From 106d3744264c7a3ff9b2ca0b0177b5eec4077220 Mon Sep 17 00:00:00 2001 From: "marcin p. joachimiak" <4625870+realmarcin@users.noreply.github.com> Date: Mon, 10 Aug 2026 23:01:30 -0700 Subject: [PATCH] SIHUMIx: chemostat, and three fields left empty on purpose (#183) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit In vitro bioreactors run chemostatically on complex intestinal medium, held anaerobic by continuously gassing the vessels with nitrogen, 250 mL. Each of the eight species is grown alone for 72 h first and the reactor inoculated with 1e9 cells of each, so the community starts from a defined, equal-per-strain inoculum rather than a mixed culture — worth recording because it is what makes SIHUMIx reproducible between labs. What is not recorded matters as much here. system_type is BIOREACTOR_UNSPECIFIED. The paper says "in vitro bioreactors" and points at prior work for the design; it never says stirred-tank. Guessing the vessel would put an unevidenced enum value where a reader takes it as read from this paper. operating_temperature is absent. The 37 °C and 175 rpm in this paper attach to strains "cultivated separately" in BHI — the eight precultures, not the community. That is the second record running where the same paper carries preculture conditions next to the community's, which is the pattern #529 names; the bioreactor's own temperature lives in the cited prior study. The 250 mL is flagged in notes as the medium volume the inoculum went into. It is the closest thing the source offers to a working volume and the source does not call it one. Co-Authored-By: Claude Opus 5 --- ...UMIx_Human_Intestinal_Model_Community.yaml | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) diff --git a/kb/communities/SIHUMIx_Human_Intestinal_Model_Community.yaml b/kb/communities/SIHUMIx_Human_Intestinal_Model_Community.yaml index 0ac0a340..eb043ecd 100644 --- a/kb/communities/SIHUMIx_Human_Intestinal_Model_Community.yaml +++ b/kb/communities/SIHUMIx_Human_Intestinal_Model_Community.yaml @@ -330,6 +330,51 @@ ecological_interactions: evidence_source: IN_VITRO snippet: Two of these novel sProteins have a potential antimicrobial function explanation: Supports potential interaction-relevant antimicrobial functions. +cultivation_setup: +- cultivation_mode: CHEMOSTAT + system_type: BIOREACTOR_UNSPECIFIED + working_volume: 250.0 + working_volume_unit: mL + instrument_detail: >- + In vitro bioreactors run chemostatically on a complex intestinal medium, held anaerobic + by continuously gassing the vessels with nitrogen. Each of the eight species was grown + individually for 72 h first, then the reactor was inoculated with 1e9 cells of each, so + the community starts from a defined and equal-per-strain inoculum rather than from a + mixed culture. + notes: >- + `system_type` is BIOREACTOR_UNSPECIFIED on purpose. The source says "in vitro + bioreactors" and refers to a prior paper for the design; it never says stirred-tank, and + guessing the vessel would put an unevidenced enum value where a reader would take it as + read from this paper. + + Operating temperature is absent for the same reason. The 37 °C and 175 rpm in this paper + belong to the sentence about strains "cultivated separately" in BHI - those are the + eight precultures, not the community, and recording them here is the error class #529 + covers. The bioreactor's own temperature is in the cited prior work. + + The 250 mL is the medium volume the inoculum went into, which is the closest thing the + source gives to a working volume; it is not called that. + evidence: + - reference: PMID:33622394 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: The SIHUMIx community was cultivated in chemostatic bioreactors + explanation: Sources both the chemostat mode and the bioreactor system type. + - reference: PMID:33622394 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: continuously cultivated in complex intestinal medium (Supplement Table 2) and + maintained under anaerobic conditions by continuously gassing the bioreactor vessels + with nitrogen + explanation: Continuous operation, the medium, and how anaerobiosis was maintained. + - reference: PMID:33622394 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: the eight bacterial species were cultivated individually for 72 h before inoculation + of the bioreactor with 1 × 109 bacterial cells per strain (total cell number = 8 × 109 + cells in 250 mL medium) + explanation: The inoculation scheme and the 250 mL the community was grown in. + environmental_factors: - name: Anaerobic Atmosphere value: Nitrogen-gassed anaerobic bioreactor