• Allison Fahrenbach

Is Gut Microbiome Testing Accurate or Worth It?

When your health takes a turn for the worse, it is natural to want to know why. Especially if it relates to digestion and gut health.


Why has my digestion changed?

Why am I getting bloated?

Why do all these foods seem to upset my stomach?

Why have my bowel habits changed?


One of the most popular answers to these “whys” right now is gut microbiome testing. Which is what I want to discuss in this blog.

The more researchers study the microbiome, the more and more the evidence concludes that gut health IS health. Your microbiota literally regulates and establishes your health.

A healthy microbiome:

  • Regulates your immune system

  • Influences your metabolism

  • Is critical to proper digestion and absorption of nutrients

  • Helps balance hormones

  • Impacts your mood


An unhealthy microbiome is associated with:

  • Inflammatory bowel diseases

  • Cancer

  • Obesity

  • Diabetes

  • Liver disease

  • Autoimmune disorders

  • Asthma

  • Mood disorders

  • Hormone imbalance

  • Weight loss and weight gain


It’s understandable to want to know what’s going on in your microbiome, especially if you're dealing with health issues.


One method of testing you might have looked into, or may be considering is microbiome testing.


Microbiome tests are abundantly available right now with dozens and dozens of companies selling them, claiming that these tests will “unlock the mysteries of your digestive issues.”

Some even offer dietary advice for fixing your microbiome, while others will custom formulate a probiotic you can buy that specifically will “balance” your microbiome.


These tests claim to be able to detect the presence of different species of microorganisms from a stool sample. From the test results, you can then get information like the richness of the gut microbiome, diversity of the gut microbiome, and how it compares to that of others.

But what does this information mean?

Is it even accurate?

And is there such a thing as the “ideal” microbiome?


How Important Is your Microbiome?

Scientists and researchers have been increasing their focus on the health of the gut and the impact of the microbiome over the last two decades.

The gut and its microbes have been called the “second brain” alluding to how important its function is to your health.


Researchers have even found the same grey matter in your gut as in the brain!

But now that statement is under question. Out of every ten communications from your brain and gut, your gut sends nine to the brain. The brain only sends one back!


This raises the question: is the brain influencing your gut, or is your gut affecting your brain?

Research is now showing us the latter.


An unhealthy gut actually changes your brain.


In studies done with IBS patients, gray matter started to deteriorate. Researchers think this is what lead to anxiety and depression in this group of people.


This would also explain why people who have poor gut health frequently experience anxiety, nervousness, depression, brain fog and cognitive/memory issues.


Beyond impacting your brain, your microbiome influences your genetics and perform thousands of functions that you cannot:

  • They synthesize a variety of vitamins and amino acids

  • They transform your bile into an even more potent health-giving chemical called TUDCA

  • Microbiota produce enzymes and break down your food to help provide you with energy

  • They produce critical chemical constituents and short chain fatty acids

  • They provide antimicrobial protection from dangerous microbes

  • They support your immune system and can help prevent allergies

  • These microbes produce hormones and neurotransmitters affecting your mood and memory

  • They even impact your sleep!

  • They affect hormone balance


It’s for reasons like these that much of eastern medicine and most alternative practitioners consider the gut to be the epicenter of health.


Hippocrates said all disease originated in the gut, and Ayurveda, one of the oldest healing practices in the world, also considers the gut to be the focal point of health.


But will gut microbiome testing give you the answers you need?


What We Know About The Microbiome

Science has come a long way in learning about the microbiome and gut health.


The problem is, the more they uncover, the more they find they need still need to discover!

The NIH Human Microbiome Project has identified about 10,000 species that can inhabit your GI tract.


But this changes. Every few years they discover and catalog about 1,500 more. The human microbiome is complex and dynamic. It’s constantly changing.

Right now they estimate that eventually, they will find 20,000 to 40,000 in total.

And each time they discover new microbes questions arise like:

  • What does this microbe do?

  • What genes does it affect?

  • How does it interact with other microbes?

  • Has it always been in the microbiome or is it new?

  • Is it supposed to be there, or should we try and get rid of it?


Doctors used to think that the number of microbes vastly outnumbered your own cells. Now that’s been revised. They presently state that the number is about the same. You have as many microbes as your own cells, yet they admit there is about a 25% variance amongst different people.

Plus, your microbiome changes continuously.


Even one bowel movement can significantly change that number!

Which Microbes Are The “Good” Ones?

Humans like to analyze, gather stats and compartmentalize. We like to put everything into neat, clean boxes.

Just as we like to label one food as “good” and another as “bad”, we want to know which microbes in the gut are friendly and which ones are not.


