A large-scale literature review to which I contributed was recently published in Nature Medicine!! Led by Dr. Jack Gilbert, a team of microbiome experts put together this paper exploring how microbiome research has evolved in the last two decades from asking fundamental questions about which microbes were present, what they were doing, and how and when microbial communities would react, to creating diagnostic tools and clinical interventions to promote health.

Gilbert, J.A., Azad, M.B., Bäckhed, F., Blaser, M.J., Byndloss, M., Chiu, C., Chu, H., Dugas, L.R., Eran Elinav, E., Gibbons, S.M., Henn, M.R., Ishaq, S.L., Ley, R.E., Lynch, S.V., Segal, E., Spector, T.D., Strandwitz, P., Suez, J., Tropini, C., Whiteson, K., Knight, R. 2025. Clinical translation of microbiome research. Nature Medicine. Accepted.

Abstract

The landscape of clinical microbiome research has dramatically evolved over the last decade. By leveraging in vivo and in vitro experimentation, multiomic approaches and computational biology, we have uncovered mechanisms of action and microbial metrics of association and identified effective ways to modify the microbiome in many diseases and treatment modalities. This Review explores recent advances in the clinical application of microbiome research over the last 5 years, while acknowledging existing barriers and highlighting opportunities. We focus on the translation of microbiome research into clinical practice, spearheaded by Food and Drug Administration (FDA)-approved microbiome therapies for recurrent Clostridioides difficile infections and the emerging fields of microbiome-based diagnostics and therapeutics. We highlight key examples of studies demonstrating how microbiome mechanisms, metrics and modifiers can advance clinical practice. We also discuss forward-looking perspectives on key challenges and opportunities toward integrating microbiome data into routine clinical practice, precision medicine and personalized healthcare and nutrition.