What your gut microbiome diversity score means

Two kinds of diversity

Alpha diversity describes the variety within your own sample: how many different types of microbes were found, and whether a few dominate or many share the space. This is usually the headline score. A common version is the Shannon index, which combines richness and evenness into a single number.

Beta diversity describes how different your sample is from another, such as a reference population or your own earlier test. Some reports show this as a dot on a scatter plot. It can help show whether your gut community has shifted over time, but it does not tell you whether the shift is good or bad.

Why scores are hard to compare

• Labs use different sequencing methods, such as targeted 16S sequencing or whole-genome (shotgun) sequencing
• Different indices produce different numbers on different scales
• Percentile rankings are usually based on the company's own customers, not a representative population
• A single stool sample varies from day to day with what you ate and how your gut was moving
• Shipping time and sample handling can affect results

What tends to raise diversity

The American Gut Project, a large citizen-science study, found that the number of different plant types people ate each week was more closely related to their microbiome than labels like vegan or omnivore. People eating more than 30 different plant foods a week had more diverse gut microbes than those eating 10 or fewer, and more microbes associated with producing short-chain fatty acids.

That is an association from an observational study, but it fits with what is known about how gut microbes feed on different fibers. Variety across vegetables, fruits, legumes, whole grains, nuts, seeds, herbs and spices all counts.

What tends to lower it

In the same study, recent antibiotic use was linked with lower microbial diversity. Other factors commonly associated with lower diversity include low-fiber diets, some medications such as acid-suppressing drugs, heavy alcohol use and older age, though findings vary between studies.

A large study of Hispanic and Latino adults also found that postmenopausal women had somewhat lower gut microbiome diversity than premenopausal women.

Why one number is not a diagnosis

Low diversity has been associated with many conditions in research, from inflammatory bowel disease to obesity. Because it is linked to so many things, it cannot point to any one of them. And plenty of healthy people have lower scores, while some people with disease have high ones.

An international consensus statement on microbiome testing published in 2025 concluded that evidence for the clinical usefulness of microbiome testing is still limited, and that direct-to-consumer tests lack proven clinical value. Your diversity score is best treated as context, not a verdict.

Other parts of the report

Beyond diversity, reports often list the relative abundance of particular bacteria, predicted functions such as the potential to make short-chain fatty acids, and sometimes pathogen screens. Predicted functions are inferred from which genes or organisms are present; they are not direct measurements of what your gut is producing.

Lists of "good" and "bad" bacteria are an oversimplification. The same species can behave differently depending on the rest of the community and on what you eat. Your clinician will focus on findings that have a clear practical meaning and will not prescribe treatments based on a single species.

How to read your report

• Note which index and method the lab used, so you can compare like with like if you retest
• Look at the score alongside your diet and recent medications, especially antibiotics
• Treat percentiles as rough guides, not population norms
• Focus on actionable patterns, such as a very low-fiber diet, rather than individual species
• Ignore any claim that a score diagnoses a specific disease

Should you retest?

Retesting makes sense only if you have made a deliberate change, such as substantially increasing plant variety for several months, and you want to see whether your community shifted. Use the same lab and method, and collect under similar conditions.

Probiotic supplements are often sold to raise diversity, but most contain a few strains and do not reliably change overall diversity. Diet variety is the more consistent lever.

How HealifyMD uses the score

Your clinician reviews the score as one piece of context alongside your symptoms, diet and other health information, and explains its limits. If you have digestive symptoms or red flags, standard evaluation comes first. The Gut Biome Analysis is $625 as a one-time test, confirmed after your eligibility review. Labs are priced separately from treatment, and there is no membership fee.