Is Microbiome Testing More Hype Than Science?

Experts say microbiome tests aren’t right for everyone.

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Scott Jackson and his wife were amused when they got the results back from a consumer microbiome test.

“One recommendation was that our diet was too carnivorous, and we needed to cut down on our meat consumption,” he told The Epoch Times.

The problem with that advice: They had eaten entirely meat-free for the week before collecting and submitting their stool samples—and the microbiome can change within days. The mismatched results illustrate a problem in the burgeoning field of gut microbiome testing—it’s an immature science that offers value in narrow circumstances.

Consumers are desperate to know what their own microbiome says about their disease risk in an environment where more than 30 companies are willing to tell you what bugs are in your gut and what that might mean. Studies have pinpointed microbial “fingerprints” associated with some of the most puzzling diseases, such as multiple sclerosis, autism, Parkinson’s disease, obesity, eczema, and inflammatory bowel disease.

Should you opt for testing, it’s helpful to know what to expect, how to pick a reputable company, and how to adjust your expectations to realistically align with developing technology.

When Testing Makes Sense

If you are healthy, there’s no need for a microbiome test. However, if you are struggling with health issues after you’ve fixed a poor diet and addressed sleep and stress, a test may offer helpful insight.

That could include testing for babies who have gut-related conditions such as colic, reflux, eczema, and food allergies, according to Kimberley Sukhum, a scientist who has studied how pathogens and antibiotics affect the gut microbiome.

Sukhum works for Tiny Health, which specializes in testing for babies and even recommends testing for asymptomatic infants. The company has collected observational yet unpublished data showing that one-third of vaginally born and breastfed babies, who tend to be the healthiest, are missing critical bacteria such as Bifidobacteria, which are important for immune system development in early childhood.

At-home microbiome tests allow consumers to collect varying amounts of stool and ship samples to a laboratory that will send back a report. One example, BiomeFx’s report, classifies the diversity and richness of your microbiome—markers generally associated with good health—and describes pathogenic microbes that may be out of range. It examines bacteria, parasites, and yeast and details whether keystone species are out of range.

“When you’re in these first three years of life, it’s really critical to check in,” Sukhum told The Epoch Times. “The microbiome has a huge impact on the rest of your health.”

Experts have long been concerned about the effects of processed food, environmental pollutants, and medication, especially antibiotics, that can cause the loss of healthy microbes.

Tiny Health combines its test results with consultations with functional health coaches who may tell you what to eat or avoid eating, as well as what probiotics and supplements to take. Additional lifestyle advice about sleeping and stress management might also be suggested.

Gastroenterologist and researcher Dr. Sabine Hazan takes a more conservative position, saying consumer testing should be limited to patients who are undergoing a fecal microbiota transplant for an overgrowth of Clostridioides difficile (C. difficile), a bacterium that can cause severe diarrhea and other intestinal problems.

The Food and Drug Administration (FDA) has approved two fecal transplant products for use with C. difficile. Patients with the bacterial infection may be interested in regular at-home microbiome tests alongside their medical treatment to track changes in their gut bacteria over time. The goal of the transplant is to graft new beneficial microbes into their microbiome, and testing can help observe this process.

Jackson, who is a molecular geneticist and a leading expert in the gut microbiome, noted that, in limited circumstances, he considers testing potentially useful. Such situations include when one is embarking on a lifestyle change, such as a radically different diet or preparing for a medical procedure, such as a fecal microbiota transplant, cancer treatment, or even a course of antibiotics.

“These are situations and scenarios in your life when you may want to monitor things over time,” he said, noting that customers ought to be aware that there are many nuances not only in the microbiome test findings but also in the way the tests are conducted.

Test Results Vary Widely

As part of a research study, Jackson ordered three microbiome tests from seven different companies, disguising his identity and submitting the same stool sample from a human gut microbiome reference developed by the National Institute of Standards and Technology.

“Not surprisingly, the results were all over the place, and each company gave strikingly different results from the next. At least one company measuring the same sample three times gave strikingly different results, which is really alarming,” he said.

