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Diet–microbiota interactions and personalized nutrition


Conceptual scientific and medical advances have led to a recent realization that there may be no single, one-size-fits-all diet and that differential human responses to dietary inputs may rather be driven by unique and quantifiable host and microbiome features. Integration of these person-specific host and microbiome readouts into actionable modules may complement traditional food measurement approaches in devising diets that are of benefit to the individual. Although many host-derived factors are hardwired and difficult to modulate, the microbiome may be more readily reshaped by environmental factors such as dietary exposures and is increasingly recognized to potentially impact human physiology by participating in digestion, the absorption of nutrients, shaping of the mucosal immune response and the synthesis or modulation of a plethora of potentially bioactive compounds. Thus, diet-induced microbiota alterations may be harnessed in order to induce changes in host physiology, including disease development and progression. However, major limitations in ‘big-data’ processing and analysis still limit our interpretive and translational capabilities concerning these person-specific host, microbiome and diet interactions. In this Review, we describe the latest advances in understanding diet–microbiota interactions, the individuality of gut microbiota composition and how this knowledge could be harnessed for personalized nutrition strategies to improve human health.

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Fig. 1: Dynamic changes in the microbiome in response to diet.
Fig. 2: Personalized microbiota and host responses to diet.
Fig. 3: Clinically relevant bacterial metabolites.
Fig. 4: Microbiota-based diet design.


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The authors thank the members of the Elinav lab and the members of the Division of Microbiome and Cancer, DKFZ, for discussions and apologize to researchers whose work was not included due to space constraints. A.A.K. was a recipient of EMBO Long Term Fellowship 2016-1088 and support from the European Union’s Horizon 2020 research and innovation programme under Marie Sklodowska-Curie Grant Agreement No. 747114. D.Z. is the recipient of a European Crohn’s and Colitis Organization (ECCO) Fellowship and is supported by the Ke Lin Program of the First Affiliated Hospital, Sun Yat-sen University. E.E. is supported by Yael and Rami Ungar, the Leona M. and Harry B. Helmsley Charitable Trust, the Adelis Foundation, the Pearl Welinsky Merlo Scientific Progress Research Fund, the Lawrence and Sandra Post Family Foundation, the Daniel Morris Trust, the Park Avenue Charitable Fund, the Hanna and Dr. Ludwik Wallach Cancer Research Fund, the Howard and Nancy Marks Charitable Fund, the Aliza Moussaieff Estate of Malka Moskowitz, the Estate of Myron H. Ackerman, the Estate of Bernard Bishin for the WIS-Clalit Program, Donald and Susan Schwarz, grants funded by the European Research Council, the Israel Science Foundation, Israel Ministry of Science and Technology, Israel Ministry of Health, the Helmholtz Foundation, the Else Kroener Fresenius Foundation, the Garvan Institute, the European Crohn’s and Colitis Organisation, Deutsch-Israelische Projektkooperation and the Wellcome Trust. E.E. is the incumbent of the Sir Marc and Lady Tania Feldmann Professorial Chair, a senior fellow of the Canadian Institute of Advanced Research (CIFAR) and an international scholar of the Bill and Melinda Gates Foundation and the Howard Hughes Medical Institute (HHMI).

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All authors researched the data for this article, made substantial contributions to discussion of the content, and wrote, reviewed and edited the manuscript before submission.

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Correspondence to Eran Elinav.

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E.E. is a paid consultant at DayTwo and BiomX. All other authors declare no competing interests.

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Personalized medicine

A medical approach in which patients are stratified into groups depending on different factors that contribute to treatment outcomes and then receive the tailored treatment predicted to be most effective.


Changes from rural to urban areas and encompasses both the flux of people from rural areas to cities and the growth of urban areas.

Metabolic derangements

Pathological states in which the host metabolism is dysregulated, which are associated with a clustering of metabolic disorders, including obesity, hypertension, insulin resistance, impaired glucose tolerance and dyslipidemia.


A short-chain fatty acid produced by bacteria in the gut from complex carbohydrates.


Proposed classification of human microbiomes into three different types, depending on which bacterial genus is most prevalent: Bacteroides, Prevotella or Ruminococcus.

Saccharolytic microorganisms

Microorganisms that break down sugar to acquire energy.


Foods, or compounds found in food, that induce the growth of bacterial species that are beneficial.


Substances found in food, used to prevent the separation of emulsions in order to achieve the desired textures of food.


Live microorganisms (bacteria or yeast) found in dietary supplements or food.

Faecal microbiota transplantation

(FMT). Process of transferring faecal matter from one or many individuals to another in order to affect the microbiome of a recipient.

Barley kernel-based bread

(BKB). Bread that is made from barley kernels, leading to high resistant starch and non-starch polysaccharide content.

Postprandial glycaemic response

(PPGR). Increase of glucose level in the blood following ingestion of a meal.

Nonalcoholic steatohepatitis

(NASH). A form of nonalcoholic fatty liver disease, characterized by at least 5% hepatic steatosis, with histological liver inflammation and hepatocyte injury.

Primary bile acids

Amphipathic molecules produced by the hepatocytes and released to the intestine to aid the digestion and absorption of lipids.

Glycaemic index

Numeric value, on a scale from 0 to 100, that represents the average glucose-level increase upon consumption of a particular food.


Lipoprotein particles, composed of cholesterol, triglicerides, phospholipids and carrier proteins, that allow the transport of fat in the blood.

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Kolodziejczyk, A.A., Zheng, D. & Elinav, E. Diet–microbiota interactions and personalized nutrition. Nat Rev Microbiol 17, 742–753 (2019).

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