Digestive Health: At-Home Microbiome Testing
By Densie Webb, PhD, RD
Today’s Dietitian
Vol. 25 No. 5 P. 10

Is it ready for clinical practice?

Research demonstrating an association between the gut microbiome and overall health keeps getting stronger. Over the last couple of decades, the state of the gut microbiome has been linked to everything from obesity and diabetes to inflammatory bowel disease and cognitive decline.

The gut contains a thriving community of trillions of bacteria that can either reduce or increase inflammation, produce needed vitamins and hormones or not, and send healthy or unhealthy signals to the brain. Dysbiosis occurs when the gut microbiome shifts away from healthy microbes and is populated with more disease-causing bacteria.

Testing for the composition of the microbiome could, in theory, provide a window to view potential health risks. Some research has deemed particular gut microbiome profiles/species as being pathogenic or protective. For example, some profiles are associated with obesity. Certain diet patterns also are linked to different profiles.

Microbiome Tests
One of the keys to good health, according to research, is to prevent dysbiosis by maintaining a balance between the so-called “good bacteria” and “bad bacteria” that make up the microbiome community. But that community is invisible to the naked eye, making it impossible to know what’s going on in the intestinal tract. Enter at-home microbiome tests.

Like at-home tests for colon cancer screening, at-home microbiome tests provide a scooper or swab to get a small stool sample to be mailed to a lab. After a few weeks, a report featuring the individual’s microbiome profile is sent back through the mail. The report indicates whether there’s an increased risk of certain diseases and disorders. It also may provide dietary and supplement recommendations (sometimes supplements developed by the test manufacturer) to improve the microbiome and overall health.

Several companies, including Day-Two, Zoe, Floré, Biohm, Ombre, Viome, Thorne, Wellnicity, and Verisana, offer microbiome tests, with prices ranging anywhere from $49 to $350. However, there’s little research to demonstrate the relevance of such tests.

“The problem is not that the tests are scientifically problematic, but more that their practical utility remains very unclear,” says Amy Loughman, PhD, MPsyc, senior research fellow at the Food & Mood Centre at The Institution for Mental and Physical Health and Clinical Translation in Melbourne, Australia. “Even if the test shows a low abundance of ‘good’ bacteria, we don’t know whether it’s possible to increase abundance of a particular microbe with a probiotic or other intervention in a long-lasting way, or how the effects that change could have on the rest of the community.”

Loughman says some of the tests identify the relative abundance of bacteria at the genus level but not the species level. Other tests identify which strains of microbes, including viruses and fungi, and their functions, are present. That’s important because microbes act differently at the strain level, she says.

Alexander Khoruts, MD, a professor of medicine at the University of Minnesota, has written that the definition of what constitutes a healthy microbiome, ie, which specific microbes should be present to improve health and prevent disease, has yet to be determined, adding that examples of specific microbiome profiles haven’t been established to reliably predict whether someone will develop a specific disease.1 To put at-home test results in perspective, there would need to be a standard against which an individual’s results are compared, similar to those for blood glucose, cholesterol, and bilirubin, for example. Currently, there’s no such standard for the microbiome. The fact that the composition of the microbiome varies greatly among individuals—even between twins—complicates matters.2

While there’s a plethora of research on the bacteria that make up the microbiome and its association with health and disease, there isn’t an empirical study that examines the validity or utility of these tests. “It’s perhaps telling that companies offering these home tests haven’t published any data on their utility,” Loughman says.

Diet and the Microbiome
Research shows that the gut microbiome responds rapidly to alterations in the diet.3 As a result, these at-home tests—even if accurate—are simply a snapshot of the makeup of the gut at a single point in time. Robert Allen, PhD, a professor of molecular biology and microbiology at Baylor College of Medicine in Houston, says it’s unrealistic to believe it’s possible to make dietary or supplement recommendations based on the results of a microbiome profile that will be relevant across time.

Nevertheless, research has demonstrated that the microbiome can affect blood glucose control. In what Loughman labels a “flagship study,” researchers in Israel showed that short-term personalized dietary interventions based on an algorithm that included parameters such as dietary habits, physical activity, and gut microbiota successfully lowered postmeal glucose.4

Current at-home tests can’t provide such sophisticated analysis. Moreover, Britton says, “There’s no single way that’s ideal to analyze a microbiome.” In other words, results from one test or one study using one type of analysis shouldn’t be compared with another test or study using a different methodology. However, among people with type 2 diabetes, it may be possible in a research setting to analyze gut microbes and tailor their diets to keep blood glucose under control.5

The mechanisms for the effect that microbiome changes have on blood glucose are believed to include alterations in bile acid metabolism, short-chain fatty acid production, gut hormone secretion, and branched-chain amino acid circulation.6

What the Future Holds
Experts agree that “we’re not there yet” in terms of home tests being reliable resources to analyze the microbiome and make specific recommendations based on the results. Loughman says these testing services are based on science that’s still in its infancy. However, while their current state isn’t ideal, she believes microbiome testing will become useful once sufficient evidence has been gathered.

While the tests hold promise, Loughman says that, for now, knowing what’s in your gut is mostly a curiosity and not a useful predictive or diagnostic tool. At some point, however, it does seem like microbiome testing, diagnosis, and subsequent dietary prescriptions will be part of the medical landscape.

“With additional research and clinical validation, we’ll be able to have some tests that use the microbiome for predicting health and disease,” Britton says.

In the meantime, RDs should continue to recommend diets that have been shown to produce healthy microbiomes. “The evidence points to a wide variety of dietary fiber being important to include in one’s diet, and that the Mediterranean diet is associated with seemingly positive microbiome compositions,” Loughman says.

— Densie Webb, PhD, RD, is a freelance writer, editor, and industry consultant based in Austin, Texas.

1. Khoruts A. A clinician’s guide to microbiome testing. KevinMD website. https://www.kevinmd.com/2018/12/a-clinicians-guide-to-microbiome-testing.html. Published December 17, 2018. Accessed February 2, 2023.

2. Vilchez-Vargas R, Skieceviciene J, Lehr K, et al. Gut microbial similarity in twins is driven by shared environment and aging. EBioMedicine. 2022;79:104011.

3. David LA, Maurice CF, Carmody RN, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2014;505(7484):559-563.

4. Zeevi D, Korem T, Zmora N, et al. Personalized nutrition by prediction of glycemic responses. Cell. 2015;163(5):1079-1094.

5. Ciubotaru I, Green SJ, Kukreja S, Barengolts E. Significant differences in fecal microbiota are associated with various stages of glucose tolerance in African American male veterans. Transl Res. 2015;166(5):401-411.

6. Utzschneider KM, Kratz M, Damman CJ, Hullar M. Mechanisms linking the gut microbiome and glucose metabolism. J Clin Endocrinol Metab. 2016;101(4):1445-1454.