Clinical success of live gut microbe transfer has led multiple pharmaceutical companies to attempt the development of microbiome drugs. The potential benefits and safety concerns associated with these drugs were discussed in a review published in The Journal of Infectious Diseases.

The most significant clinical benefits to date for patients with Clostridiodes difficile infection (CDI) has occurred with fecal microbiota transplantation (FMT). The benefits have included prevention of recurrence, decolonization, and treatment of active infection, making FMT the current standard recommended treatment for CDI.

Beyond CDI, FMT has shown positive results for decolonizing other pathogenetic microbes and may possibly be used as therapy for patients with gut antibiotic-resistant bacteria or recurrent urinary tract infections.

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On the basis of FMT success, several pharmaceutical companies have begun working toward developing and gaining approval for microbiome drugs. This process is not without challenges: discerning the optimal ecological interactions among a complex web of microorganisms is a substantial task. In addition, certain patients or disease conditions may require personalized microbiome drugs, and producing them entails unique logistical challenges.

The review authors highlighted 3 main aspects of microbiome drug development that remain significant roadblocks: safety, consistency, and delivery.

Safety is an important aspect of any drug development program. In this case, it is of particular importance because of long-standing safety concerns about FMT, primarily due to the Food and Drug Administration failing to impose mandatory safety standards. For the drug development process, a rigorous donor screening program combined with standardized processing measures must be formulated and implemented.

Another vital step in the drug developmental process would be to establish uniformity processes. Incidents of variable donor-based efficacy have been observed among patients treated for CDI or ulcerative colitis, but little is understood about the cause of this variation. A potential process for mitigating heterogeneity among donors would be to pool donor samples. This methodology, however, requires rigor testing.

The optimum delivery method for FMT has not been satisfactorily determined. FMT can be delivered via upper or lower endoscopies, naso-enteric tubes, enemas, or capsules with fresh, frozen, or thawed preparations. Further studies and new metrics are needed to determine which method would be the most efficacious and whether disease-specific delivery methods are required.

The review authors concluded microbiome drugs have the potential to transform patient care for microbe-mediated diseases. Despite the early clinical success of FMT, significant challenges remain for the effective translation of FMT to microbiome drug products.

Disclosure: Several authors declared affiliations with industry. Please refer to the original article for a full list of disclosures.


Geradin Y, Timberlake S, Allegretti JR, Smith MB, Kassam Z. Beyond fecal microbiota transplantation: developing drugs from the microbiome. J Infect Dis. Published online December 7, 2020. doi:10.1093/infdis/jiaa700

This article originally appeared on Infectious Disease Advisor