Precision fermentation is the microbial-host branch of cellular agriculture: engineered yeast and other microbes are used to secrete recombinant growth factors, media proteins, and animal-protein analogues that feed or replace the animal-cell side of the field. Genome-scale metabolic models (GEMs) of the standard production hosts are the reference substrate for that work — they parameterize media and feed design, predict growth and secretion on defined carbon sources, and provide the constraint-based scaffold that strain-engineering campaigns optimize against. This page collects the consensus GEMs for the two dominant precision-fermentation hosts, Saccharomyces cerevisiae and Komagataella phaffii (Pichia pastoris). Like the human and CHO reference pages in this directory, these are host-organism reference reconstructions rather than cultivated-meat-species data — the modeling substrate the precision-fermentation side of cell-ag builds on.
GEMs are SBML-formatted reconstructions of an organism’s metabolic network — every reaction, metabolite, and gene-protein-reaction mapping — and are the input data structure for the constraint-based modeling tools in Software.md / Metabolic Modeling & Strain Design. The reconstructions below are the microbial-host counterparts to the mammalian GEMs on the CHO and Human reference pages.
Yeast9 — Saccharomyces cerevisiae (precision-fermentation host reference)
Yeast9 is the community-curated consensus genome-scale metabolic model for Saccharomyces cerevisiae (Zhang, Sánchez, Li, et al. 2024, Molecular Systems Biology), the latest generation of the long-running consensus S. cerevisiae reconstruction. It ships as versioned SBML with continuous community curation at SysBioChalmers/yeast-GEM. S. cerevisiae is the workhorse chassis for precision-fermentation routes to recombinant proteins and food molecules, so Yeast9 is the reference network for media and feed design, flux prediction, and strain-design campaigns on the yeast side of cell-ag — including the S. cerevisiae fermentation-aroma modeling in Papers.md ref #27 (Du et al. 2025). Published: 10.1038/s44320-024-00060-7.
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iMT1026 / iMT1026 v3.0 — Komagataella phaffii (Pichia pastoris)
iMT1026 is the genome-scale metabolic reconstruction of Komagataella phaffii (Pichia pastoris), integrating and validating earlier Pichia models with updated protein-glycosylation, lipid, and energy metabolism (Tomàs-Gamisans, Ferrer, & Albiol 2016, PLOS ONE). The v3.0 update fine-tunes the model for improved prediction of growth on methanol or glycerol as sole carbon sources (Tomàs-Gamisans, Ferrer, & Albiol 2018, Microbial Biotechnology) — the carbon sources that matter most for methylotrophic Pichia bioprocesses. K. phaffii is a leading host for secreted recombinant proteins, and constraint-based media/feed design on this model is directly the kind of work cell-ag precision fermentation depends on — the Bayesian-optimization media campaign that lifted recombinant-protein productivity in K. phaffii in Papers.md ref #58 (Narayanan et al. 2025) is a worked example of that host. The SBML reconstructions are distributed as supplementary files with the two source publications; there is no dedicated code repository. Published: 10.1371/journal.pone.0148031 (iMT1026); 10.1111/1751-7915.12871 (iMT1026 v3.0).
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