Tier 0 · open
anaerobic digestion: glucose -> methane (methanogen<->fermenter syntrophy)
SUPER-ADDITIVE CONSORTIUM (reducible)
corpus v0.3.0 · hash 3574ed92836e…
Model licensing
This run includes model(s) we cannot re-serve. They are named and cited so you can obtain them directly from the source. Naming a model in a result is not redistribution.
- link-only: Unconfirmed (repo MIT; vmh.life data license not confirmed, preprint noted CC-BY-NC 4.0) -- obtain a license from the source before reuse; source: https://vmh.life/files/reconstructions/AGORA2/version2.01/
The remaining models are openly redistributable (CC-BY).
Provenanced sample report (Syntropa discovery, role-aware Stage-1). Corpus v0.3.0 (15717 models, fingerprint 3574ed92836e) · tools v0.1.0 (git 38fbc04, code 7965284a0cdb) · env py3.13.13 win32 swiglpk5.0.13+osqp1.1.3+highspy1.15.1+pyscipopt6.2.1+optlang1.9.1 (deps fec80ac6eed5). Feed={'glucose': 10} target=methane mode=produce. Report id af618d0abdb8 (content-addressed to config + EXACT corpus + EXACT tools -> reproducible/auditable). Honest-by-construction: read the caveats.
Verdict: SUPER-ADDITIVE CONSORTIUM (reducible)
the consortium produces FAR more than any single member (super-additive), but a feasible SUBSET already produces the target, so the full set is NOT irreducibly required. Honest framing.
Validation (why this result is trustworthy)
Flagship anchor, validated FOUR independent ways (2026-07-24): (1) ENGINE-PATH confirmed -- the signal survives the real closed-medium emergence path, not the leaky open-medium one (baseline collapses 9.3->0.046); (2) adversarial review -- the two most serious objections were refuted by direct test; (3) OUT-OF-SAMPLE -- on a provably-disjoint held-out set the positive class hit 22/30 (emergent + feedstock-dependent) vs 0/60 for both decoy classes, Fisher one-sided p=1.1e-14; (4) THERMODYNAMICS -- the net transform glucose->3CH4+3CO2 is feasible at dG'm=-431 kJ/mol (eQuilibrator component-contribution, class-level).
Honest limits:
- Breadth is n=1: this clean non-circular structural anchor is METHANE-SPECIFIC (a rare, specific exchange signature). Broadening to common-intermediate targets (sulfate reduction, chain elongation) needs a reaction-marker index, not yet built -- so this is ONE rigorously-validated anchor, not a general claim.
- Hit propensity is model-source-dependent (CarveMe/AGORA reconstructions secrete the H2 intermediate readily, embl_gems less so), so candidates are read WITH their source.
- Thermo is CLASS-LEVEL + necessary-only: per-hit community transforms are 'unknown' (amino-acid cross-feeding unmapped), so each hit's ledger thermo_verdict stays NULL -- never faked.
Frozen rigor records are archived with the release.
Super-additivity + honest scope
- Best consortium reaches 16.304 (no single-organism baseline exceeded 0).
- The 31 feedstock-dependent candidates are COMBINATIONS over a diverse front-end core and largely SHARE the finisher(s) ['agora2_methanobrevibact_ruminantiumm1', 'agora2_methanobrevibact_smithiiatcc35061'] -- they are variations on a small number of core relays, NOT 31 independent discoveries. The biological finding is the finisher + its best partners, not the raw count.
Ranked feedstock-dependent candidates (top 10 of 31)
| rank | n | production | emergence | members |
|---|---|---|---|---|
| 1 | 2 | 16.304 | super-additive/reducible | agora2_methanobrevibact_ruminantiumm1 (AGORA2 v2.01 (Heinken 2023)/semi-curated) + cme_gcf000025265 (CarveMe 1.6.6 reconstruction from NCBI RefSeq proteome/draft) |
| 2 | 2 | 16.290 | super-additive/reducible | agora2_methanobrevibact_ruminantiumm1 (AGORA2 v2.01 (Heinken 2023)/semi-curated) + cme_gcf900021175 (CarveMe 1.6.6 reconstruction from NCBI RefSeq proteome/draft) |
| 3 | 2 | 16.282 | super-additive/reducible | agora2_methanobrevibact_ruminantiumm1 (AGORA2 v2.01 (Heinken 2023)/semi-curated) + cme_gcf001263205 (CarveMe 1.6.6 reconstruction from NCBI RefSeq proteome/draft) |
| 4 | 2 | 16.072 | super-additive/reducible | agora2_methanobrevibact_smithiiatcc35061 (AGORA2 v2.01 (Heinken 2023)/semi-curated) + cme_gcf900021175 (CarveMe 1.6.6 reconstruction from NCBI RefSeq proteome/draft) |
| 5 | 2 | 16.066 | super-additive/reducible | agora2_methanobrevibact_ruminantiumm1 (AGORA2 v2.01 (Heinken 2023)/semi-curated) + cme_gcf002291425 (CarveMe 1.6.6 reconstruction from NCBI RefSeq proteome/draft) |
| 6 | 2 | 15.955 | super-additive/reducible | agora2_methanobrevibact_ruminantiumm1 (AGORA2 v2.01 (Heinken 2023)/semi-curated) + cme_gcf009388985 (CarveMe 1.6.6 reconstruction from NCBI RefSeq proteome/draft) |
| 7 | 2 | 15.884 | super-additive/reducible | agora2_methanobrevibact_ruminantiumm1 (AGORA2 v2.01 (Heinken 2023)/semi-curated) + cme_gcf900178525 (CarveMe 1.6.6 reconstruction from NCBI RefSeq proteome/draft) |
| 8 | 2 | 15.321 | super-additive/reducible | agora2_methanobrevibact_ruminantiumm1 (AGORA2 v2.01 (Heinken 2023)/semi-curated) + cme_gcf034651555 (CarveMe 1.6.6 reconstruction from NCBI RefSeq proteome/draft) |
| 9 | 2 | 15.255 | super-additive/reducible | agora2_methanobrevibact_ruminantiumm1 (AGORA2 v2.01 (Heinken 2023)/semi-curated) + cme_gcf055385405 (CarveMe 1.6.6 reconstruction from NCBI RefSeq proteome/draft) |
| 10 | 2 | 15.109 | super-additive/reducible | agora2_methanobrevibact_ruminantiumm1 (AGORA2 v2.01 (Heinken 2023)/semi-curated) + cme_gcf006716235 (CarveMe 1.6.6 reconstruction from NCBI RefSeq proteome/draft) |
Attribution
Every model above is credited by id + source. Model authors: your reconstruction appears in this result. (Impact-ledger stamping = flywheel, pending.)
Caveats (disclosed up front)
- FBA proves a route is stoichiometrically POSSIBLE, not that a living cell will do it.
- Every consortium here is a HYPOTHESIS until cultured; nothing is wet-lab validated.
- Feedstock-dependence is the anti-medium-artifact control: withdraw the feed and the product must collapse (a NOT-feedstock-dependent result is flagged SUSPECT, not a discovery).
- The ranking score is a documented heuristic for human review, not a truth or biology claim.
- Stage-1 selects finisher x diverse front-ends; multi-finisher relays are out of scope. Stage-2 expansion of winners is pending -- these are PRELIMINARY until it runs.