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Microbiome-Targeted Medicines

An overview of medicines that aim at the microbiome, from the two FDA-approved products to investigational consortia, phages and fecal transplant uses.

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

The big picture

A microbiome-targeted medicine is a treatment designed to change the community of microbes in the body in order to prevent or treat a disease. A 2026 review groups them as additive (adding microbes: fecal transplant, live biotherapeutics, defined consortia), subtractive (removing a target: targeted antibiotics, bacteriocins, phages, CRISPR-based antimicrobials) and modulatory (changing host and microbe interactions such as bile acid metabolism and spore germination). C. difficile infection is called the most extensively studied model. [1] Evidence labels: approved medicine, promising but limited, mixed, insufficient evidence.

What is still investigational

ApproachCondition studiedBest evidence readLabel
Donor-stool productsRecurrent C. difficileRandomized trials; US-approved products [5][6]approved medicine
Defined consortium (VE303)C. difficile recurrencePhase 2, 79 adults [7]promising but limited
FMTUlcerative colitisMeta-analysis of 16 trials [8]promising but limited
FMTIrritable bowel syndrome13 trials, very low certainty [9]mixed
FMT plus immunotherapyMelanoma20-person single-arm trial [10]insufficient evidence
Single-species product (Akkermansia)Insulin resistanceSmall pilot [11]promising but limited
PhagesResistant infectionsMixed trials [12][13]mixed

See Fecal Microbiota-Based Therapies, Defined Microbial Products and Bacteriophage Research.

Why the field is hard

  • The microbiome varies person to person, and apparent links to disease may reflect lifestyle or medicines rather than cause. See Microbiome Studies: Association vs Causation.
  • Products differ: donor-stool, spores, single species, and phages are not interchangeable, and one approval does not carry over to another.
  • Small trials and short follow-up are common. The Akkermansia trial enrolled 40 people for three months. [11]

How to evaluate claims

Ask which product, which condition, which regulator, and whether the study measured symptoms or only microbes. Supplements sold as "microbiome support" are not these medicines; see Probiotics vs Microbiota-Based Medicines and Live Biotherapeutic Products.

Frequently asked questions

Are there approved microbiome medicines?

In the US, FDA lists REBYOTA and VOWST for preventing recurrent C. difficile infection. [4]

Are probiotics microbiome medicines?

Not as a rule. NCCIH says in most instances it is unknown which probiotics help. [14]

Could microbiome medicines treat depression or obesity?

Not established. The trials read here concern infections, bowel disease, cancer treatment and a pilot in insulin resistance.

What does "additive, subtractive, modulatory" mean?

Adding microbes, removing a target microbe, or changing host-microbe interactions. [1]

Should I try a fecal transplant for another condition?

Speak with a specialist; the evidence outside C. difficile is still investigational.

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.

What is approved (United States)
FDA lists two fecal microbiota products: REBYOTA and VOWST, each to prevent recurrence of Clostridioides difficile infection in adults 18 and older after antibiotic treatment. [2][3] Read 2026-10-22. These are approved for that indication only. This section found no approved microbiome-targeted medicine for obesity, mood, autism, or most other conditions; FDA's page lists only these two. [4] Approval elsewhere was not verified.
Safety
Live-microbe products can cause infection; risk is greater in severe illness or weakened immunity per NCCIH, which was discussing probiotics. [14] FDA reported serious infections after a stool-bank FMT product in 2020. [15] These medicines belong under clinician supervision. This section gives no instructions for fecal transplant, culture or phage preparation.
References
  1. Microbiome-based therapeutics for C. difficile infection: additive, subtractive, and modulatory strategies. Gut Microbes 2026. PubMed 42657533. Read 2026-10-22.
  2. US FDA, REBYOTA product page. Read 2026-10-22.
  3. US FDA, VOWST product page. Read 2026-10-22.
  4. US FDA, Fecal Microbiota Products. Read 2026-10-22.
  5. SER-109, an oral microbiome therapy for recurrent Clostridioides difficile infection. NEJM 2022. PubMed 35045228. Read 2026-10-22.
  6. Final results from a phase 2b randomized, placebo-controlled trial of RBX2660. Infect Dis Ther 2023. PubMed 36544075. Read 2026-10-22.
  7. VE303, a defined bacterial consortium, for prevention of recurrent C. difficile infection: randomized clinical trial. JAMA 2023. PubMed 37060545. Read 2026-10-22.
  8. Fecal microbiota transplantation in ulcerative colitis: updated systematic review and meta-analysis. Adv Ther 2026. PubMed 41945234. Read 2026-10-22.
  9. Fecal microbiota transplantation for symptom improvement in irritable bowel syndrome: systematic review and meta-analysis. Gastroenterology 2026. PubMed 42162772. Read 2026-10-22.
  10. FMT with anti-PD1 in advanced melanoma: final results of the MIMic phase 1 trial. J Immunother Cancer 2025. PubMed 40759441. Read 2026-10-22.
  11. Supplementation with Akkermansia muciniphila in overweight and obese human volunteers: proof-of-concept exploratory study. Nat Med 2019. PubMed 31263284. Read 2026-10-22.
  12. Efficacy and tolerability of a cocktail of bacteriophages to treat burn wounds infected by Pseudomonas aeruginosa (PhagoBurn). Lancet Infect Dis 2019. PubMed 30292481. Read 2026-10-22.
  13. Intravesical bacteriophages for treating urinary tract infections in patients undergoing transurethral resection of the prostate. Lancet Infect Dis 2021. PubMed 32949500. Read 2026-10-22.
  14. NCCIH, Probiotics: Usefulness and Safety. Read 2026-10-22.
  15. US FDA, Safety Alert Regarding Use of FMT and Risk of Serious Adverse Events (March 12, 2020). 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.