diff --git a/docs/communities/DIETsimp_Lignocellulose_to_Methane_DIET_Consortia.html b/docs/communities/DIETsimp_Lignocellulose_to_Methane_DIET_Consortia.html index 31851b00..32916333 100644 --- a/docs/communities/DIETsimp_Lignocellulose_to_Methane_DIET_Consortia.html +++ b/docs/communities/DIETsimp_Lignocellulose_to_Methane_DIET_Consortia.html @@ -409,6 +409,7 @@

DIET-based Simplified Lignocellulose-to-Methane Consortia (DIETsimp)

+ @@ -771,6 +772,47 @@

Evidence

+
+

Knowledge gaps & discussions (1)

+ +
+

+ KNOWLEDGE_GAP + OPEN + Are the S. globosa→M. mazei and C. aceticum→M. mazei DIET pathways experimentally validated (direct interspecies electron transfer vs H2/formate mediation), and is there any causal dependency between the two parallel donor→methanogen relationships? + +

+

An Edison causal-graph pass (PMID:42229598) found no justifiable directed causal edge for this consortium: both interactions are recorded as "Proposed DIET pathway", the primary full text was inaccessible, and no perturbation (donor-removal, inhibitor, mono-/co-culture, or knockout) evidence was retrieved. The source supports two parallel donor→methanogen proposals, not a causal dependency of one on the other, so no `downstream` edge was added. Neutral-red-mediated electron delivery to M. mazei reported in a different system must not be imported here without exact-system verification. +

+ +

Attaches to: ecological_interactions#DIET syntrophy from S. globosa to M. mazei, ecological_interactions#DIET syntrophy from C. aceticum to M. mazei

+ + + +
+ 1 evidence item(s) + +
+
+ IN_VITRO + PARTIAL + + + + PMID:42229598 + + +
+

during anaerobic digestion of lignocellulose that S. globosa and C. aceticum metabolized intermediates

+

The consortium role is stated at the level of intermediate metabolism / proposed DIET, without a validated or perturbation-tested causal mechanism — the basis for the knowledge gap.

+
+ +
+ + +
+ +
diff --git a/docs/communities/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture.html b/docs/communities/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture.html index bd482439..2b367fb2 100644 --- a/docs/communities/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture.html +++ b/docs/communities/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture.html @@ -409,6 +409,7 @@

Dehalococcoides-Syntrophomonas TCE Dechlorination Coculture

+ @@ -631,6 +632,15 @@

Butyrate Fermentation Supporting TCE Dechlorination

+
+ Downstream Effects: + +
+ → Reductive Dechlorination by Dehalococcoides +
+ +
+

Evidence

@@ -802,6 +812,15 @@

Aggregation-Enhanced Hydrogen Flux

+
+ Downstream Effects: + +
+ → Reductive Dechlorination by Dehalococcoides +
+ +
+

Evidence

diff --git a/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html b/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html index de34cff3..f7acff03 100644 --- a/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html +++ b/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html @@ -409,6 +409,7 @@

Syntrophomonas-Methanococcus Butyrate Growth Coordination Coculture

+ @@ -645,6 +646,15 @@

Syntrophic Butyrate Oxidation and Methanogenesis

+
+ Downstream Effects: + +
+ → Population Ratio Convergence During Growth +
+ +
+

Evidence

@@ -815,6 +825,47 @@

Evidence

+
+

Knowledge gaps & discussions (1)

+ +
+

+ KNOWLEDGE_GAP + OPEN + Does syntrophic aggregation / cell-to-cell attraction causally enhance butyrate oxidation or methanogenesis in this coculture, and is direct interspecies electron transfer (e.g. the reported carbon-nanotube methane stimulation) involved rather than only H2/formate transfer? + +

+

Aggregation and disturbance-resistant cell-to-cell attraction are observed, but no experiment demonstrates that aggregation increases butyrate oxidation or methane production in this exact coculture, so no aggregation→enhancement `downstream` edge was added. Likewise, carbon-nanotube acceleration of methane production is reported, but DIET "does not always explain the enhancement of methane production" and was not directly proven here, so a DIET mechanism is not asserted. +

+ +

Attaches to: ecological_interactions#Syntrophic Aggregation and Cell-to-Cell Attraction

+ + + +
+ 1 evidence item(s) + +
+
+ IN_VITRO + PARTIAL + + + + PMID:34603271 + + +
+

suggesting the cell-to-cell attraction between Syntrophomonas and Methanococcus

+

Attraction/aggregation is observed, but its causal contribution to metabolic performance is untested — the basis for the knowledge gap.

