Microbiome diversity is one of the most frequently discussed measurements in gut-health research.
This article is part of the AKK Knowledge Centre, our guide hub for gut health, Akkermansia and microbiome research.
You may have seen claims such as:
“A diverse microbiome is a healthy microbiome.”
There is some truth behind the idea — but it is too simple.
Higher gut microbiome diversity is often associated with certain healthy dietary and lifestyle patterns, but a higher diversity score is not automatically proof of better gut health.
A microbiome can be diverse and still contain undesirable features.
Another microbiome can have lower measured diversity while functioning well for that individual.
The most useful approach is to treat diversity as one ecological measurement among many, not as a universal health grade.
Key Takeaways
- Microbiome diversity describes the variety and distribution of microorganisms in a sample.
- Alpha diversity measures diversity within a microbial community.
- Beta diversity compares differences between microbial communities.
- Lower diversity is associated with several disease states, but association does not prove that low diversity caused disease.
- Higher diversity has not been proven to be universally healthier.
- Antibiotics, diet, age and environment can all change diversity.
- Function, resilience and host health matter alongside diversity.
- Consumer microbiome diversity scores should not be treated as medical diagnoses.
What Is Alpha Diversity?
Alpha diversity describes variation within one sample.
It can reflect:
- how many different microbial groups are detected,
- how evenly those organisms are distributed,
- or a combination of richness and evenness.
Researchers use several mathematical indices, including:
- Shannon index,
- Simpson index,
- Chao1,
- observed species or ASVs.
These different methods measure slightly different ecological properties.
That means two microbiome reports can calculate “diversity” differently.
What Is Beta Diversity?
Beta diversity measures how different two microbial communities are from each other.
For example, researchers may compare:
- people following two different diets,
- samples before and after antibiotics,
- people with a condition versus controls,
- or one person's microbiome across time.
A significant beta-diversity difference means the communities differ in overall composition.
It does not automatically mean one is healthier.
Why Did Diversity Become Associated With Health?
Many observational studies found reduced microbial diversity in people with certain diseases or highly disrupted microbiomes.
Antibiotics can also sharply reduce microbial richness and change community structure.
Meanwhile, diets containing a greater range of fermentable plant substrates are often associated with broader microbial functions.
These observations encouraged the idea that greater diversity may represent ecological resilience.
But the relationship is not universal.
Higher Diversity Is Not Automatically Better
A 2025 review in Nature Reviews Gastroenterology & Hepatology on antibiotic-perturbed microbiota highlighted an important distinction:
Although low diversity is associated with several diseases, higher diversity has not been causally linked to good health in the host.
That matters.
A microbial ecosystem should be evaluated in relation to:
- function,
- resilience,
- metabolic outputs,
- host symptoms,
- immune status,
- and the surrounding environment.
A diversity score alone does not provide that information.
What Is Microbiome Resilience?
Resilience describes the ability of a microbial ecosystem to withstand or recover from disruption.
For example, the microbiome may change after:
- antibiotics,
- infection,
- major dietary change,
- travel,
- or illness.
A resilient ecosystem can often move back toward a stable state.
This may be more biologically meaningful than having the maximum number of detected species at one point in time.
Can a Diverse Microbiome Still Be Unhealthy?
Yes.
Imagine a microbial community containing many different organisms, including organisms associated with inflammation or infection.
The community could technically be highly diverse.
That does not automatically make it desirable.
Ecology depends on who is present, what they are doing, where they are located and how the host responds.
Can a Low-Diversity Microbiome Be Healthy?
Potentially.
Normal diversity varies with:
- age,
- geography,
- diet,
- population,
- sampling method,
- and body site.
Some microbial communities naturally have lower diversity than others.
For example, the infant microbiome is very different from the adult microbiome.
A low numerical diversity score should therefore not be interpreted without context.
What Changes Gut Microbiome Diversity?
Antibiotics
Antibiotics can sharply alter microbial community structure and reduce some populations.
Recovery varies between people.
Diet
Diet changes which substrates are available to microbes.
A varied diet can support a wider range of microbial metabolic pathways.
Age
Microbial communities change across infancy, adulthood and older age.
Illness and Medication
Many medications and diseases are associated with microbial changes.
Environment and Geography
Urbanisation, sanitation, food systems and local lifestyle influence microbiome composition.
