From ea3dbcb947945a5339c064190753a607d36226a8 Mon Sep 17 00:00:00 2001 From: "marcin p. joachimiak" <4625870+realmarcin@users.noreply.github.com> Date: Mon, 10 Aug 2026 22:23:17 -0700 Subject: [PATCH] Record the reactor, not the precultures beside it (#183) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Clostridium_Ljungdahlii_Kluyveri_Syngas_Alcohol_Coculture: a 2 L Biostat M at 1 L working volume, 37 °C by water jacket, pH controlled by KOH, agitation raised from 200 to 400 rpm at hour 475, fed continuously with syngas (60% CO, 35% H2, 5% CO2) recirculated through the headspace. Two judgements are recorded rather than assumed. The mode is CONTINUOUS, not CHEMOSTAT, even though the vessel is sold as a chemostat and the paper calls it one. Cells were retained, giving a bleed rate of a quarter of the applied dilution rate, so biomass is not washed out at the dilution rate and the defining property of a chemostat does not hold. What the equipment is called is not evidence about how it was run. feed_or_dilution_rate is unset: 80 mL/h in Phase 1, 40 mL/h in Phases 2-5, and the phases are the experiment. A single value would assert a steady state the paper does not claim — the same call made for the thiocyanate retention time and the Caldicellulosiruptor dilution sweep. The same paper carries serum-bottle conditions — 160 mL bottles, 10 to 50 mL working volume, 35 °C — and none of them are here. Those are the two strains' separate precultures. Recording them as the community's setup is exactly the error #529 was filed for, and this record is where that guard first had something to be careful about. Co-Authored-By: Claude Opus 5 --- ...lii_Kluyveri_Syngas_Alcohol_Coculture.yaml | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) diff --git a/kb/communities/Clostridium_Ljungdahlii_Kluyveri_Syngas_Alcohol_Coculture.yaml b/kb/communities/Clostridium_Ljungdahlii_Kluyveri_Syngas_Alcohol_Coculture.yaml index 0a4b807f..05f188ec 100644 --- a/kb/communities/Clostridium_Ljungdahlii_Kluyveri_Syngas_Alcohol_Coculture.yaml +++ b/kb/communities/Clostridium_Ljungdahlii_Kluyveri_Syngas_Alcohol_Coculture.yaml @@ -292,6 +292,56 @@ ecological_interactions: evidence_source: IN_VITRO snippet: two bioprocesses compete for intermediates explanation: Supports competition for carboxylate intermediates between chain elongation and biological reduction. +cultivation_setup: +- cultivation_mode: CONTINUOUS + system_type: STIRRED_TANK_BIOREACTOR + manufacturer_model: Biostat M (Braun, Allentown, PA), 2 L vessel + working_volume: 1.0 + working_volume_unit: L + operating_temperature: 37.0 + operating_temperature_unit: °C + ph_controlled: true + temperature_controlled: true + instrument_detail: >- + A single-stage 2 L Biostat M run at 1 L working volume, fed continuously from a medium + reservoir and sparged with syngas (60% CO, 35% H2, 5% CO2) into the headspace, with the + gas recirculated. Temperature held by water jacket. + controls_notes: >- + pH controlled by 2 M KOH alone until hour 1510, and by a second addition thereafter. + Agitation began at 200 rpm and was raised to 400 rpm at hour 475. + notes: >- + Recorded as CONTINUOUS rather than CHEMOSTAT even though the vessel is sold as one. Cells + were retained, giving a bleed rate of a quarter of the applied dilution rate, so biomass + is not washed out at the dilution rate and the defining property of a chemostat does not + hold. The paper's own word for the equipment is not evidence about how it was operated. + + `feed_or_dilution_rate` is left unset for the same reason the ramped cases elsewhere are: + it was 80 mL/h in Phase 1 and 40 mL/h in Phases 2-5, and a single value would assert a + steady state across a run whose phases are the experiment. + + Nothing here comes from the serum-bottle passages in the same paper - 160 mL bottles at + 10, 20 or 50 mL working volume, 35 °C. Those are the two strains' separate precultures, + not the coculture, and recording them as the community's setup is the error class #529 + was filed for. + evidence: + - reference: PMID:27877166 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: One 2 L Biostat M chemostat (Braun, Allentown, PA) with a 1 L working volume was + used for the reactor experiment + explanation: The vessel, its model and the working volume. + - reference: PMID:27877166 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: The temperature was controlled at 37°C by a water jacket + explanation: Sources operating_temperature and temperature_controlled. + - reference: PMID:27877166 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: this setup resulted in a rate of cell withdrawal (bleed rate) of 1/4 of the applied + dilution rate + explanation: Cell retention, which is why the mode is CONTINUOUS and not CHEMOSTAT. + environmental_factors: - name: Syngas feed value: 60% CO, 35% H2, and 5% CO2