The industry doesn’t have any testing standards. Each step in the testing process could be tainted, according to an editorial in The Lancet Gastroenterology and Hepatology. Some reasons are:

• Use of different collection, storage, processing, and analysis methods across labs
• Use of different chemicals in kits to stabilize the samples during transit
• Use of various technologies and software to identify microbes
• Use of different data sets for comparison—some labs may compare results with those of customers with chronic diseases rather than a healthy standard
• Use of varying styles of reports on findings
• Presence of conflicts of interest when companies selling reports also sell supplements or food plans

Downstream, discrepancies may cause invalid clinical recommendations. The Lancet editorial writers said that recommended interventions given to customers as part of the test ought to be the result of “rigorous randomised trials.”

The authors suggested that products should clearly state they are not intended for medical use or people with chronic conditions and that the testing process should be standardized—from sample collection to reporting.

Another exploration of at-home microbiome tests found issues with the standardization of terminology. Companies use terms such as “high,” “low,” “favorable,” and “average” to describe levels of microbes without providing a key or reference that allows users or doctors to quantify the microbes in a meaningful way.

The article emphasized that although at-home test reports don’t need to explain every technical detail, both patients and health care professionals deserve clear, informative results. Without knowing how the data were gathered and analyzed, the authors wrote, “it is impossible to interpret microbiome data.”

Different Tests, Different Results

There are two types of metagenomic consumer microbiome tests: one that tells you the composition of microbes and another that offers a deeper perspective on the function of your microbes.

The type of functional testing that can collect DNA data on microbes is called shotgun metagenomics. One example of what this testing can reveal is whether someone’s microbiome lacks bacteria for fiber digestion, which could cause symptoms such as gas, bloating, constipation, and diarrhea, according to Sukhum.

More cursory in nature, 16S sequencing tends to be cost-effective but offers a more reductive assessment of microbial diversity without functional insights. It is less accurate about species-level bacteria and doesn’t include fungi and parasites.

“You’ll get your unique microbial fingerprint, but it will be really hard to know what it’s doing,” Sukhum said.

Doctors who offer microbiome tests typically use culture-based stool tests that incubate microbes from your stool sample in a petri dish or targeted polymerase chain reaction tests to quantify common pathogens. These testing styles are limited to a more narrow perspective of the microbiome—a point of contention for those in favor of the technology.

The Debate Over At-Home Microbiome Tests

Experts in favor of direct-to-consumer testing claim that enough is known about some microbes for patients and providers to discover potential problems, and they’ve said that personal testing will help advance microbiome knowledge.

Personal microbiome tests can increase visibility of the field and improve willingness to participate in research, according to Krystal Thomas-White, a senior scientist at Evvy, a company that makes tests.

“From a provider perspective, there is a growing scientific and medical understanding that the presence of certain combinations of organisms can cause health issues, and a frustration that physicians are treating the symptoms without understanding the underlying cause,” Thomas-White wrote in a rebuttal to one of several editorials calling for regulation of direct-to-consumer microbiome testing.

Jackson countered that microbiome testing can mislead and overwhelm patients, especially those with significant gastrointestinal distress who feel let down by the traditional medical system. Desperate for answers, they may turn to testing, only to be misled by promises the tests can’t deliver on—and that, he warned, can lead to harmful or ineffective treatments.

Jackson said there can be conflicts of interest when companies sell both the test and the recommended probiotics.

The FDA has not approved any consumer microbiome tests. That means the test cannot be used to diagnose or treat a disease—a legal disclaimer that all microbiome tests should include.

The Role of Patients

Hazan suggested that people research companies and ask how they verify their tests and avoid following the advice of social media influencers. Patients can do more to advance the science by participating in clinical research.

Sukhum said that although it’s ideal to have decades of research before clinical applications become the norm, there is already enough evidence showing strong correlations between health conditions and the gut microbiome to support some interventions.

“You can’t deny that there’s a really strong relationship here, and it’s not an area we can ignore,” she said.