Constraint-based stoichiometric modelling from single organisms to microbial communities.
Microbial communities are ubiquitously found in Nature and have direct implications for the environment, human health and biotechnology. The species composition and overall function of microbial communities are largely shaped by metabolic interactions such as competition for resources and cross-feeding. Although considerable scientific progress has been made towards mapping and modelling species-level metabolism, elucidating the metabolic exchanges between microorganisms and steering the community dynamics remain an enormous scientific challenge. In view of the complexity, computational models of microbial communities are essential to obtain systems-level understanding of ecosystem functioning. This review discusses the applications and limitations of constraint-based stoichiometric modelling tools, and in particular flux balance analysis (FBA). We explain this approach from first principles and identify the challenges one faces when extending it to communities, and discuss the approaches used in the field in view of these challenges. We distinguish between steady-state and dynamic FBA approaches extended to communities. We conclude that much progress has been made, but many of the challenges are still open.
Systems Bioinformatics, Amsterdam Institute for Molecules, Medicines and Systems, VU University Amsterdam, De Boelelaan 1087, 1081 HV Amsterdam, The Netherlands.
Willi
0000-0002-6502-1393
W
Gottstein
Systems Bioinformatics, Amsterdam Institute for Molecules, Medicines and Systems, VU University Amsterdam, De Boelelaan 1087, 1081 HV Amsterdam, The Netherlands.
Brett G
BG
Olivier
Systems Bioinformatics, Amsterdam Institute for Molecules, Medicines and Systems, VU University Amsterdam, De Boelelaan 1087, 1081 HV Amsterdam, The Netherlands.
Frank J
FJ
Bruggeman
Systems Bioinformatics, Amsterdam Institute for Molecules, Medicines and Systems, VU University Amsterdam, De Boelelaan 1087, 1081 HV Amsterdam, The Netherlands b.teusink@vu.nl.
Bas
B
Teusink
D059013:Microbial Consortia / Q000502:physiology*; D008954:Models, Biological
community flux balance analysis; derivation of flux balance analysis; genome-scale stoichiometric models; growth strategies; metabolic interactions; microbial communities