From bd7d8bfe458a595de2505c9730c27ad1269f6b8d Mon Sep 17 00:00:00 2001 From: "marcin p. joachimiak" <4625870+realmarcin@users.noreply.github.com> Date: Tue, 11 Aug 2026 00:21:31 -0700 Subject: [PATCH] =?UTF-8?q?Static=2060=20=C2=B0C=20anaerobic=20culture,=20?= =?UTF-8?q?and=20why=20static=20is=20a=20setting=20(#183)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Clostridium_Thermoanaerobacterium_JN4_GD17_Cellulosic_Biofuel_Coculture: CTFUD medium in anaerobic tubes or serum bottles, 60 °C incubator, no agitation. "Without agitation" is in the record rather than dropped as an absence, because it is a choice. These are thermophilic cellulose degraders and C. thermocellum works through a surface-attached cellulosome, so leaving the substrate settled is part of the design. A reader who saw no agitation field would assume it went unmentioned. No working volume: the source offers "tubes/serum bottles", either, and never a fill volume — and the two would not imply the same one. This is the first of the recent batch where the #529 question answers itself. The cited sentence names "the reconstructed coculture of the two bacteria" among what was grown this way, alongside each strain alone, so the conditions are explicitly the community's rather than inferred from a member count. It is also why the paper's monoculture and coculture results are comparable at all. Co-Authored-By: Claude Opus 5 --- ...JN4_GD17_Cellulosic_Biofuel_Coculture.yaml | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/kb/communities/Clostridium_Thermoanaerobacterium_JN4_GD17_Cellulosic_Biofuel_Coculture.yaml b/kb/communities/Clostridium_Thermoanaerobacterium_JN4_GD17_Cellulosic_Biofuel_Coculture.yaml index d4787ea1..6ce590ea 100644 --- a/kb/communities/Clostridium_Thermoanaerobacterium_JN4_GD17_Cellulosic_Biofuel_Coculture.yaml +++ b/kb/communities/Clostridium_Thermoanaerobacterium_JN4_GD17_Cellulosic_Biofuel_Coculture.yaml @@ -337,6 +337,37 @@ ecological_interactions: evidence_source: IN_VITRO snippet: relieves the carbon catabolite repression of C. thermocellum JN4 explanation: Supports the narrower mechanism that GD17 can also relieve carbon catabolite repression. +cultivation_setup: +- cultivation_mode: BATCH + system_type: SERUM_BOTTLE + operating_temperature: 60.0 + operating_temperature_unit: °C + instrument_detail: >- + Anaerobic tubes or serum bottles of CTFUD medium in a 60 °C incubator, static. The same + conditions were used for each strain alone and for the reconstructed coculture, which is + what makes the monoculture and coculture results in this paper comparable. + notes: >- + "Without agitation" is recorded because it is a choice rather than an omission: these are + thermophilic cellulose degraders and C. thermocellum works through a surface-attached + cellulosome, so leaving the substrate settled is part of the design, not a detail that + went unmentioned. + + No working volume. The source names the vessel type - tubes or serum bottles, either - + but never a fill volume, and the two would not imply the same one. + + Unlike several neighbouring #183 records, the cited conditions are explicitly the + coculture's as well as the monocultures': the sentence names "the reconstructed coculture + of the two bacteria" among what was grown this way. That is the check #529 asks for, and + here it passes on the sentence itself rather than on a member-name count. + evidence: + - reference: PMID:31551972 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Clostridium thermocellum JN4, T. thermosaccharolyticum GD17 and the reconstructed + coculture of the two bacteria were grown using CTFUD media in anaerobic tubes/serum bottles + in an incubator at 60°C without agitation + explanation: Vessel, medium, temperature and static operation, stated for the coculture itself. + environmental_factors: - name: Cellulose-rich lignocellulosic substrate value: cellulose