Genome-scale metabolic models for a synthetic soil microbial community as a path for understanding community functioning
- 1Swiss Federal Institute of Technology (EPFL)
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.
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BibTeX
@misc{keshk2026genomescale,
title = {{Genome-scale metabolic models for a synthetic soil microbial community as a path for understanding community functioning}},
author = {O. Keshk and E. Vayena and S. Causevic and A. Sintsova and D. Wijaya and J. R. van der Meer and V. Hatzimanikatis},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.16.759588},
url = {https://www.biorxiv.org/content/10.64898/2026.10.16.759588v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - Genome-scale metabolic models for a synthetic soil microbial community as a path for understanding community functioning
AU - O. Keshk
AU - E. Vayena
AU - S. Causevic
AU - A. Sintsova
AU - D. Wijaya
AU - J. R. van der Meer
AU - V. Hatzimanikatis
PY - 2026
DA - 2026/10/16
PB - bioRxiv
DO - 10.64898/2026.10.16.759588
UR - https://www.biorxiv.org/content/10.64898/2026.10.16.759588v1
AB - 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.
ER -