There is a great deal of excitement around microbiome research as it confirms, and debunks, long-held beliefs. Investigators have shown, for example, that proton-pump inhibitors can alter the microbiome’s composition and that interventions such as fecal microbiota transplants may support engraftment of beneficial organisms. Yet these findings pose a challenge to gastroenterologists seeking to determine how best to translate into concrete clinical advice.
Despite this uncertainty, numerous at-home microbiome testing companies have already entered the market, offering kits to the public, typically priced between $100 and $500. Many are eligible for health savings accounts or flexible spending accounts, which may give an unwarranted sense of clinical legitimacy.
Because many companies also sell probiotics or prebiotics based on test findings, their utility can be misleading. At best, these tests reveal microbiome imbalances that prompt helpful dietary changes; at worst, they open the door to unnecessary purchases.
Tests Clinically Useful?
Gastroenterologists are increasingly fielding questions from patients about these at-home tests. This makes it more critical than ever to weigh their clinical value when deciding whether they have a role in medical decision-making.
Najwa El-Nachef, MD, a gastroenterologist at Henry Ford Health Hospital in Detroit told Medscape Medical News that diagnosing conditions such as inflammatory bowel disease or irritable bowel syndrome requires far more than an at-home stool test.For inflammatory bowel disease, clinicians still must obtain a detailed family history, evaluate symptoms, and perform a colonoscopy for direct visualization of inflammation. “Lab markers are supportive, but you need the endoscopic diagnosis,” she said. Irritable bowel syndrome is even more nuanced, she added, because it often does not appear endoscopically and is “almost always” a diagnosis of exclusion.
While diagnostic tools continue to evolve, at-home microbiome tests currently on the market are “not clinically validated” for these conditions, El-Nachef noted.
Max Brondfield, MD, a gastroenterologist at the University of California San Francisco, who specializes in celiac disease, agrees that these tests lack clinical value for diagnosing or treating this condition. They may, however, offer limited utility as part of a broader evaluation for suspected small intestinal bacterial overgrowth (SIBO).
At-home microbiome tests analyze stool, which extrapolates information from across the entire intestinal tract. But the small intestine and colon have different biomes, Brondfield noted, limiting the precision of these tests. Even so a test can identify dysbiosis in the microbiome, leading gastroenterologists to order a SIBO breath test or adjust treatment in a patient already diagnosed with SIBO who is not improving.
In many cases though, a standard stool test ordered by a gastroenterologist provides equivalent or better clinical information.
“It’s fair to say for most of the conditions I’m treating, a standard stool test will do,” Brondfield said.
Testing Methods Lead to Quality Concerns
At-home microbiome tests use varying sequencing methods, such as shotgun metagenomics or 16S rRNA sequencing. Crucially, they do not analyze metabolomics, a key component in understanding how the microbiome actually affects the gastrointestinal tract, El-Nachef noted.
Brondfield added that proprietary technologies used with these tests make it difficult to assess quality or transparency. Shotgun metagenomic analysis can be particularly oversensitive, leading to false positives for different infections.
“Shotgun metagenomics are capturing every scrap in [the intestinal track], and that’s not necessarily relevant,” Brondfield said. “I generally prefer standardized lab tests because they’re more transparent.”
However, Brondfield has ordered one type of at-home microbiome test, Genova Diagnostics, for some patients. Available by physician order only, this test serves as a diagnostic tool, and they only sell diagnostic tests, not supplements.
Both Brondfield and El-Nachef cautioned clinicians and patients to be skeptical of companies that use microbiome testing as a means of selling additional products.
“If someone is selling a probiotic, I would worry about that recommendation,” El-Nachef said.
She also stressed that “healthy” microbiomes vary widely by geography, diet, and genetics. Results with an at-home test can even differ by the day for some individuals depending on what they ate.
Looking Ahead
El-Nachef is encouraged by emerging research on fecal microbiota transplants for ulcerative colitis and potentially Crohn’s disease, although the latter is comparatively less studied.
“Each paper on fecal transplant is a pearl of wisdom,” she said.
The wealth of incoming microbiome research can make it feel like “drinking from a firehose,” she noted, and it’s going to take time to incorporate these at-home microbiome tests in a meaningful way. She estimated it will take years to reproduce evidence on the microbiome and disease states in enough patient cohorts for true validation.
El-Nachef believes that this gap in evidence leaves clinicians and patients vulnerable to commercial hype, with private companies selling these products “taking advantage of interest in the field,” especially given the lack of strong clinical guidance.
However, she reassured her colleagues that they are not missing out by exercising caution in how they approach at-home microbiome tests.
“I tell almost the same thing to all of my patients,” she said. “The test provides interesting insider information, and if you’re interested in the data, you can do it, but it may not change our action plan.”
El-Nachef disclosed receiving grant funding from Takeda, AbbVie, and Abivax. Brondfield reported consulting for Ferring on behalf of REBYOTA.
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