But scientists still aren’t entirely sure what a “perfect” microbiome looks like, or which microbes are good, or which are bad.


For example some bacteria are commensal (friendly) but only in certain amounts. If there’s an overgrowth then even some good bacteria can become pathogenic.

So microbiome testing is still in its infancy in terms of understanding what your data means.

It’s clear that gut health is important. But does your “perfect” microbiome look the same as what would be perfect for someone else? Is there one “ideal” microbiome?


The answer seems to be no.


The combination of microbes that create gut health differs from person to person. It even changes from region to region. Some underlying microbes remain relatively constant between you and everyone else. But there is also some unexpected diversity.

Researchers studied a rural tribe in Africa to hopefully get some answers. They felt this group would be a good representation of what a microbiome would look like before being introduced to a Western diet saturated with processed food.

These people had dramatically more variety of microbes in their gut. They had some “bad” microbes that would probably give someone in a Western community diarrhea. They also completely lacked one microbe that has been proven to be “good.” Yet they were very healthy.


The microbiome is like a city with different people and businesses. Each has a particular function to make the city (your gut) run smoothly and for everyone’s needs to be met.


Yet the amenities in each city are different. The needs of a city with lots of rain will be different than those of a city that gets lots of snow. If you think of this analogy it makes sense that microbes differ from person to person and region to region.


And ultimately research is still not clear as to what each microbe does and what they do when combined.


This is one reason why microbiome testing can’t nail down your perfect “community” of microbes.


The Microbiome Isn’t “Fixed”- It Changes

Not only are researchers not sure which microbes each of us need, but the microbiome is also forever changing. Even within the same day!


Some things that influence the changing of your microbiome are:

  • Exercise (some microbes die off when you exercise)

  • Age

  • The foods you eat

  • When you eat

  • Fasting

  • The amount of light you get

  • Medications

  • Supplements

  • Where you are in the world (you are exposed to new microbes when you travel)

  • Stress- What you encounter in your day and how you perceive it can even change your microbiome. Scientist discovered that immediately after stress, your levels of “good” bugs go down. This lets the “bad” bugs go up in number, specifically one associated with loose stools.

Microbiome Testing Is A Shot In The Dark

Scientists have many kinks to iron out before they can really understand what a gut test is saying.


Considering that having a little stress or eating a strange food right before your test could change the outcome, how accurate are these tests?


These tests are closer to a snapshot of a moment and don’t necessarily correspond with your gut ecosystem.


Personally, I did two microbiome tests from the same company (Viome), spaced a few days apart and got two different results.


Different microbes are more active at certain times of the day than at other times. Your microbiome composition can vary as much as 60% throughout the day. Even a morning and evening gut test will be radically different.


Also,the content in your stools isnt necessarily the best reflection of what is going on in your gut.

Internal biopsies reveal that the microbiota present in your stool sample can be completely different from what is actually colonized in your intestines. An entirely different set of microbes can appear “dominant” in your stool than what is actually in your gut. There is typically a much higher diversity in a biopsy than a stool sample gut test.


That being said, if you have ulcerative colitis, the opposite can happen. When researchers looked at biopsies and stool samples from ulcerative colitis patients, they were astounded. There was very little microbe colonization in their intestines. Yet there were many microbes in their stools. This could give you a false positive. You might think your intestines are teeming with good microbes, when in fact there is almost none.


A gut test only tells you what is coming out of your body, not what’s actually in it.


One answer you might specifically be looking for with a stool test is, do I have parasites?


It may or may not be able to tell that. Most parasites die soon after they leave their host. Most of them release chemicals and enzymes that start to decompose their bodies shortly after death. By the time your gut test gets to the testing lab to be analyzed, those parasites might dissolve completely. You won’t get an accurate answer to whether you have a parasitic infection.


The BEST way to test for a parasite given the available methods is what’s called an Ova and Parasite test. It’s a fecal test. It’s also known as microscopy. The test takes feces, processes it, concentrates it, stains it, and then places it onto a microscope slide.


A technician then looks at the feces through a microscope and visually inspects and records what parasites, and parasite eggs (called ova) they observe.


In todays high tech world, this "manual" method of parasite detection seems old fashioned but when it comes to real world parasite infections, this is typically the most effective and reliable test for the following reasons:

  1. Samples are collected over 3-8 days - making it unlikely that the parasites will be missed while the parasite spends part of its life cycle outside of the intestines in other organs.

