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  1. Focus Areas of Regulatory Science Report

Focus Area: Microbiome Research

Skin Microbiota
Gut Bacteria Microbiome

Importance to FDA

FDA regulates many products and devices that interact directly or indirectly with the human and animal microbiomes. Microbiota refers to the community of microbial species connected by physical location, inter-relationships of function, and microbiome to the collective genomes. For example, the human body’s microbiome is made up of trillions of beneficial, neutral, and pathogenic microbes.

FDA’s microbiome research spans microbiology, toxicology, nutrition, immunology, and antimicrobial resistance because animal and environmental microbiota play important roles in states of health and disease. Diet, antibiotics, drug and chemical residues in food, cosmetics, and metabolites of all of these factors may influence complex processes regulated by the microbiome that are important to human health. FDA regulates some products that are composed of or impact microbes and/or microbial communities, such as fecal microbiota for transplantation (FMT), live biotherapeutic products, live microbes in foods, dietary supplements, and tobacco products.


FDA researchers address key issues related to FDA-regulated products and their impact on the microbiota, often through studies of the microbiome.

  • Developing and using an animal model to assess FMT: Using infection by the gastrointestinal pathogen Clostridioides difficile (C. diff.) as a model, researchers are assessing safety methods, seeking to understand how manufacturing procedures alter microbial composition, and are working to identify biomarkers of an effective microbial community to assess the potency of FMT products. This work uses next generation sequencing methods and an animal (murine) model with a unique microbiome that is naturally resistant to C. diff.
  • Addressing the impact of FDA-regulated medical products on gut microbiota and natural immune response to highlight the different physical reactions to gut microbiota. Uncovering the gut microbiota response to a drug or biological product may help identify individuals in the population more likely to positively respond to therapy. Thus, these gut microbiota responses may inform recommendations to facilitate development of biologics and small molecule drugs.
  • FDA scientists are optimizing an intestine-on-a-chip model for measuring the impact of drug residues on the human intestinal microbiome – for use as a potential alternative in vitro model to support evaluation of new animal drug products. Developing a qualified model that can serve as a potential alternative to animal testing represents a substantial step forward in the evaluation of new animal drug products and aligns with FDA’s efforts to reduce or refine reliance on animals for research.
  • Many products available to the consumer, such as dietary supplements and foods, contain intentionally added live microorganisms that may provide a human health benefit. This has led to an increased production of these commodities to meet the demand for these new health related supplements. Consumers rely on product labels that report identity and viability to be accurate and true. However, species are often misclassified, or absent, and products are occasionally contaminated with species not listed on the label. High-throughput next generation sequencing (NGS) can support metagenomic investigations as a feasible means to analyze these products and eliminate any bias of culture-based sampling, or the inability to isolate all microbes present. of live microbes in pre and probiotic products. However, products containing live microorganisms are sometimes misclassified or which is of concern for products marketed to pregnant or lactating people. Research is ongoing to develop an analytical pipeline to assess the content and purity of dietary supplements available to women in the US.
  • Studying the degree to which tobacco use is associated with negative effects on the oral microbiome and oral health through the National Health and Nutrition Examination Survey. Such data may be used to inform review of tobacco product applications.




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