Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome - INRAE - Institut national de recherche pour l’agriculture, l’alimentation et l’environnement Access content directly
Journal Articles Cell Metabolism Year : 2015

Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome

Julien Chilloux
Lesley Hoyles
Marc e. Dumas
Jens Nielsen
Edi Prifti
Nicolas Pons
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  • IdHAL : nicolas-pons
Emmanuelle Le Chatelier
Benoit Quinquis
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  • PersonId : 1205563
Florence Levenez
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  • PersonId : 1068837
Nathalie Galleron
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  • PersonId : 1205248
Jean-Michel Batto
  • Function : Contributor
Stanislav D. Ehrlich
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  • PersonId : 1068832
Emmanuelle Maguin


The human gut microbiome is known to be associated with various human disorders, but a major challenge is to go beyond association studies and elucidate causalities. Mathematical modeling of the human gut microbiome at a genome scale is a useful tool to decipher microbe-microbe, diet-microbe and microbe-host interactions. Here, we describe the CASINO (Community And Systems-level INteractive Optimization) toolbox, a comprehensive computational platform for analysis of microbial communities through metabolic modeling. We first validated the toolbox by simulating and testing the performance of single bacteria and whole communities in vitro. Focusing on metabolic interactions between the diet, gut microbiota, and host metabolism, we demonstrated the predictive power of the toolbox in a diet-intervention study of 45 obese and overweight individuals and validated our predictions by fecal and blood metabolomics data. Thus, modeling could quantitatively describe altered fecal and serum amino acid levels in response to diet intervention.
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hal-02634319 , version 1 (08-01-2024)


Attribution - NonCommercial - NoDerivatives



Saeed Shoaie, Pouyan Ghaffari, Petia Kovatcheva-Datchary, Adil Mardinoglu, Partho Sen, et al.. Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome. Cell Metabolism, 2015, 22 (2), pp.320-331. ⟨10.1016/j.cmet.2015.07.001⟩. ⟨hal-02634319⟩
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