Sleep and Exercise
Both are associated with microbiome differences, although human intervention results are not always consistent.
Do More Plant Foods Increase Diversity?
Plant foods provide many different:
- fibres,
- resistant carbohydrates,
- polyphenols,
- and other compounds.
These can support different microbial metabolic pathways.
This is one reason dietary diversity is commonly recommended for gut health.
However:
plant diversity does not guarantee a specific microbiome diversity score.
Individual responses still vary.
Does a High-Fibre Diet Always Increase Diversity?
No.
Fibre effects depend on:
- fibre type,
- dose,
- habitual diet,
- baseline microbiome,
- and study duration.
Some fibres selectively increase particular bacterial groups without dramatically increasing overall diversity.
That may still be beneficial.
What Happens to Diversity After Antibiotics?
Antibiotics can cause substantial short-term disruption.
Some microbial populations recover quickly.
Others can take longer.
Some may not return to their previous detectable level during the study period.
Recovery also differs depending on:
- antibiotic class,
- dose,
- duration,
- prior exposure,
- baseline microbiome,
- diet,
- and the individual.
This is why “restoring diversity” is not a simple one-product problem.
Do Probiotics Restore Microbiome Diversity?
Not necessarily.
Specific probiotics can reduce the risk of certain antibiotic-associated adverse effects.
But a major 2025 review concluded that current evidence does not support the general claim that probiotics restore the antibiotic-disrupted microbiota to its pre-antibiotic state.
A probiotic can have a clinical benefit without “rebuilding the microbiome.”
These are different questions.
Can You Increase Diversity With a Supplement?
There is no universal supplement proven to maximise healthy microbial diversity.
Prebiotics can selectively stimulate microorganisms.
Probiotics deliver defined live microorganisms.
Postbiotics deliver inactivated microorganisms or their components with demonstrated benefits.
But none of these concepts means:
“more species is always the goal.”
What Should Matter More Than a Diversity Score?
A more complete gut-health picture considers:
- gastrointestinal symptoms,
- digestion,
- bowel function,
- barrier function,
- microbial metabolites,
- resilience,
- immune interactions,
- and overall health.
Diversity is useful for research because it summarises ecological structure.
It is not a complete measure of how the system functions.
Should You Compare Your Diversity Score With Other People?
Be careful.
Different commercial microbiome companies may use:
- different sequencing methods,
- different sample processing,
- different databases,
- different algorithms,
- and different reference populations.
A “72/100 diversity score” from one service may not be directly comparable with a score from another.
Even repeat samples from the same person can vary.
Frequently Asked Questions
Is higher microbiome diversity better?
Not automatically. Higher diversity is sometimes associated with healthy patterns, but it is not a universal measure of health.
What is a good microbiome diversity score?
There is no single clinically accepted consumer diversity score that defines a healthy gut for everyone.
Can diet improve microbiome diversity?
Diet can alter microbiome structure and function. A varied diet provides a wider range of substrates, but individual responses vary.
Do antibiotics reduce diversity?
They can substantially disrupt microbial composition and often reduce certain measures of diversity, although the effect depends on the antibiotic and individual.
Do probiotics increase diversity?
Not necessarily. Probiotic benefits are strain- and outcome-specific and do not require an overall increase in diversity.
The Bottom Line
Microbiome diversity is useful — but it is not the same thing as gut health.
A higher diversity score can sometimes reflect a richer ecological community, but scientists cannot simply rank every person from “low diversity = bad” to “high diversity = good.”
A better goal is a gut ecosystem that is functional, resilient, adaptable and compatible with normal gastrointestinal health.
Continue Learning
- What Is the Gut Barrier?
- Is akkermansia naturally present in everyone?
- How the gut microbiome relates to metabolic health
Selected Scientific References
- Szajewska H, Scott KP, de Meij T, et al. Antibiotic-perturbed microbiota and the role of probiotics. Nature Reviews Gastroenterology & Hepatology. 2025.
- Marco ML, Cunningham M, Bischoff SC, et al. The International Scientific Association for Probiotics and Prebiotics consensus statement on the definition and scope of gut health. Nature Reviews Gastroenterology & Hepatology. 2026.
Educational Disclaimer
This article is for general education only and should not be used to diagnose gut or microbiome disorders.