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Perspective: Leveraging the Gut Microbiota to Predict Personalized Responses to Dietary, Prebiotic, and Probiotic Interventions

Gibbons, Sean M.; Gurry, Thomas; Lampe, Johanna W; Chakrabarti, Anirikh; Dam, Veerle; Everard, Amandine; Goas, Almudena; Gross, Gabriele; Kleerebezem, Michiel; Lane, Jonathan; Maukonen, Johanna; Penna, Ana Lucia Barretto; Pot, Bruno; Valdes, Ana M.; Walton, Gemma; Weiss, Adrienne; Zanzer, Yoghatama Cindya; Venlet, Naomi V; Miani, Michela


Sean M. Gibbons

Thomas Gurry

Johanna W Lampe

Anirikh Chakrabarti

Veerle Dam

Amandine Everard

Almudena Goas

Gabriele Gross

Michiel Kleerebezem

Jonathan Lane

Johanna Maukonen

Ana Lucia Barretto Penna

Bruno Pot

Gemma Walton

Adrienne Weiss

Yoghatama Cindya Zanzer

Naomi V Venlet

Michela Miani


Humans often show variable responses to dietary, prebiotic, and probiotic interventions. Emerging evidence indicates that the gut microbiota is a key determinant for this population heterogeneity. Here, we provide an overview of some of the major computational and experimental tools being applied to critical questions of microbiota-mediated personalized nutrition and health. First, we discuss the latest advances in in silico modeling of the microbiota-nutrition-health axis, including the application of statistical, mechanistic, and hybrid artificial intelligence models. Second, we address high-throughput in vitro techniques for assessing interindividual heterogeneity, from ex vivo batch culturing of stool and continuous culturing in anaerobic bioreactors, to more sophisticated organ-on-a-chip models that integrate both host and microbial compartments. Third, we explore in vivo approaches for better understanding of personalized, microbiota-mediated responses to diet, prebiotics, and probiotics, from nonhuman animal models and human observational studies, to human feeding trials and crossover interventions. We highlight examples of existing, consumer-facing precision nutrition platforms that are currently leveraging the gut microbiota. Furthermore, we discuss how the integration of a broader set of the tools and techniques described in this piece can generate the data necessary to support a greater diversity of precision nutrition strategies. Finally, we present a vision of a precision nutrition and healthcare future, which leverages the gut microbiota to design effective, individual-specific interventions.


Gibbons, S. M., Gurry, T., Lampe, J. W., Chakrabarti, A., Dam, V., Everard, A., …Miani, M. (2022). Perspective: Leveraging the Gut Microbiota to Predict Personalized Responses to Dietary, Prebiotic, and Probiotic Interventions. Advances in Nutrition, 13(5), 1450-1461.

Journal Article Type Article
Acceptance Date Jun 28, 2022
Online Publication Date Feb 9, 2023
Publication Date Sep 1, 2022
Deposit Date Feb 17, 2023
Journal Advances in Nutrition
Print ISSN 2156-5376
Electronic ISSN 2156-5376
Publisher Elsevier BV
Peer Reviewed Peer Reviewed
Volume 13
Issue 5
Pages 1450-1461
Keywords Prebiotic; probiotic; diet; microbiome; microbiota; personalized nutrition; personalized healthcare; precision nutrition; precision healthcare
Public URL
Publisher URL
Additional Information This article is maintained by: Elsevier; Article Title: Perspective: Leveraging the Gut Microbiota to Predict Personalized Responses to Dietary, Prebiotic, and Probiotic Interventions; Journal Title: Advances in Nutrition; CrossRef DOI link to publisher maintained version: