Emergence of microbial diversity due to cross-feeding interactions in a spatial model of gut microbial metabolism

BMC Systems Biology
Milan J A van Hoek, Roeland M H Merks

Abstract

The human gut contains approximately 1014 bacteria, belonging to hundreds of different species. Together, these microbial species form a complex food web that can break down nutrient sources that our own digestive enzymes cannot handle, including complex polysaccharides, producing short chain fatty acids and additional metabolites, e.g., vitamin K. Microbial diversity is important for colonic health: Changes in the composition of the microbiota have been associated with inflammatory bowel disease, diabetes, obesity and Crohn's disease, and make the microbiota more vulnerable to infestation by harmful species, e.g., Clostridium difficile. To get a grip on the controlling factors of microbial diversity in the gut, we here propose a multi-scale, spatiotemporal dynamic flux-balance analysis model to study the emergence of metabolic diversity in a spatial gut-like, tubular environment. The model features genome-scale metabolic models (GEM) of microbial populations, resource sharing via extracellular metabolites, and spatial population dynamics and evolution. In this model, cross-feeding interactions emerge readily, despite the species' ability to metabolize sugars autonomously. Interestingly, the community requires cross-feeding for...Continue Reading

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Software Mentioned

Matlab
BRENDA
MOVECELL
COBRA Toolbox
NEUROtiker
Metacyc
FBAwMC
Flux Balance Analysis with Molecular Crowding ( FBAwMC )
FBAwMC )

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