

There are many different gut microbiome tests these days, and it can be tempting to want the “official verification” of a test to tell you what is wrong with your gut and how to fix it. But the results don’t live up to the hype—yet. 

We’re still studying and learning new things about the microbiome every day. While testing technology is advancing steadily, it’s not yet able to give you an accurate picture of your gut microbiome and how to optimize it. 

Instead, it’s much more actionable to use your symptoms (and ideally a clinical evaluation) to guide the diet, lifestyle, and other recommendations that can heal your gut. Skeptical? Let’s dive into the promises and shortcomings of at-home microbiome testing. 

The Promise of Gut Microbiome Mapping

Gut microbiome tests (aka microbiome mapping) use algorithms that compare the DNA of your gut’s microbial composition to databases of other people’s microbiomes [1]. These tests have become more popular in recent years as awareness around gut health has increased and people learn that gut health is important for overall health and well-being [2]. 

Fun Fact: In a study of Google searches from 2007 to 2022, Google searches for the term “gut microbiome” grew more than 1,400% [3]!

Using your microbial DNA, gut microbiome tests promise to identify certain bacterial species, fungi, and even parasites currently residing in your gut. The goal is to identify anything that could be contributing to anything from irritable bowel syndrome (IBS) to mental health conditions to immune system dysregulation. Often, the tests simply identify “abnormal” microbes, leaving you to figure out how these imbalances relate to your digestive health.

You might then use this information to treat an underlying gut infection, take certain probiotics to replenish your gut bacteria, or address a leaky gut. And depending on the test, it might come with guidance on diet and other lifestyle factors that are supposed to improve your health based on your personal gut microbiome. For example: 

• A testing company called Zoe offers microbiome mapping, claiming they can use the results to personalize nutrition for reducing inflammation, increasing energy, reducing hunger between meals, inducing weight loss, and improving bowel movements [4].
• A company called Viome has developed a Gut Intelligence test kit, which uses metatranscriptomics (RNA sequencing technology) to “see every organism in your gut microbiome and analyze” the organisms’ activity in just a few weeks [5]. 
• A company called DayTwo offers microbiome mapping and claims the results can be used to create personalized diets to reduce the incidence of metabolic disease, including obesity and type-2 diabetes [6].

These and similar gut microbiome tests can be tempting when you’re trying to figure out what is going on with your gut and find relief from your symptoms. I get it—I used to rely on them often in my practice and for my own health. 

But unfortunately, microbiome tests are just not reliable. 

In fact, when you compare two or more of these popular tests, you’ll often get completely contradictory results. More often than not, this leads people on a wild goose chase, trying to treat something that isn’t present at all, or treating the wrong thing. 

If you’re curious, check out my YouTube video below showing the test results from two different microbiome tests using the exact same stool sample. I bet you’ll be surprised by the results. 

Don’t Rely on Gut Microbiome Tests for Your Gut Health—For Now

Let’s dig a little deeper into the faulty reasoning behind at-home microbiome testing from the standpoints of test accuracy and interpretation. 

Again, at-home microbiome testing should NOT be used for diagnostic and treatment purposes [7]. Here are the reasons why.

Reason #1 

Different gut microbiome tests will almost always show different results, even from the exact same stool sample. This goes back to the video I shared above, wherein we submitted the same stool sample to two different microbiome test labs and got completely different results from each one. The testing technology simply isn’t advanced enough yet to give an accurate snapshot of your microbiome health at a particular point in time. And as I’ll discuss next, that snapshot might not even be a useful data point in the first place.

Reason #2

Our trillions of gut microbes are constantly changing, depending on our diet, sleep quality, stress levels, and many other factors [8]. So, during the week or two when you send in your sample, the lab processes it, compiles your results, sends them to you or your health provider, and you review those results, your microbiome could change a lot. Even if your results were accurate at the time, they may no longer represent your gut microbiome once you view them. 

Reason #3

Everyone has a unique microbiome, and some microorganisms that would be considered “pathogenic” in one individual are completely normal and don’t cause symptoms in another. For example, you may be one of a large percentage of people who have Clostridium difficile bacteria as part of their normal microbial flora. A microbiome test may flag this as something you need to treat, yet when you take antibiotics, you feel worse because C. diff was simply part of your normal gut flora, much of which the antibiotics harmed. 

Reason #4

Along those same lines, there is no clear definition of a “normal” gut microbiota [9, 10]. We use the term dysbiosis to refer to an altered microbiome that’s associated with a specific disease or condition when compared to the microbiome of a healthy control patient [10]. But no microbiome signature has been conclusively found for any particular disease [7]. By no means are we clear on what causes dysbiosis, or even what defines it. This makes microbiome testing even more murky and unreliable because we have no standard point of comparison.

Reason #5

Finally, many doctors are not current on the basics of microbiome science and struggle to interpret microbiome mapping results [7]. Genomic sequencing technologies have evolved faster than the analytical tools that evaluate the data they provide. This often results in false diagnoses that may cause lasting physical, mental, and emotional harm to patients who end up chasing a condition they don’t actually have [7]. As a clinician, it breaks my heart when these patients end up in my office and have spent weeks, months, or even years stressing out over these faulty test results. 

It simply doesn’t have to be this way. While I value testing in certain cases, there are many other ways to assess gut symptoms and begin a plan to get you feeling better as soon as possible. 

How to Bypass Microbiome Testing and Heal Your Gut

Fortunately, you don’t need a microbiome test to start healing. Evaluating your symptoms is a reliable indicator of your gut health and can inform you of the next steps to restore your gut.

For example, symptoms like abdominal pain, excessive gas, bloating, diarrhea, constipation, food reactions, brain fog, fatigue, headaches, joint pain, skin problems, anxiety, and depression tend to be good indicators that your gut health may be off. 

