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  • Review Article
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Utilization of the microbiome in personalized medicine

Nature Reviews Microbiology volume 22, pages 291–308 (2024)Cite this article

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Abstract

Inter-individual human variability, driven by various genetic and environmental factors, complicates the ability to develop effective population-based early disease detection, treatment and prognostic assessment. The microbiome, consisting of diverse microorganism communities including viruses, bacteria, fungi and eukaryotes colonizing human body surfaces, has recently been identified as a contributor to inter-individual variation, through its person-specific signatures. As such, the microbiome may modulate disease manifestations, even among individuals with similar genetic disease susceptibility risks. Information stored within microbiomes may therefore enable early detection and prognostic assessment of disease in at-risk populations, whereas microbiome modulation may constitute an effective and safe treatment tailored to the individual. In this Review, we explore recent advances in the application of microbiome data in precision medicine across a growing number of human diseases. We also discuss the challenges, limitations and prospects of analysing microbiome data for personalized patient care.

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Fig. 1: Utilization of microbiome data for screening and personalized prevention of disease.
Fig. 2: Site-specific microbiome assessment in disease prediction and diagnosis.
Fig. 3: Utilization of the microbiome in disease treatment.
Fig. 4: Microbiome-mediated modulation of cancer treatment.

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Acknowledgements

K.R. is supported by The Nehemia Levtzion Scholarship for Outstanding Doctoral Students. D.C. received postdoctoral fellowship funding from the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement No 101068352. S.K.A. is supported by the Israeli Ministry of Science and Technology Zvi Yanai Fellowship. E.E. is supported by the Leona M. and Harry B. Helmsley Charitable Trust, Adelis Foundation, Ben B. and Joyce E. Eisenberg Foundation, Estate of Bernard Bishin for the WIS-Clalit Program, Jeanne and Joseph Nissim Center for Life Sciences Research, Miel de Botton, Swiss Society Institute for Cancer Prevention Research, Belle S. and Irving E. Meller Center for the Biology of Aging, Sagol Institute for Longevity Research, Sagol Weizmann-MIT Bridge Program, Norman E. Alexander Family M Foundation Coronavirus Research Fund, Mike and Valeria Rosenbloom Foundation, Daniel Morris Trust, Isidore and Penny Myers Foundation and Vainboim Family, and by grants funded by the European Research Council, Israel Science Foundation, Israel Ministry of Science and Technology, Israel Ministry of Health, German–Israeli Helmholtz International Research School: Cancer-TRAX (HIRS-0003), Helmholtz Association’s Initiative and Networking Fund, Minerva Foundation, Garvan Institute, European Crohn’s and Colitis Organization, DeutschIsraelische Projektkooperation, IDSA Foundation, WIS-MIT grant, Emulate, Charlie Teo Foundation, Mark Foundation for Cancer Research and Welcome Trust; is the incumbent of the Sir Marc and Lady Tania Feldmann Professorial Chair of immunology; is a senior fellow at the Canadian Institute of Advanced Research; and is an international scholar at the The Bill & Melinda Gates Foundation and Howard Hughes Medical Institute.

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  1. These authors contributed equally: Karina Ratiner, Dragos Ciocan, Suhaib K. Abdeen.

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  1. Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel

    Karina Ratiner, Dragos Ciocan, Suhaib K. Abdeen & Eran Elinav

  2. Division of Cancer–Microbiome Research, DKFZ, Heidelberg, Germany

    Eran Elinav

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Glossary

Dysbiosis

An altered microbiome configuration, characterized by imbalances in the microbial community structure such as composition, metabolic activities or distribution, that can be associated with disease.

Next-generation probiotics

Microbial taxa, experimentally evaluated as therapeutic living microorganisms, that would be optimized for human colonization, while featuring a reproducible safety and efficacy in promoting health.

Personalized nutrition

An experimental predictive approach that incorporates multi-faceted information, including data derived from the microbiome, to optimize the precision and efficacy of tailored dietary recommendations.

Postbiotics

Small molecules — metabolites — of varying chemical composition that are produced, degraded or modified by commensal microorganisms, or released following bacterial lysis.

Prebiotics

Nutritional supplements, such as fibres, that are selectively utilized by host microorganisms, conferring a health benefit by promoting the growth of commensal microorganisms.

Probiotics

Living microorganisms that are consumed to confer a health benefit to the host; despite widespread popularity, no probiotic preparations were approved to date by the US and European regulatory agencies as medical treatment or prevention.

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Ratiner, K., Ciocan, D., Abdeen, S.K. et al. Utilization of the microbiome in personalized medicine. Nat Rev Microbiol 22, 291–308 (2024). https://doi.org/10.1038/s41579-023-00998-9

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