diff --git a/kb/communities/Kombucha_KMC_IMBG1_Fermentation_Community.yaml b/kb/communities/Kombucha_KMC_IMBG1_Fermentation_Community.yaml index b7319756..59518c82 100644 --- a/kb/communities/Kombucha_KMC_IMBG1_Fermentation_Community.yaml +++ b/kb/communities/Kombucha_KMC_IMBG1_Fermentation_Community.yaml @@ -207,4 +207,31 @@ associated_datasets: evidence_source: IN_VITRO snippet: submitted to the GenBank database under an accession numbers KF908872-KF90879 explanation: Supports the associated GenBank sequence-accession range reported by the study. +related_ingredients: +- preferred_term: sucrose + chebi_term: + id: CHEBI:17992 + label: sucrose + relevance: > + Sucrose is the primary fermentable carbon source added to the black-tea substrate that sustains + the KMC-IMBG1 yeast and acetobacterial community. + evidence: + - reference: PMID:26061774 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: black tea (Lipton, 1.2%, w/v) extract with sucrose (3.0%, w/v) + explanation: Names sucrose as the sweetener added to the black-tea fermentation medium. +- preferred_term: cellulose + chebi_term: + id: CHEBI:18246 + label: (1->4)-beta-D-glucan + relevance: > + Cellulose is produced by the acetobacterial members and forms the surface pellicle that physically + structures the kombucha community. + evidence: + - reference: doi:10.1186/s13568-015-0124-5 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: cellulose-based pellicles created by the cellulose-producing bacteria + explanation: Names cellulose as the pellicle material produced by community bacteria. metal_relevance: NOT_APPLICABLE diff --git a/kb/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.yaml b/kb/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.yaml index cd5b455c..82320713 100644 --- a/kb/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.yaml +++ b/kb/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.yaml @@ -238,6 +238,72 @@ environmental_factors: evidence_source: IN_VITRO snippet: from air, water, phosphate, trace metals, and sunlight explanation: Supports trace metals as reported inorganic inputs. +related_ingredients: +- preferred_term: sucrose + chebi_term: + id: CHEBI:17992 + label: sucrose + relevance: > + Sucrose is the cross-fed carbon currency: engineered cscB S. elongatus exports sucrose, and the + coculture cannot grow without a sucrose-exporting S. elongatus partner. + evidence: + - reference: PMID:27232890 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: sucrose-exporting S. elongatus + explanation: Names sucrose export by S. elongatus as required for coculture growth. +- preferred_term: polyhydroxybutyrate + chebi_term: + id: CHEBI:53389 + label: poly(3-hydroxybutyrate) + relevance: > + Polyhydroxybutyrate (PHB) is the industrially relevant biopolymer the designed coculture was shown + to produce from simple inorganic inputs and light. + evidence: + - reference: PMID:27232890 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: polyhydroxybutyrate (PHB) and alginate + explanation: Names polyhydroxybutyrate as an industrially relevant product of the system. +- preferred_term: alginate + chebi_term: + id: CHEBI:58187 + label: alginate + relevance: > + Alginate is named as a second industrially relevant biopolymer the coculture has the potential to + produce alongside PHB. + evidence: + - reference: PMID:27232890 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: polyhydroxybutyrate (PHB) and alginate + explanation: Names alginate as a potential industrially relevant product of the coculture. +- preferred_term: glutamate + chebi_term: + id: CHEBI:18237 + label: glutamic acid + relevance: > + Glutamate was supplied in the initial coculture studies that established the cross-feeding model + between S. elongatus and A. vinelandii. + evidence: + - reference: PMID:27232890 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: media with glutamate + explanation: Names glutamate as a medium component in the initial cross-feeding studies. +- preferred_term: phosphate + chebi_term: + id: CHEBI:18367 + label: phosphate(3-) + relevance: > + Phosphate is one of the simple inorganic inputs from which the coculture concept was designed to + drive chemical photoproduction. + evidence: + - reference: PMID:27232890 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: from air, water, phosphate, trace + explanation: Names phosphate among the simple inorganic inputs for photoproduction. growth_media: - name: Light-driven Synechococcus-Azotobacter coculture composition: diff --git a/kb/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml b/kb/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml index 1a721a14..48ff4098 100644 --- a/kb/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml +++ b/kb/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml @@ -232,5 +232,20 @@ associated_datasets: url: https://doi.org/10.1186/s13068-017-0736-x description: Open-access study reporting growth, sucrose use, ROS, biomass, and lipid measurements for S. elongatus-yeast artificial lichen cocultures. +related_ingredients: +- preferred_term: sucrose + chebi_term: + id: CHEBI:17992 + label: sucrose + relevance: > + Sucrose is the central exchanged metabolite of this synthetic lichen coculture: engineered + cscB+ Synechococcus elongatus secretes it as photosynthate and Rhodotorula glutinis consumes it + as its carbon source for growth and lipid production. + evidence: + - reference: doi:10.1186/s13068-017-0736-x + supports: SUPPORT + evidence_source: IN_VITRO + snippet: sucrose-secreting cyanobacterium Synechococcus elongatus + explanation: Names sucrose as the metabolite secreted by the engineered cyanobacterial partner. metal_relevance: NOT_APPLICABLE