Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome

Saeed Shoaie; Pouyan Ghaffari; Petia Kovatcheva-Datchary; Adil Mardinoglu; Partho Sen; Estelle Pujos-Guillot; Tomas de Wouters; Catherine Juste; Salwa Rizkalla; Julien Chilloux; Lesley Hoyles; Jeremy K Nicholson; Joel Dore; Marc E Dumas; Karine Clement; Gert Fredrik Bäckhed; Jens Nielsen; MICRO-Obes Consortium

doi:10.1016/j.cmet.2015.07.001

Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome

Saeed Shoaie, Pouyan Ghaffari, Petia Kovatcheva-Datchary, Adil Mardinoglu, Partho Sen, Estelle Pujos-Guillot, Tomas de Wouters, Catherine Juste, Salwa Rizkalla, Julien Chilloux, Lesley Hoyles, Jeremy K Nicholson, Joel Dore, Marc E Dumas, Karine Clement, Gert Fredrik Bäckhed, Jens Nielsen, MICRO-Obes Consortium

218 Citations (Scopus)

Abstract

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.

Original language	English
Journal	Cell Metabolism
Volume	22
Issue number	2
Pages (from-to)	320-31
Number of pages	12
ISSN	1550-4131
DOIs	https://doi.org/10.1016/j.cmet.2015.07.001
Publication status	Published - 4 Aug 2015

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Shoaie, S., Ghaffari, P., Kovatcheva-Datchary, P., Mardinoglu, A., Sen, P., Pujos-Guillot, E., de Wouters, T., Juste, C., Rizkalla, S., Chilloux, J., Hoyles, L., Nicholson, J. K., Dore, J., Dumas, M. E., Clement, K., Bäckhed, G. F., Nielsen, J., & MICRO-Obes Consortium (2015). Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome. Cell Metabolism, 22(2), 320-31. https://doi.org/10.1016/j.cmet.2015.07.001

Shoaie, S, Ghaffari, P, Kovatcheva-Datchary, P, Mardinoglu, A, Sen, P, Pujos-Guillot, E, de Wouters, T, Juste, C, Rizkalla, S, Chilloux, J, Hoyles, L, Nicholson, JK, Dore, J, Dumas, ME, Clement, K, Bäckhed, GF, Nielsen, J & MICRO-Obes Consortium 2015, 'Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome', Cell Metabolism, vol. 22, no. 2, pp. 320-31. https://doi.org/10.1016/j.cmet.2015.07.001

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title = "Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome",

abstract = "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.",

author = "Saeed Shoaie and Pouyan Ghaffari and Petia Kovatcheva-Datchary and Adil Mardinoglu and Partho Sen and Estelle Pujos-Guillot and {de Wouters}, Tomas and Catherine Juste and Salwa Rizkalla and Julien Chilloux and Lesley Hoyles and Nicholson, {Jeremy K} and Joel Dore and Dumas, {Marc E} and Karine Clement and B{\"a}ckhed, {Gert Fredrik} and Jens Nielsen and {MICRO-Obes Consortium}",

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AU - Shoaie, Saeed

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AU - Mardinoglu, Adil

AU - Sen, Partho

AU - Pujos-Guillot, Estelle

AU - de Wouters, Tomas

AU - Juste, Catherine

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AU - Chilloux, Julien

AU - Hoyles, Lesley

AU - Nicholson, Jeremy K

AU - Dore, Joel

AU - Dumas, Marc E

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AU - Nielsen, Jens

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N2 - 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.

AB - 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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VL - 22

SP - 320

EP - 331

JO - Cell Metabolism

JF - Cell Metabolism

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Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome

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