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Article Summary:

• The microbiome is a collection of microorganisms that live within the human gastrointestinal tract and perform many significant health-promoting functions.
• Stool sample microbiome testing is the standard for detection of microbiome bacterial species in the functional medicine realm, and whether or not you have certain ones in particular ratios is supposed to be a helpful diagnostic tool.
• When researchers checked the stool microbial population and then checked the community within the gut itself, they found that the results were completely different.
• If testing stool samples for parasites is so inaccurate, it only makes sense to assume that looking at the stool to do microbiome testing is inaccurate as well.
• The often heard “status quo” is that bacteria within the body outnumber the body’s human cells by about 10:1 However, newer research shows that the ratio between microbes and human cells is more likely to be 1:1.
• Furthermore, the ratio of numbers of bacteria to numbers of human cells is close enough that each bowel movement may flip the ratio to favor human cells over bacteria, as many bacteria are expelled in the feces.
• Recent research published in February 2019 shows 2000 newly discovered gut bacteria. 
• Stool sample testing uses DNA fragments to identify what bacteria are present, but it can’t be accurate if we don’t know and can’t test for the whole scope of bacterial species that can live in the gut.
• Numerous other variables cast doubt on microbiome stool testing as an accurate analysis of the gut population.
• A single stool sample is a snapshot that provides information about a person’s microbiome profile only at the time and location that the sample was collected.
• The microbiome is dynamic and ever-changing, even on a daily basis, and many factors influence it.
• You’ll likely be better served by skipping the microbiome analysis and turn your attention toward cleansing, clearing, and supporting the microbiome.
• Ways to support the microbiome include: Eating locally and seasonally-sourced whole foods, fiber-rich foods, and fermented foods, getting the bacteria you need from the environment, and getting exposure to different ecosystems.
• If you need support along the way, my programs can help. You can work through my At-Home Program on your own.

Busting the Myths & Questioning the Status Quo About Stool Microbiome Analysis

The intestinal microbiome is a collection of microorganisms that live within the gastrointestinal (GI) tract, and perform many significant health-promoting functions. The intestinal microbes aid in the breakdown of food products into absorbable nutrients, stimulate the immune system, prevent the growth of pathogenic microbes, and produce a wide variety of biologically relevant compounds.

Stool sample testing is the standard for detection of microbiome bacterial species in functional medicine, and whether or not you have certain ones in particular ratios is supposed to be a helpful diagnostic tool. However, when researchers checked the stool to see the viability of stool tests and then checked the population within the gut itself, they found that the results were completely different.¹ Maybe what is being seen in the stool are microbes that the body doesn’t need anymore. So, perhaps to understand what’s in the gut, it is better to look at what is in the gut, not at what is being expelled as waste.

Think About Parasite Testing, For Example

Consider, for example, the practice of diagnosing parasites by examining stool samples. Many doctors will typically say, “Well, let’s run a lab.” Unfortunately, parasite diagnosis through stool samples is substantially inadequate.

Parasites don’t always come out in every stool sample. Plus, many labs are typically pretty busy, they’re trying to do numerous samples in an hour. The lab technicians spend maybe three minutes or so examining a sample, and if they don’t find anything in that time period, it’s ruled negative.

A further complication is that, when parasites die, some of them actually release an enzyme that will dissolve their bodies. So considering the transit time the sample takes to get to a lab, and the time it takes for the lab to look at it, there may not be anything left to see. There could have been parasites, but now they’re gone or not recognizable.

Additionally, there are thousands of types of parasites. You can’t test for all of those. And we don’t have sufficient knowledge and understanding of many of them. The results of a study released in November 2018 revealed that when scientists compared the genomes of 81 species of roundworm and flatworm parasites, including 45 species that had never been sequenced before, they discovered upwards of a million new genes that had not previously been seen.² 

So, if testing stool samples for parasites is so inaccurate, why do we assume that looking at the stool to do microbiome testing is accurate as well?

The Ratio of Gut Microbes to Human Cells is NOT 10:1

The often heard “status quo” about the bacteria in the gut microbiome and other places within the body is that they outnumber the body’s human cells by about 10:1. That’s a busted myth that should be quickly forgotten. In truth, newer research shows that the ratio between microbes and human cells is more likely to be 1:1.³

The ratio can vary among individuals—one person might have twice as many or half as many bacteria as another person, for example—but nowhere near the 10:1 ratio of bacteria to human cells commonly assumed.

Furthermore, the ratio of numbers of bacteria to numbers of human cells is close enough that each bowel movement may flip the ratio to favor human cells over bacteria, as many bacteria are expelled in the feces.

The 10:1 myth that has become the “standard” theory came from a 1972 estimate by a microbiologist named Thomas Luckey. This one testament to microbiome numbers was probably never meant to be widely quoted and accepted as the status quo decades later.

