Syntrophy setup, and the fumarate that must not be in it (#183) - #539
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Syntrophy setup, and the fumarate that must not be in it (#183)#539realmarcin wants to merge 1 commit into
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Syntrophobacter_Methanobacterium_Syntrophy: 1 L flasks with 550 mL medium, in triplicate, 37 °C, under a pressurised N2/CO2 (80:20) gas phase at 172 kPa. The headspace is not merely an anaerobic blanket — syntrophic propionate oxidation is thermodynamically feasible only while the partner keeps H2 and formate low, so the gas composition and pressure are part of the experiment. The cited sentence says "all organisms", which here covers the cocultures as well as the axenic controls, so these are the community's conditions. That is the #529 check passing on the wording rather than on a member-name count. Deliberately excluded: the 20 mM propionate and 60 mM fumarate supplement, which the source attaches to "the medium for the pure cultures". Fumarate is an electron acceptor that lets S. fumaroxidans grow without a partner, so carrying it into the coculture's setup would describe a condition that abolishes the syntrophy this record exists to document. Same shape as the precultures excluded from the last three records, but with a sharper consequence. Also fixes two reference-validation failures already on main for this record. The snippets wrote strain designations as `MPOB T`, `JF1 T`, `MF T`; the cached text renders the superscript type-strain marker closed up, `MPOBT`, `JF1T`, `MFT`. A rendering artefact, not a misquotation — the record now validates at zero issues rather than two. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Network integrity findingsWarnings only — a member with no interaction yet, or a participant matched by ontology id rather than by name, or one on a community-level interaction that resolves to no member. Reported, but does not fail the build. The full report is attached to the workflow run as an artifact. |
This was referenced Aug 11, 2026
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What
Syntrophobacter_Methanobacterium_Syntrophy— 1 L flasks with 550 mL medium, in triplicate, 37 °C, under a pressurised N₂/CO₂ (80:20) gas phase at 172 kPa.The headspace is recorded because it is not merely an anaerobic blanket. Syntrophic propionate oxidation is thermodynamically feasible only while the methanogenic partner keeps H₂ and formate low, so the gas composition and pressure are part of the experiment rather than background.
The #529 check passes on the wording
The cited sentence says "All organisms were batch cultured…", which in this paper covers the cocultures as well as the axenic controls. So these are the community's conditions, established from the sentence itself rather than inferred from a member-name count — as with the JN4/GD17 record.
What is deliberately excluded, and why it matters more than usual
The source also gives 20 mM propionate and 60 mM fumarate — attached specifically to "the medium for the pure cultures".
Fumarate is an electron acceptor that lets S. fumaroxidans grow without a partner. Carrying it into the coculture's
cultivation_setupwould describe a condition that abolishes the very syntrophy this record exists to document. Same shape as the precultures excluded from the last three records, with a sharper consequence: not just a wrong number, but a setup that contradicts the record's subject.Also fixes two failures already on
mainThis record had 2 reference-validation errors before this PR. Its snippets wrote strain designations as
MPOB T,JF1 T,MF T; the cached text renders the superscript type-strain marker closed up —MPOBT,JF1T,MFT.A rendering artefact, not a misquotation. Corrected, so the record now validates at 0 issues rather than 2.
Checks
just validate— no issuesjust validate-references— Total checks: 0 (was 2)just validate-strict,just lint,just check-docs-current— exit 0uv run pytest tests/— 2375 passed, 16 skippedPart of #183.
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