From 49150110a7da040ddb59cb3efce53d7c7f28c640 Mon Sep 17 00:00:00 2001 From: "marcin p. joachimiak" <4625870+realmarcin@users.noreply.github.com> Date: Mon, 10 Aug 2026 23:40:31 -0700 Subject: [PATCH] Both arms of the biofilm consortium, not an average of them (#183) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Clostridium_Phytofermentans_Ecoli_Cellobiose_Biofilm_Consortium gets two cultivation_setup entries, because the paper ran two experiments on the same consortium and its result is the contrast between them. The planktonic arm: 18 x 150 mm Balch anaerobic tubes, 10 mL mGS-2, 150 rpm, 37 °C, with medium held under 5% H2 / 5% CO2 / 90% N2 in a Bactron II chamber until use. The biofilm arm: biofilms on medium plates moved to a fresh plate every two days, 37 °C, in an anoxic chamber, an oxic incubator, or both depending on the experiment — the oxygen regime is the variable, not a setting, so it is described rather than reduced to a field. Two enum approximations are labelled as such rather than left to look exact. A Balch tube is recorded as SERUM_BOTTLE, the nearest value for a butyl-stoppered anaerobic vessel, with the real vessel in instrument_detail. A surface-attached biofilm on a plate is OTHER, because FLASK or any reactor type would assert a containment this had none of. Unlike the last two records, neither arm here is a preculture — both are experiments on the consortium — so both belong. Co-Authored-By: Claude Opus 5 --- ...s_Ecoli_Cellobiose_Biofilm_Consortium.yaml | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) diff --git a/kb/communities/Clostridium_Phytofermentans_Ecoli_Cellobiose_Biofilm_Consortium.yaml b/kb/communities/Clostridium_Phytofermentans_Ecoli_Cellobiose_Biofilm_Consortium.yaml index 988023d9..165bedad 100644 --- a/kb/communities/Clostridium_Phytofermentans_Ecoli_Cellobiose_Biofilm_Consortium.yaml +++ b/kb/communities/Clostridium_Phytofermentans_Ecoli_Cellobiose_Biofilm_Consortium.yaml @@ -249,6 +249,58 @@ ecological_interactions: evidence_source: IN_VITRO snippet: C. phytofermentans resided primarily in the anoxic bottom of the biofilm explanation: Supports spatial oxygen niche partitioning in the consortium biofilm. +cultivation_setup: +- cultivation_mode: BATCH + system_type: SERUM_BOTTLE + working_volume: 10.0 + working_volume_unit: mL + operating_temperature: 37.0 + operating_temperature_unit: °C + instrument_detail: >- + The planktonic arm. 18 x 150 mm Balch anaerobic culture tubes holding 10 mL of mGS-2 + medium, shaken at 150 rpm. Medium was held in a Bactron II anaerobic chamber under + 5% H2 / 5% CO2 / 90% N2 until use. + notes: >- + SERUM_BOTTLE is the nearest enum value: a Balch tube is a butyl-stoppered anaerobic + culture vessel of the same kind, and the enum has no tube. The exact vessel is in + instrument_detail so the approximation is visible rather than implied. + evidence: + - reference: PMID:33268782 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Planktonic experiments were performed using 18 × 150 mm Balch anaerobic culture + tubes in containing 10 mL of mGS-2 medium in a shaker operated at 150 revolutions per + minute and 37 °C + explanation: Vessel, working volume, agitation and temperature for the planktonic arm. + - reference: PMID:33268782 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Media was kept in an anaerobic chamber (Bactron II, Sheldon Manufacturing Inc.) + with 5% H2, 5% CO2, and 90% N2 until it was used + explanation: How anaerobiosis was maintained up to inoculation. +- cultivation_mode: BATCH + system_type: OTHER + operating_temperature: 37.0 + operating_temperature_unit: °C + instrument_detail: >- + The biofilm arm, and the one the record is about. Biofilms on medium plates, moved to a + fresh plate every 2 days, incubated at 37 °C in an anoxic chamber, an oxic incubator, or + both depending on the experiment - the oxygen regime is the variable, not a setting. + notes: >- + A surface-attached biofilm on a plate has no enum value; OTHER with the description is + honest where FLASK or a reactor type would not be. Recorded as a second entry rather + than merged with the planktonic arm because the two are different experiments on the + same consortium, and the paper's result is the contrast between them - temporal + partitioning of anaerobic and aerobic metabolism within the biofilm. + evidence: + - reference: PMID:33268782 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Biofilms were incubated at 37 °C in an anoxic chamber and/or oxic incubator depending + on experiment. Biofilm cultures were aseptically transferred to a new medium plate every + 2 days + explanation: Temperature, the alternating oxygen regime, and the 2-day transfer schedule. + environmental_factors: - name: Modified GS-2 medium value: mGS-2