Quantifying diet-induced metabolic changes of the human gut microbiome

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. ORCID: 0000-0002-6418-342X, Nicholson, J.K., MICRO-Obes Consortium, , Dore, J., Dumas, M.E., Clement, K., Bäckhed, F. and Nielsen, J., 2015. Quantifying diet-induced metabolic changes of the human gut microbiome. Cell Metabolism, 22 (2), pp. 320-331. ISSN 1550-4131

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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 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.

Item Type: Journal article
Publication Title: Cell Metabolism
Creators: 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., MICRO-Obes Consortium, , Dore, J., Dumas, M.E., Clement, K., Bäckhed, F. and Nielsen, J.
Publisher: Cell Press
Date: 4 August 2015
Volume: 22
Number: 2
ISSN: 1550-4131
Identifiers:
NumberType
10.1016/j.cmet.2015.07.001DOI
S1550413115003307Publisher Item Identifier
Divisions: Schools > School of Science and Technology
Depositing User: Jill Tomkinson
Date Added: 09 Aug 2018 09:57
Last Modified: 09 Aug 2018 09:57
URI: http://irep.ntu.ac.uk/id/eprint/34295

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