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

Hopital Pitie Salpetriere

Inserm Transfert

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

Hopital Pitie Salpetriere

Pierre and Marie Curie University (UPMC)

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)

Vol. 22 2 320-331

Metagenomics in Cardiometabolic Diseases (METACARDIS)

European Commission (FP7), 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

More information

Latest update

1/18/2019