Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome
Journal article, 2015
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
Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology
Pouyan Ghaffari Nouran
Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology
P. Kovatcheva-Datchary
University of Gothenburg
Adil Mardinoglu
Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology
Partho Sen
Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology
E. Pujos-Guillot
INRA Centre de Clermont-Ferrand-Theix
T. de Wouters
Microbiologie de l'Alimentation au Service de la Sante Humaine
C. Juste
Microbiologie de l'Alimentation au Service de la Sante Humaine
S. Rizkalla
Inserm Transfert
Assistance publique – Hôpitaux de Paris (AP-HP)
J. Chilloux
Imperial College London
L. Hoyles
Imperial College London
J. K. Nicholson
Imperial College London
J. Dore
Microbiologie de l'Alimentation au Service de la Sante Humaine
M. E. Dumas
Imperial College London
K. Clement
Pierre and Marie Curie University (UPMC)
Assistance publique – Hôpitaux de Paris (AP-HP)
Inserm Transfert
Fredrik Bäckhed
University of Copenhagen
University of Gothenburg
Jens B Nielsen
Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology
Cell Metabolism
1550-4131 (ISSN) 19327420 (eISSN)
Vol. 22 2 320-331Metagenomics in Cardiometabolic Diseases (METACARDIS)
European Commission (EC) (EC/FP7/305312), 2012-11-01 -- 2017-10-31.
Subject Categories
Cell Biology
Infrastructure
C3SE (Chalmers Centre for Computational Science and Engineering)
Areas of Advance
Life Science Engineering (2010-2018)
DOI
10.1016/j.cmet.2015.07.001
PubMed
26244934