Then, in 2014, a molecular biologist at the U.S. National Institutes of Health questioned the status quo and expressed his doubts about the 10:1 claim. He pointed out that there were very few good estimates for the ratio of human vs. microbial cells in the body. Other scientists undertook re-estimating the numbers by reviewing recent experimental data. The measurements suggest that there are fewer bacteria in stool samples than Luckey thought.

The researchers conducted a microbiome stool sample and then compared it with a physical exam of the colon to check the cultures inside it, and found that the results were vastly different, reflecting poorly on the accuracy of a stool sample for microbiome testing. The latest research defines the ratio of microbial to human cells for an average man to be 1.3:1, with a wide degree of uncertainty.

The Complete Spectrum of Gut Bacteria Varieties is Unknown

Recent research published in February 2019 shows 2000 newly discovered gut bacteria.⁴ Stool sample testing uses DNA fragments to identify what bacteria are present, but if we don’t know and can’t test for the whole scope of bacterial species that can live in the gut, then how do we know that the test results are accurate?

Taking the gut species matter a step farther: How sure are we that specific gut bacteria are good, and others are bad? They may even have differing roles, depending on the circumstances. And when these bacteria function as part of a colony, do they behave differently than if they were just individual bacteria? There seem to be more and more questions without concrete answers, making the information you can get from a microbiome test appear less and less helpful as a diagnostic tool.

Other Variables That Cast Doubt on Microbiome Diagnosis

Sample Collection

The sample needs to be collected with a bit of precision.⁵ Many microbiome testing companies instruct the person taking the test to obtain a sample at home, and how it is collected and then stored may have a substantial impact on the analysis and results.

Intra-Stool Variability

It turns out that there can be differences between the microbes taken from two different parts of the same sample.⁶

Changes During the Shipping Process

The shipping process allows the growth of certain bacteria that would not usually exist in fresh samples. Some testing companies will account for this and filter their reported results accordingly.⁷ However, arbitrary filtering may only amount to a “best guess” scenario and may vary among testing companies.

DNA Extraction and More

The way DNA extraction is done can make a significant difference in the results. DNA profiling technologies, computer programs, and analysis methods may differ among companies and are still being perfected.

It’s a Singular Snapshot

A single stool sample will provide information about a person’s microbiome profile only at the time and location that the sample was collected. The microbiome is dynamic and ever-changing, even on a daily basis. Some factors that influence the microbiome include:

• Your age: Researchers found that the older you get, the more diverse your microbiome becomes, regardless of where you live.⁸ Other research also found that the flora in your gut could play a role in the rate at which you age.⁹
• Your gender: Research has shown that men and women have different bodily microbial communities, which could be related to differences in hormone levels.¹⁰
• Your exercise regimen: A study of athletes found that they had a higher diversity of bacteria in their gut compared to a control group.¹¹ These results suggest that getting exercise can be beneficial for increasing the friendly bacteria that live in the GI tract.
• The medications you take: Medications have a substantial impact on the gut. It is widely known that antibiotics disrupt the microbiome wiping out both good and bad gut flora. Beyond antibiotics, metformin (a drug often prescribed for diabetes) and antipsychotic medications are linked to reduced microbiome diversity. Proton-pump inhibitors (drugs that decrease stomach acid production), NSAIDs, opioids, and statins can also change the microbiome.¹² Anticancer drugs, including chemotherapeutic and immunotherapeutic drugs, can also significantly affect the microbiome composition.¹³
• Your stress levels: Chronic stress not only causes persistent inflammation in the body but also adversely impacts gut health. Research suggests that stress-related hormones alter the intestinal lining, relocating the microbes from where they should be.¹⁴
• Eating and fasting: Short-term, intermittent fasting can induce long-lasting gut health.¹⁵ Intermittent fasting can produce a reconfiguration of the microbiota resulting in greater numbers of certain friendly bacterial species and a reduction of others.¹⁶
• What you eat: What you eat has a huge impact on your microbiome. Foods that contain chemical additives and ultra-processed foods disrupt the gut environment and increase the risk of disease. Alcohol and artificial sweeteners like aspartame, sucralose, and saccharine also have an adverse effect on the gut flora.¹⁷ These upset the microbiome’s metabolism of microbes and reduce gut diversity. However, organic produce, whole foods, high fiber foods, and fermented foods can promote a healthy microbiome.¹⁸
• Your pets: People who own a dog tend to have more bacterial species in common with other dog owners—more so than those who don’t own a pet or own a cat. Dogs tend to go outside more frequently, where they pick up a variety of different bacteria, which they bring into the house and spread to humans.
• Where you are in the world: The microbiome is also affected by the environment. Someone native to one country will likely have a different microbiome than someone born in another country. ¹⁹
• Poor sleep patterns: Poor sleep patterns and disruptions in light to dark cycles (from exposure to artificial light or stimulating blue light from phone and computer screens), alters the natural circadian rhythm of the body, resulting in microbial dysbiosis.²⁰
• Alterations in circadian rhythm: Gut microbes display time-specific changes in composition and functions that align with the human circadian clock. They contribute to distinct activities throughout the day, such as ramping up energy metabolism during daytime and the detoxification pathways at night. Jet-lagged people, those who do shift work, or those who don’t otherwise live according to light and dark cycles can develop intestinal flora imbalances.²¹
• Your exposure as an infant: Babies developing in the womb encounter no microbes until birth. Most infants get their first big dose of microorganisms when they are born while traveling through the birth canal. If an infant experiences a cesarean section birth, they can be exposed to a different set of flora than what they would receive from natural birth. Plus, babies pick up more microbes while breastfeeding, so bottle-fed infants may not get the same microorganisms as a naturally fed baby.²²

