{
  "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.",
  "abstract_shown": true,
  "affiliations": [
    "Swiss Federal Institute of Technology (EPFL)"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 7,
  "authors": [
    {
      "name": "O. Keshk"
    },
    {
      "name": "E. Vayena"
    },
    {
      "name": "S. Causevic"
    },
    {
      "name": "A. Sintsova"
    },
    {
      "name": "D. Wijaya"
    },
    {
      "name": "J. R. van der Meer"
    },
    {
      "affs": [
        0
      ],
      "name": "V. Hatzimanikatis"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/6sn54n9wkymvy.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.10.16.759588",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.10.16.759588v1.full",
  "id": "6sn54n9wkymvy",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.10.16.759588v1",
  "language": null,
  "licence": "CC-BY-NC-ND",
  "licence_label": "CC BY-NC-ND",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc-nd/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "systems biology"
    ],
    [
      "openalex",
      "1312|Microbial Metabolic Engineering and Bioproduction"
    ]
  ],
  "openalex": "W7222960277",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.10.16.759588v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-16",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/6sn54n9wkymvy.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:28:34Z",
      "native_id": "10.64898/2026.10.16.759588",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.10.16.759588v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:systems biology",
      "subfield": "systems-synthetic"
    }
  ],
  "title": "Genome-scale metabolic models for a synthetic soil microbial community as a path for understanding community functioning",
  "title_text": "Genome-scale metabolic models for a synthetic soil microbial community as a path for understanding community functioning",
  "type": "preprint",
  "updated_at": "2026-10-30T12:28:34Z",
  "url": "https://research.draconitic.com/paper/6sn54n9wkymvy",
  "venue": "bioRxiv",
  "versions": []
}