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Gut Microbiome Research: What Is Known

An overview of what gut microbiome research has established, what it links to health, which microbiome-based medicines are approved, and what is still unproven.

Content last updated . This page has not been medically reviewed.

Where the field stands

The gut holds the largest and best-studied human microbial community. Research there has produced solid descriptions of what the community looks like, a small number of approved medicines, and a much larger body of associations that have not been shown to be causes. Evidence labels used on this page: approved medicine, established, promising but limited, insufficient evidence and preclinical (cells/animals only).

What is reasonably well established

  • The gut community is individual and fairly steady. Healthy people differ widely in their gut microbes, [1] and in 37 US adults followed for up to five years most strains looked like residents for decades. [2] Label: established.
  • It responds to disturbance. In a small study of three people, ciprofloxacin cut diversity within three to four days, and communities often returned only incompletely. [3] Label: established as an observation in small samples.
  • It responds to diet in the short term. In a feeding study, entirely animal-based or entirely plant-based diets changed community structure within days. [4] This is a change in microbes, not a health outcome.
  • Everyday factors explain much of the variation. Stool consistency showed the largest effect size and medication explained the largest share of variance in a population analysis. [5]

What it is linked with, without proof of cause

A Danish study found that adults with low gut bacterial richness (about 23% of the group) had more overall fat, insulin resistance and inflammation than those with high richness. [6] A study of about 3,400 people found gut microbes associated with roughly 150 host features, including lifestyle and blood markers. [7] When cases and controls were matched on lifestyle and physiology, apparent disease associations shrank. [8] Label: promising but limited. See Microbiome Studies: Association vs Causation.

Experts reviewing the field in 2019 concluded that it is not established whether dysbiosis is a cause, consequence or both of changes in gut function and disease. [9]

Probiotics and other products

The US National Center for Complementary and Integrative Health says much remains to be learned about whether probiotics are helpful and safe for various conditions, and that in most instances it is still unknown which probiotics help and which do not. [12] The NHS says probiotics may help ease some symptoms of irritable bowel syndrome, but there is little evidence for many health claims. [13] Label: mixed. Ingredient guides are in Supplements; start with Probiotic Supplements Explained.

Why results are hard to compare

Gut studies vary in sample type, DNA extraction, handling and analysis, and these choices explained most variation in a 15-laboratory comparison. [14] A reporting checklist (STORMS) exists to improve consistency. [15]

What is not yet shown

Frequently asked questions

What is the gut microbiome?

It is the community of microbes in the digestive tract. The word "microbiome" means the community of microorganisms in a particular environment. [16]

Is a fecal transplant an approved treatment?

In the United States, FDA-listed fecal microbiota products are indicated to prevent recurrence of C. difficile infection in adults after antibiotic treatment. [10][11] This is a medical treatment decided with a clinician.

Do probiotics fix the gut microbiome?

Not reliably. NCCIH says it is mostly unknown which probiotics help for which conditions. [12]

Does low diversity mean poor health?

Low richness was linked with some metabolic measures in a Danish study, but this is an association. [6]

Can a gut microbiome test tell me what to eat?

Not in a validated way. Experts say normal ranges and validated microbiome indicators are still needed. [9]

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.

Approved medicines that act on the gut community
Two products made from human stool microbes are on the US FDA list of biologic products. This is approved medicine for one specific use:
  • REBYOTA (fecal microbiota, live-jslm) is indicated to prevent recurrence of Clostridioides difficile infection in people 18 and older, after antibiotic treatment for recurrent infection. [10]
  • VOWST (fecal microbiota spores, live-brpk) has the same type of indication for adults 18 and older. [11]

Both statements come from the FDA's own product pages, read 2026-10-22, and apply to the United States only. They do not mean that other uses, other products or do-it-yourself preparations are safe or effective. This guide gives no instructions for fecal transplants. Learn more in Fecal Microbiota-Based Therapies.

Safety note
Persistent diarrhea, blood in the stool, unexplained weight loss or severe abdominal pain need medical assessment, not a microbiome product. People with weakened immune systems should talk with their clinician before taking live-microbe products. For everyday digestion see Gut and Digestive Health.
References
  1. Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature 2012. PubMed 22699609. Read 2026-10-22.
  2. Faith JJ et al. The long-term stability of the human gut microbiota. Science 2013. PubMed 23828941. Read 2026-10-22.
  3. 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.
  4. David LA et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature 2014. PubMed 24336217. Read 2026-10-22.
  5. Falony G et al. Population-level analysis of gut microbiome variation. Science 2016. PubMed 27126039. Read 2026-10-22.
  6. Le Chatelier E et al. Richness of human gut microbiome correlates with metabolic markers. Nature 2013. PubMed 23985870. Read 2026-10-22.
  7. 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.
  8. Vujkovic-Cvijin I et al. Host variables confound gut microbiota studies of human disease. Nature 2020. PubMed 33149306. Read 2026-10-22.
  9. 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.
  10. US FDA, REBYOTA product page. Read 2026-10-22.
  11. US FDA, VOWST product page. Read 2026-10-22.
  12. NCCIH, Probiotics: Usefulness and Safety. Read 2026-10-22.
  13. NHS, Probiotics. Read 2026-10-22.
  14. Sinha R et al. Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium. Nat Biotechnol 2017. PubMed 28967885. Read 2026-10-22.
  15. Mirzayi C et al. Reporting guidelines for human microbiome research: the STORMS checklist. Nat Med 2021. PubMed 34789871. Read 2026-10-22.
  16. National Human Genome Research Institute, Talking Glossary: Microbiome. Read 2026-10-22.
Education, not medical advice. This page is for general information. It does not diagnose or treat any condition and is not a substitute for care from a qualified health professional. Natural does not automatically mean safe. Ask a clinician or pharmacist before changing your care, especially if you take medication, are pregnant or breastfeeding, or have a health condition.