  2. Experienced technicians can identify a huge range of parasites that PCR and antibody/antigen tests can't identify.

  3. The severity of the infection can be judged by an experienced technician.

  4. This test doesn't confuse prior infections, with current infections (unlike PCR and antibody/antigen tests). If the test is negative for parasites, and symptoms are gone, then it's very likely that the parasite has been removed.


The second best method of testing is PCR, which is what Diagnostics Solutions GI MAP uses. This method is still flawed, however. This article does a good job explaining the PCR method.

Different Tests, Different Outcomes

If all those variables were not enough to affect your microbiome testing results, the type of test changes what gets revealed as well.

Different companies have different methods. This includes how a sample is: collected, transported, stored and analyzed.

For example, some testing labs freeze your sample. That can preserve some aspects of your test, but it can ruin others. Some microbiota is well preserved this way, but others tend to disappear which could skew your results.


Some labs are more efficient at extracting the DNA from samples than others.

These labs also try and detect toxins in your sample. The delay between taking your sample and analyzing it can change what they detect.


The taking and handling of these tests need refinement before we can rely on their conclusions. Analyzing your microbiome is trickier than you think.

Okay- so now what?

If gut tests aren’t accurate, what’s the answer?

The answer isn‘t necessarily to NOT test, but to keep in mind the potential inaccuracies and indiscepencies of testing.

While I may recommend testing to clients, I have often found it to be more impactful to stop looking for a “why“ and instead focus on “what’s next.”


In other words focus on what helps your microbiome be healthy and vibrant, not whether it might be sick.


1. Get Your Gut Moving!

Your GI tract is the primary way your body gets rid of metabolic wastes and dangerous chemicals. If you struggle with constipation, it will dramatically impact the health, and balance, of your microbiome.


Studies show that being constipated changes what microbes are dominant in your gut.


The ones associated with pathogenic diseases take over your GI tract. Get this drainage pathway moving regularly -- at least one- three times a day. This will tip the microbes in your favor!

2. Make Sure Your Liver Is Open

One of the jobs a healthy microbiome loves is to take your bile salts and turn them into TUDCA. Tauroursodeoxycholic acid, or TUDCA is a bile acid derivative that’s naturally occurring in the body. A healthy person produces very small amounts of TUDCA, re-circulating some 95% of their bile salts. However, poor diet, decreased liver function, and certain medications can impair this process. A lack of TUDCA changes the microbiome and can activate other diseases.


A healthy, open liver bile duct will dramatically change your microbiome.

3. Feed Your Friendly Microbes With Fiber

Most people eating the SAD (standard American diet) eat far below the amount of fiber needed to keep their little intestinal community happy. You can’t digest fiber, but bacteria love it.

When you don’t feed them fiber, they start to die. The ones left over scrounge for whatever they can find. Unfortunately, they are not very friendly and often feed on your intestinal wall, degrading the mucosal barrier in your GI tract. This not only harms your intestines but also leads to “leaky gut” which leaves you open for infection from dangerous pathogens.

Eating a variety of vegetables and low sugar fruits is a natural, healthy way to increase good fiber and keep your microbes satisfied. This leads to better gut health.

4. Eat Fermented Foods

Fermented foods are a good source of fiber and microbes that can help increase your microbiome diversity. For example kimchi and sauerkraut have fiber, nutrients, and good microbes.

Fermented food consumption dates back for thousands of years. It’s associated with good gut health and even mental health, so try adding fermented foods to your diet.

5. Seek Support From a Professional

The area of gastrointestinal health is complex and multi factorial. It can really help to work one-on-one with a certified health coach, a functional medicine practitioner or a registered dietician with gut health experience.

These types of professionals can help you address your gut health concerns through a holistic lens. Which basically means they will look at the interconnectedness of your symptoms and help you to identify the underlying cause.


Rather then investing in unreliable and inconclusive testing, it may be preferable to invest in someone with the education and expertise to successfully help you navigate your symptoms and optimize your digestive system.


The takeaway:

It’s human nature to want to know why. And wanting to know why isn’t a bad thing!

But it doesn’t necessarily fix the problem, especially since there is a lot science still needs to uncover about our microbes.


In my opinion, focusing on testing rather than overcoming can leave you hanging instead of healthy. Especially if you’re relying on a testing method, like microbiome testing, which isn’t proven to be reliable and whose methodology varies wildly from one company to the next.

The science doesn’t support microbiome tests as being advanced enough for accurate conclusions to be made about your microbiome.


Choosing to spend your time and money in actions towards health, instead of analyzing why it’s missing, can help you break free from what’s holding you back.

If you’d like help putting the pieces together and reclaiming your health, take a moment to fill out this form for a FREE coaching consultation!!




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