How to set up and manage a microbiome research facility

BACKGROUND: The increasing number of therapeutic intervention studies in the microbiome field has sparked broad interest among clinicians and scientists to incorporate microbiome analyses in their research. However, microbiome study design, data generation, bioinformatics, and statistical data analysis are typically of a complexity that require specific domain expertise to avoid biases, spurious findings, and other analysis pitfalls. As such, academic hospitals and research institutes are increasingly recognizing the need for dedicated microbiome research facilities that support every step in human microbiome research to a high standard. OBJECTIVES: We aimed to offer an experience-based approach on what we consider essential aspects of such a microbiome research facility. SOURCES: Insights and recommendations are based on our experiences with establishing and running a microbiome research facility at the Leiden University Medical Center (Leiden, the Netherlands), which was initiated in 2017. CONTENT: This review uses an existing microbiome research facility as an example to provide information on its advantages, structure, and financial and legal frameworks. In addition, key portfolio items of such an expertise centre are discussed. IMPLICATIONS: A dedicated microbiome research facility can support microbiome research in clinical studies, and provides opportunities to centralize activities, innovate and validate analytical and computational methodology, foster industrial collaborations, and support competitive funding applications through a dedicated infrastructure. Central facilities to support clinicians and scientists in the design, execution, and interpretation of microbiome analyses constitutes a key step towards conducting high-quality gut microbiome research and education.