BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities.

ABSTRACT: Recent advances focusing on the metabolic interactions within and between cellular populations have emphasized the importance of microbial communities for human health. Constraint-based modeling, with flux balance analysis in particular, has been established as a key approach for studying microbial metabolism, whereas individual-based modeling has been commonly used to study complex dynamics between interacting organisms. In this study, we combine both techniques into the R package BacArena (https://cran.r-project.org/package=BacArena) to generate novel biological insights into Pseudomonas aeruginosa biofilm formation as well as a seven species model community of the human gut. For our P. aeruginosa model, we found that cross-feeding of fermentation products cause a spatial differentiation

SUBMITTER: Bauer E 

PROVIDER: S-EPMC5460873 | biostudies-literature | 2017 May

REPOSITORIES: biostudies-literature