Ideally, you can work with a knowledgeable and experienced clinician who can help you qualify your symptoms and address them. If not, there’s still a lot you can do yourself—just be sure to listen to your body, and don’t do anything that doesn’t feel right to you. 

Once you evaluate your symptoms, you can begin a series of reasonable low-risk, high-reward experiments with various interventions that tend to resolve gastrointestinal issues in most individuals. 

Let’s look at the experiments my patients regularly undergo with success, in order, one by one. 

Diet

Diet remains a controversial topic for many people, but I first recommend at least following a whole foods, anti-inflammatory diet along the lines of a Paleo-type diet. An anti-inflammatory diet like Paleo helps to reduce common allergens and processed ingredients that cause inflammation and irritation in the gut for many people [11, 12]. This usually means significantly reducing or eliminating things like gluten, grains, and most dairy products for a time, but not forever. Once my patients complete their gut experiments and their digestion is back to a good place, most of them can go back to eating some grains and dairy with no issues. 

If eating a Paleo-type diet is right for their gut and body, people typically see improvements in 2–3 weeks. If not, it’s time to move on to a low-FODMAP diet, which restricts certain fermentable carbohydrates that often contribute to symptoms like bloating, gas, and constipation [13, 14]. If, after another 2–3 weeks, this diet still isn’t helping, then the problem may not be dietary. (Yes, this can happen!) Then, we move on to the next phase. 

Probiotics

Whether modifying the diet helps some or not at all, we add in probiotics. Probiotics help to restore a healthy bacterial community that produces essential metabolites like butyrate and keeps unhealthy microbes to a minimum [15, 16, 17]. Just like with diet, the options are flexible. There are three main categories of probiotic supplements to try: a Lactobacillus-Bifidobacterium blend, Saccharomyces boulardii (a beneficial yeast), or a soil-based probiotic.

It’s up to my patients whether they want to try one or all three based on their symptoms and the support they need, but I typically recommend they try all three at once. At the Ruscio Institute, we pioneered triple therapy probiotics, an all-in-one supplement that combines all three types for the most robust approach. Some people notice a shift within 4 weeks, and most people find the greatest improvement within 2–3 months. 

Elemental Diet

Okay, let’s say a patient has changed their diet and added in probiotics, but they’re still not seeing an improvement in symptoms. Or they’ve hit a plateau but aren’t quite where they want to be. At this point, I recommend trying an elemental diet. 

An elemental diet replaces one, two, or three daily meals with a delicious, easy-to-digest, and nutritionally complete meal replacement shake. Substituting one or more meals with an elemental diet allows the gut to heal and recover while starving any overgrowths or microbial imbalances that may be causing symptoms [18, 19]. 

The nice thing about an elemental diet is that you can decide how often, how long, and how intensively you want to use it. I’ve had some patients simply replace their breakfast and possibly lunch with a shake for several days, while others have chosen to do a total replacement of all their meals for up to two weeks. And after the elemental diet is complete and you transition back to a healthy, whole-food diet, you can choose to use the shake as a periodic gut reset to maintain your progress. 

Herbal Antimicrobials

Finally, step #4 is herbal antimicrobials. When my patients have experimented with all of the above but still have gut symptoms, it’s time to trial an herbal antimicrobial formula. Herbal antimicrobials can safely target and kill potential gut pathogens to allow the gut and microbiome to recover [20, 21]. This step is best done with support from a knowledgeable practitioner.

You might wonder, why not just start with antimicrobials? The reason you shouldn’t start here is because the earlier steps are crucial to set the foundation for the antimicrobials to be effective. If you were to start here, using herbal antimicrobials might not be very effective. Or, they might only be temporarily effective, since the gut and microbiome weren’t properly nourished beforehand. 

Think of it like a garden—going straight to antimicrobials would be like adding weed killer without first tending to the soil or nourishing the plants you want to grow in the garden. You might have killed the weeds, but you wind up with poisoned soil and a pretty sad garden! Following the steps in order tends to produce positive results in most people. 

Aim for an Adaptable, Resilient Microbiome

At the risk of sounding like a broken record, I’ll say it one more time: You don’t need expensive stool tests to identify microbial genes or pathogens in order to take action and improve your gut as soon as possible. The tests are often inaccurate, and many pathogens and gut symptoms respond to an anti-inflammatory diet, probiotics, an elemental diet, and herbal antimicrobials. Instead of testing, you can let your symptoms guide you and experiment with these science-backed steps known to improve gut health.

When I think about what a healthy microbiome “should” look like, it’s not a specific microbiome composed only of beneficial bacteria or absent of all pathogens. It’s a complex ecosystem of microbes that can easily and efficiently adapt to different circumstances and conditions that change to some degree every day. 

A microbiome that can change and adapt is what we want to keep up with our ever-changing lives. And for right now, microbiome tests can’t show us what that looks like nearly as well as our symptoms (and a good clinical evaluation) can. 

If you want to learn more about the steps to improve your digestive issues and overall gut health—no testing required—check out my book Healthy Gut, Healthy You. And if you’re looking for a clinician to guide you to better gut health without unnecessary testing, reach out to us at the clinic.

The Ruscio Institute has developed a range of high-quality formulations to help our patients and audience. If you’re interested in learning more about these products, please click here. Note that there are many other options available, and we encourage you to research which products may be right for you.

Dr. Michael Ruscio is a DC, Naturopathic Practitioner, researcher, and clinician. He serves as an Adjunct Professor at the University of Bridgeport and has published numerous papers in scientific journals as well as the book Healthy Gut, Healthy You. He also founded the Ruscio Institute of Functional Health, where he helps patients with a wide range of GI conditions and serves as the Head of Research.