{
  "abstract": "Quantifying intracellular fluxes through 13C-metabolic flux analysis (13C-MFA) provides a detailed view of cellular metabolism. While model formulation, including biomass synthesis reactions, is known to influence flux estimations, the degree to which biomass composition affects 13C-MFA outcomes in Escherichia coli remains debated. Here, we reconstructed a genome-scale 13C-MFA model of E. coli incorporating explicit nucleotide biosynthesis and a modular biomass formulation that separates protein, RNA, and other components. Using isotopic labeling experiments and systematic perturbations of biomass composition, we demonstrate that 13C-MFA can robustly differentiate subtle shifts in the protein/RNA ratio, with deviations as small as 2-3% producing statistically significant but biologically interpretable changes in model fit. Reaction-level analyses revealed consistent flux adjustments across amino acid and nucleotide biosynthesis, while pathways in one-carbon metabolism, particularly serine, glycine, and threonine interconversions, exhibited the strongest responses. Collectively, these results highlight the robustness and discriminative power of 13C-MFA and also demonstrate the importance of accurate biomass composition measurement in E. coli 13C-MFA, given the intrinsic sensitivity of the method to macromolecular stoichiometry.",
  "abstract_shown": true,
  "affiliations": [
    "University of Michigan"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 2,
  "authors": [
    {
      "name": "Y. Cai"
    },
    {
      "affs": [
        0
      ],
      "name": "M. R. Antoniewicz"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/4exep02hexsv0.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.10.21.760808",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.10.21.760808v1.full",
  "id": "4exep02hexsv0",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.10.21.760808v1",
  "language": null,
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "systems biology"
    ],
    [
      "openalex",
      "1312|Microbial Metabolic Engineering and Bioproduction"
    ]
  ],
  "openalex": "W7223404259",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.10.21.760808v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-21",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/4exep02hexsv0.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:29:16Z",
      "native_id": "10.64898/2026.10.21.760808",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.10.21.760808v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:systems biology",
      "subfield": "systems-synthetic"
    }
  ],
  "title": "The Sensitivity of 13C-Metabolic Flux Analysis to Biomass Composition Underscores the Need for Accurate Biomass Formulation in Escherichia coli",
  "title_text": "The Sensitivity of 13C-Metabolic Flux Analysis to Biomass Composition Underscores the Need for Accurate Biomass Formulation in Escherichia coli",
  "type": "preprint",
  "updated_at": "2026-10-30T12:29:16Z",
  "url": "https://research.draconitic.com/paper/4exep02hexsv0",
  "venue": "bioRxiv",
  "versions": []
}