Microbial Carbon Use Efficiency Predicted from Genome-Scale Metabolic Models

The Science

Characterizing variation in microbial carbon use efficiency (CUE) across taxa and substrate types in soils.

The Impact

  • A wide range in average potential CUE (0.62 ± 0.17) across taxa with structuring at subphylum levels.
  • CUE declines with increasing genome size, while larger genomes are able to access a wider range of C substrate types.
  • These findings provide a framework for predicting CUE from genomic traits and for inferring potential impacts of shifts in bacterial community composition on C cycling.
  • Phylogenetic variation in microbial CUE can dramatically alter patterns in soil C cycling over time.


  • Generated theoretical predictions of CUE for more than 200 taxa using genome-scale constraint-based metabolic modeling.
  • Used genome-scale metabolic models to predict microbial physiology based on genes.
  • Developed hypotheses on CUE structure across taxa and substrate types.

Principal Investigator(s)

Mustafa Saifuddin
Boston University


Saifuddin, M. et al. “Microbial carbon use efficiency predicted from genome-scale metabolic models.” Nature Communications 10, 3568 (2019). [DOI:10.1038/s41467-019-11488-z]