From 80ce041a749e2d53ed598dec3c08700f1257dc7f Mon Sep 17 00:00:00 2001 From: "marcin p. joachimiak" <4625870+realmarcin@users.noreply.github.com> Date: Tue, 11 Aug 2026 06:03:30 -0700 Subject: [PATCH] Cheese rind: the in vitro arm only, and OMM12 refused (#183, #543) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Cheese_Rind_InSitu_InVitro_Model_Community: communities reconstructed on cheese curd agar from roughly equal inocula, followed over time by pulling agar plugs from 96-well plates and counting CFUs, plates at room temperature. Only the in vitro arm is recorded. The record also covers an in situ survey, and sampled cheese rind is not a cultivation — the same distinction that made Avena_Rhizosphere unenrichable, except that here one paper supplies both and only one belongs in this slot. system_type is OTHER: an agar-plug community in a 96-well plate has no enum value, and FLASK or a reactor type would assert a liquid culture this is not. No operating_temperature either — the source says "room temperature", and turning that into 20 or 25 °C would invent precision the paper declined to give. OMM12_Gnotobiotic_Mouse_Gut_Community was checked and refused. Its in vitro step is per-strain revival from glycerol cryostocks into 100 ml serum bottles before the mixture is inoculated into germ-free mice; the community itself lives in the animal. Recording those bottles would be the preculture error, and a gnotobiotic mouse is not a CultivationSetup. Two of the thirteen full-text candidates in #543 are now known to be host-associated or environmental rather than cultured. The remaining plant SynComs and the second gut community likely need the same check before anyone treats that list as a work queue. Co-Authored-By: Claude Opus 5 --- ...e_Rind_InSitu_InVitro_Model_Community.yaml | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/kb/communities/Cheese_Rind_InSitu_InVitro_Model_Community.yaml b/kb/communities/Cheese_Rind_InSitu_InVitro_Model_Community.yaml index f19a8c89..fd9329a0 100644 --- a/kb/communities/Cheese_Rind_InSitu_InVitro_Model_Community.yaml +++ b/kb/communities/Cheese_Rind_InSitu_InVitro_Model_Community.yaml @@ -181,6 +181,43 @@ ecological_interactions: evidence_source: IN_VITRO snippet: succession in vitro was highly reproducible amongst replicates explanation: Supports reproducible temporal assembly in the reconstructed natural-rind community. +cultivation_setup: +- cultivation_mode: BATCH + system_type: OTHER + instrument_detail: >- + The in vitro arm. Communities reconstructed on cheese curd agar, inoculated with roughly + equal numbers of each member and followed over time; growth monitored by removing agar + plugs from 96-well plates, homogenising in PBS and counting CFUs. Plates at room + temperature. + notes: >- + `system_type` is OTHER because an agar-plug community in a 96-well plate has no enum + value, and FLASK or any reactor type would assert a liquid culture this is not. The + format is in instrument_detail instead. + + No operating_temperature: the source says "room temperature" rather than a figure, and + turning that into 20 or 25 °C would invent precision the paper declined to give. + + This record covers an in situ survey as well as this in vitro reconstruction, and only + the reconstruction is a cultivation. The in situ side is sampled cheese rind - the same + distinction that made Avena_Rhizosphere unenrichable (#543), except that here the paper + supplies both and only one of them belongs in this slot. + + The medium is the point rather than a detail: cheese curd agar is what makes the in vitro + system recapitulate the in situ succession, which is the paper's central claim. + evidence: + - reference: PMID:25036636 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: We inoculated approximately equal numbers of each together onto cheese curd agar and + followed membership of the in vitro rind communities over time + explanation: The medium and the equal-inoculum design of the reconstructed community. + - reference: PMID:25036636 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Plates were incubated at room temperature, and after colony and foci formation, CFUs + of each strain were counted + explanation: Incubation temperature as stated, and how the community was followed. + environmental_factors: - name: rind moisture value: natural-rind treatment drier than undried plates