Microbial Diversity and Health Associations
What microbial diversity means, what large studies link it to, and why a higher or lower diversity number is not a reliable measure of anyone's health on its own.
Content last updated . This page has not been medically reviewed.
What "diversity" means
In microbiome research, diversity describes how many different kinds of microbes a sample holds and how evenly they are spread. Richness is the simpler part: the count of different types. Studies report these numbers from DNA sequencing of a sample, usually stool. The question here is whether those numbers tell us anything about health. The honest answer so far is: they are linked with some health measures in some groups, and that link is an association, not proof of cause.Evidence labels used below: promising but limited, mixed, insufficient evidence, and preclinical (cells/animals only). A study that only finds two things occurring together shows an association. See Microbiome Studies: Association vs Causation.
What larger studies found
| Study | People | What it measured | What it found |
|---|---|---|---|
| Danish cohort, 2013 | 123 non-obese and 169 obese adults | Number of gut microbial genes (richness) | About 23% had low richness. They had more overall fat, insulin resistance, unhealthy blood fats and inflammation than the high-richness group. [1] |
| Population analysis, 2016 | Two cohorts of about 1,100 people each, plus global data | Gut genera and 69 clinical and questionnaire factors | A 14-genus core was found; stool consistency had the largest effect size and medication explained the largest share of total variance. [2] |
| Large cohort, 2020 | About 3,400 people | Gut microbes and about 150 host features | Both known and unknown links with blood markers and lifestyle; a putative diversity maximum along one major axis of variation. [3] |
The Danish study also reported that obese people in the low-richness group gained more weight over time. [1] It sampled a population of white adults, so it cannot be assumed to apply to everyone. Label: promising but limited.
Why the link is hard to interpret
- Other factors move both diversity and health. Matching cases and controls on host variables reduced differences in the microbiota and spurious disease associations in a 2020 analysis; alcohol intake and bowel movement quality were unexpectedly strong sources of variation. [4]
- Medications matter. Medication explained the largest share of variance in the 2016 population analysis. [2]
- Antibiotics lower diversity. In three people given ciprofloxacin, diversity fell within three to four days and the recovery was often incomplete. [5]
- Diet changes the community quickly. A short study of entirely animal-based or plant-based diets saw community structure change within days. [6]
- Time matters. Individual communities tend to stay stable over months to years, with fluctuation especially during disease and early development. [7][8]
A 2019 expert workshop concluded that mechanistic links between specific changes in gut microbiome structure and markers of human health are not yet established, and that normal ranges for microbiome-based indicators still need to be determined and validated. [9] Label: insufficient evidence for using a diversity number to judge an individual.
What this means for claims
- A "diversity score" on a consumer report is not a validated health measure on its own. Read Microbiome Scores and Indexes.
- More types of microbes is not automatically healthier, and fewer is not automatically a disease. The same 2019 workshop said dysbiosis (a shift away from a typical community) may be a cause, a consequence or both. [9] See Why There Is No Single Universal Healthy Microbiome.
- A diversity change after a food or supplement is a biomarker change, not a clinical outcome.
Frequently asked questions
Is high microbial diversity always good?
Not necessarily. Studies link low richness with some metabolic measures in one Danish group, [1] but experts say mechanisms linking microbiome structure with health markers are not yet established. [9]
What affects gut microbial diversity?
Medication, stool consistency, diet, alcohol use and antibiotics all showed links with gut microbiome composition or diversity in the studies above. [2][4][5]
Can I test my diversity and act on it?
Consumer scores are not validated for personal decisions. See the guide on commercial stool tests.
Does low diversity cause obesity?
That has not been shown. The Danish study found an association, which cannot show which came first. [1]
More details: evidence, limits and cautions
The details behind this page: cautions, limits of the evidence and where sources disagree. Open any note to read it.
Safety note
References
- Le Chatelier E et al. Richness of human gut microbiome correlates with metabolic markers. Nature 2013. PubMed 23985870. Read 2026-10-22.
- Falony G et al. Population-level analysis of gut microbiome variation. Science 2016. PubMed 27126039. Read 2026-10-22.
- Manor O et al. Health and disease markers correlate with gut microbiome composition across thousands of people. Nat Commun 2020. PubMed 33060586. Read 2026-10-22.
- Vujkovic-Cvijin I et al. Host variables confound gut microbiota studies of human disease. Nature 2020. PubMed 33149306. Read 2026-10-22.
- Dethlefsen L, Relman DA. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. PNAS 2011. PubMed 20847294. Read 2026-10-22.
- David LA et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature 2014. PubMed 24336217. Read 2026-10-22.
- Faith JJ et al. The long-term stability of the human gut microbiota. Science 2013. PubMed 23828941. Read 2026-10-22.
- Lozupone CA et al. Diversity, stability and resilience of the human gut microbiota. Nature 2012. PubMed 22972295. Read 2026-10-22.
- McBurney MI et al. Establishing what constitutes a healthy human gut microbiome: state of the science, regulatory considerations, and future directions. J Nutr 2019. PubMed 31373365. Read 2026-10-22.