COMMIT: Consideration of metabolite leakage and community composition improves microbial community reconstructions
Fig 6
Reduction of biomass flux upon blocking the uptake of metabolites whose import was added during conditional gap filling of the Schlaeppi community.
The uptake of every metabolite whose uptake was included during conditional gap filling was blocked separately and the growth rate under this condition was divided by the growth rate for that particular model. A threshold of 0.99 was applied to avoid false-positive responses. Biomass flux ratios were calculated for all metabolic models in the Schlaeppi community. The models were annotated to classes based on the taxonomy published by Bai et al. [38]. The metabolites were grouped based on KEGG BRITE br08001, which was manually refined. Hierarchical clustering was performed using average linkage with Euclidean distance. Cells in dark red indicate low biomass whereas yellow cells indicate a smaller reduction of biomass.