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