With this many variables, it’s easy to see that the microbiome is merely a snapshot taken from a stool sample and even an internal gut check depends on the particular influences at that given moment in time.

Ain‘t No Party Like a Microbiome Party

There are many avenues to get your stool sample tested, but honestly, I would say: don’t waste your money. You may be better served to put the expenditure of finances toward cleansing, clearing, and supporting the microbiome. Want to know how to keep your microbiome party going strong? Here are four tips to keep your resident microbes happy, diverse, and well-fed.

Feed the Gut Microbes with Fiber

Your friendly intestinal microbes love a good fiber-filled meal of vegetables, legumes, and low sugar fruits to keep them partying hearty. Unfortunately, most people eat far below the amount of fiber needed to keep the party going strong. Without fiber, the little critters can start to die off. As die-off continues, the party-goers will feed on whatever they can find—which will likely be the intestinal wall. This intestinal wall feeding frenzy degrades and destroys the mucosal barrier in your GI tract, and leaves it open to infection from dangerous pathogens.²³

Get the Bowels Moving

The body gets rid of metabolic wastes and toxic chemicals through the GI tract. If you are are not evacuating your bowels regularly, the wastes and chemicals sitting in your intestine can be reabsorbed, poisoning you and your microbiome.

When the microbiomes of constipated patients are compared with those of regular evacuators, there are noticeable differences in the composition of the intestinal microbiota.²⁴ Studies show that being constipated changes what microbes are dominant in your gut. That gives the microbes associated with pathogenic diseases a greater opportunity to crash the party and take over your GI tract.

Plus, evidence indicates that alterations of intestinal gut flora may actually contribute to constipation and constipation-related symptoms. The large intestine is a vital drainage pathway that needs to be moving regularly—at least two times (or more) a day is ideal.

Keep the Liver/Bile Duct Open

The liver/bile duct is another critical drainage pathway to keep open and free-flowing for a healthy microbiome. A key function of a healthy microbiome is to take the bile salts and turn them into TUDCA (tauroursodeoxycholic acid). TUDCA is a water-soluble bile acid that can cleanse the liver, counteract the toxicity of regular bile, and aid in cellular protection.²⁵

TUDCA also has impressive health benefits for the microbiome. If your liver/bile duct is blocked, the intestinal microbes will be starved of the bile salts needed to produce TUDCA. Insufficient TUDCA changes the gut flora and may activate other diseases.²⁶

Taking TUDCA in supplement form can help with unclogging the liver/bile duct. Herbs and botanicals can also support improved liver function. Coffee enemas open up the liver bile duct and purge toxins that are interfering with the healthy functioning of the body and the gut flora. You can learn more about coffee enemas in my Ultimate Coffee Enema Program.

Consume Fermented Foods

Your partying pals love it when you feast on fermented foods. Not only will you be giving them the fiber that they crave, but you are also adding new guests to the party—microbes that may increase the diversity of the microbiome. Kimchi and sauerkraut are two fermented foods that have fiber, nutrients, and friendly bacteria. Fermented food consumption is associated with a healthy gut, so chow down on those fermented foods. You can check out my video on how to make fermented vegetables at home—it’s easier than you think! 

Support Microbiome Health and Promote Diversity

The take-home message from the above information is that if you are getting information from a single sample microbiome stool test, you probably need to take the results with a grain of salt. It seems that with all the variables, you simply cannot get a good picture of your microbiome from a single stool sample. And even an internal gut probe might not give the best picture, taking into account all the things that can influence the gut flora at any given time.

You’ll likely be better served by eating the right foods and getting the bacteria you need from the environment. Clean up the microbiome and feed it seasonally-sourced local whole foods so that it can flourish. Get diversity through fermented foods. Get exposure to different ecosystems that have a variety of microbes not native to your home location.

If you need support along the way, my programs can help. You can work through my At-Home Program on your own.

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