From bacbf137a0bc88a8214fd0a5f84f640474a3de92 Mon Sep 17 00:00:00 2001 From: "marcin p. joachimiak" <4625870+realmarcin@users.noreply.github.com> Date: Tue, 11 Aug 2026 04:28:01 -0700 Subject: [PATCH] A deliberately partial setup, labelled as one (#183) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Bifidobacterium_Ruminococcus_Infant_HMO_CrossFeeding gets a cultivation_setup with no system_type, no working_volume and no operating_temperature. What the source does state, for "all cultivation work", is the atmosphere: a Coy Labs anaerobic chamber under 70% N2 / 25% CO2 / 5% H2, with media sparged and reduced with l-cysteine and sugar solutions equilibrated in the chamber for 48 h before use. That phrasing covers the B. breve / R. gnavus cocultures, so it is theirs. For a strict-anaerobe gut community the chamber composition is a real fact about how it was grown, not a placeholder. The paper then defers the coculture's vessel, volume and temperature to "(Methods)", which the cached text does not carry. The 37 °C with shaking that does appear belongs to a 48 h inoculum recovery step, so recording it would be #529 for the sixth time in this batch. Padding the block out would have been easy and wrong. The empty fields and the reason for each are in notes, so a later curator with the full methods knows exactly what to add rather than having to re-derive what was already checked. Co-Authored-By: Claude Opus 5 --- ..._Ruminococcus_Infant_HMO_CrossFeeding.yaml | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/kb/communities/Bifidobacterium_Ruminococcus_Infant_HMO_CrossFeeding.yaml b/kb/communities/Bifidobacterium_Ruminococcus_Infant_HMO_CrossFeeding.yaml index 3bbc4853..750d3a97 100644 --- a/kb/communities/Bifidobacterium_Ruminococcus_Infant_HMO_CrossFeeding.yaml +++ b/kb/communities/Bifidobacterium_Ruminococcus_Infant_HMO_CrossFeeding.yaml @@ -147,6 +147,43 @@ ecological_interactions: evidence_source: IN_VITRO snippet: HMO utilization can vary with an individual's microbiome explanation: Supports the inter-individual variability of HMO utilization. +cultivation_setup: +- instrument_detail: >- + All cultivation was done inside a Coy Labs anaerobic chamber under 70% N2 / 25% CO2 / + 5% H2. Media were sparged with N2 and reduced with l-cysteine hydrochloride, and sugar + solutions were equilibrated in the chamber for at least 48 h before use, so the carbon + source itself was anoxic at the point of mixing. + controls_notes: >- + Atmosphere controlled by the chamber rather than by a headspace in each vessel, which is + why gas composition is recorded here and not as a per-culture setting. + notes: >- + Deliberately partial, and worth saying so rather than padding. The source states the + chamber and its gas mix for "all cultivation work", which covers the B. breve / + R. gnavus cocultures - so that much is theirs. It then defers the coculture's vessel, + volume and temperature to "(Methods)", which the cached text does not carry. + + So no `system_type`, no `working_volume`, no `operating_temperature`. The 37 °C with + shaking elsewhere in the paper belongs to a 48 h inoculum recovery step, not to the + cocultures (#529), and the gas mix is a genuine fact about how this community was grown + rather than a placeholder for the ones that are missing. + + The cocultures were run with 2'-fucosyllactose, or its constituents l-fucose and + d-lactose, as the sole carbohydrate source; that design is the cross-feeding this record + documents and is described in the interactions rather than repeated here. + evidence: + - reference: PMID:37973815 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: All cultivation work was performed in the same anaerobic chamber (Coy Labs; 70% N2, + 25% CO2, 5% H2) + explanation: The atmosphere, stated for all cultivation and so covering the cocultures. + - reference: PMID:37973815 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: Sugar solutions were loosely capped and stored in the anaerobic chamber for at least + 48 h before mixing with BHI-based media for cultivation + explanation: The carbon source was anoxic before it reached the culture. + environmental_factors: - name: 2'-fucosyllactose supplementation value: 2'FL HMO substrate