Genome-scale metabolic models for a synthetic soil microbial community as a path for understanding community functioning

Authors

Keshk, O., Vayena, E., Causevic, S., Sintsova, A., Wijaya, D., van der Meer, J. R., Hatzimanikatis, V.

Abstract

Microbial communities drive essential ecosystem processes, yet community-level behavior often deviates from predictions based on single-species studies. This mismatch reflects the context-dependent nature of nutrient dependencies, metabolic interactions, and resource availability in complex environments. Here, we present a mechanistic, species-resolved framework to dissect metabolism and nutrient exchange in a defined 21-member soil synthetic community spanning five bacterial phyla. For each isolate, we reconstructed and manually curated thermodynamically constrained genome-scale metabolic models, reconciling predictions with growth phenotypes across rich and minimal media. We mapped minimal nutrient requirements, cataloged environment-specific uptake and secretion profiles, and compared metabolic pathways to identify potential competitive and cooperative interactions. Using community-scale metabolomics, we assigned putative producers and consumers for detected metabolites and revealed medium-dependent shifts in niche overlap. This approach exposes metabolic strategies that govern community function and resilience, offering a predictive basis for understanding and manipulating microbiomes. Our findings highlight how species-level metabolic maps can clarify why microbial interventions succeed or fail and guide targeted manipulations in soil ecosystems.

Preprint server: bioRxiv
The authors list and abstract were imported from bioRxiv on 20 Oct 2026.

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