+
+ +
+ + +
+ +
diff --git a/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html b/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html index 0961904e..f6ed0b4b 100644 --- a/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html +++ b/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html @@ -409,6 +409,7 @@

Trichococcus-Syntrophomonas-Methanospirillum Butyrate Coculture

+ @@ -765,6 +766,15 @@

Aggregation With Syntrophic Partners

+
+ Downstream Effects: + +
+ → Fermenter-Stimulated Butyrate Oxidation and Methane Production +
+ +
+

Evidence

@@ -830,6 +840,15 @@

Proteome Response in the Syntrophic Partners

+
+ Downstream Effects: + +
+ → Fermenter-Stimulated Butyrate Oxidation and Methane Production +
+ +
+

Evidence

@@ -919,6 +938,47 @@

Associated Datasets

+
+

Knowledge gaps & discussions (1)

+ +
+

+ KNOWLEDGE_GAP + OPEN + Does T. flocculiformis ES5 improve the S. wolfei / M. hungatei syntrophy via co-aggregation-based spatial bridging (possible DIET) or via the observed proteomic changes, and is either mechanism causal rather than correlative? + +

+

The ES5-driven increase in butyrate consumption (120%) and methane (150%) is perturbation-supported, but the mediating mechanism is unresolved: aggregation and the partner proteome response are observed correlates, not demonstrated causal mediators (the two `downstream` edges here are flagged HYPOTHESIZED accordingly). Direct interspecies electron transfer was not experimentally demonstrated for this tri-culture, and the exact ES5 bridging role remains an open question per the source. +

+ +

Attaches to: ecological_interactions#Aggregation With Syntrophic Partners, ecological_interactions#Proteome Response in the Syntrophic Partners

+ + + +
+ 1 evidence item(s) + +
+
+ IN_VITRO + PARTIAL + + + + PMID:35699440 + + +
+

T. flocculiformis ES5 to aggregate with the syntrophic partners

+

Aggregation is reported as an association accompanying the ES5 effect, without a demonstrated causal-mediation or DIET mechanism — the basis for the knowledge gap.

+
+ +
+ + +
+ +
diff --git a/kb/communities/DIETsimp_Lignocellulose_to_Methane_DIET_Consortia.yaml b/kb/communities/DIETsimp_Lignocellulose_to_Methane_DIET_Consortia.yaml index 06a8d5d0..659622fe 100644 --- a/kb/communities/DIETsimp_Lignocellulose_to_Methane_DIET_Consortia.yaml +++ b/kb/communities/DIETsimp_Lignocellulose_to_Methane_DIET_Consortia.yaml @@ -237,3 +237,32 @@ growth_media: snippet: during anaerobic digestion of lignocellulose that S. globosa and C. aceticum metabolized intermediates explanation: Confirms cultivation is anaerobic (anaerobic digestion of lignocellulose). +discussions: +- discussion_id: kg-dietsimp-proposed-diet-no-causal-edge + prompt: > + Are the S. globosa→M. mazei and C. aceticum→M. mazei DIET pathways + experimentally validated (direct interspecies electron transfer vs + H2/formate mediation), and is there any causal dependency between the two + parallel donor→methanogen relationships? + kind: KNOWLEDGE_GAP + status: OPEN + attaches_to: + - ecological_interactions#DIET syntrophy from S. globosa to M. mazei + - ecological_interactions#DIET syntrophy from C. aceticum to M. mazei + rationale: > + An Edison causal-graph pass (PMID:42229598) found no justifiable directed + causal edge for this consortium: both interactions are recorded as "Proposed + DIET pathway", the primary full text was inaccessible, and no perturbation + (donor-removal, inhibitor, mono-/co-culture, or knockout) evidence was + retrieved. The source supports two parallel donor→methanogen proposals, not a + causal dependency of one on the other, so no `downstream` edge was added. + Neutral-red-mediated electron delivery to M. mazei reported in a different + system must not be imported here without exact-system verification. + evidence: + - reference: PMID:42229598 + supports: PARTIAL + evidence_source: IN_VITRO + snippet: during anaerobic digestion of lignocellulose that S. globosa and C. aceticum + metabolized intermediates + explanation: The consortium role is stated at the level of intermediate metabolism / proposed + DIET, without a validated or perturbation-tested causal mechanism — the basis for the knowledge gap. diff --git a/kb/communities/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture.yaml b/kb/communities/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture.yaml index 870e76cc..15725dda 100644 --- a/kb/communities/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture.yaml +++ b/kb/communities/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture.yaml @@ -141,6 +141,13 @@ ecological_interactions: term: id: GO:0044419 label: biological process involved in interspecies interaction between organisms + downstream: + - target: Reductive Dechlorination by Dehalococcoides + description: > + Hydrogen produced during syntrophic butyrate oxidation by S. wolfei + supplies the electron donor D. mccartyi 195 uses for TCE dechlorination; + the coupling is demonstrated by nanomolar aqueous H2 during dechlorination + and the strain-195 minimum H2 threshold. evidence: - reference: PMID:25576615 supports: SUPPORT @@ -230,6 +237,13 @@ ecological_interactions: term: id: GO:0044419 label: biological process involved in interspecies interaction between organisms + downstream: + - target: Reductive Dechlorination by Dehalococcoides + description: > + Cell aggregation shortens the interspecies distance and sustains the + hydrogen flux required for the observed TCE dechlorination rates + (supported by the reported need for aggregation; lower-confidence than the + direct H2-threshold edge). evidence: - reference: PMID:25576615 supports: SUPPORT diff --git a/kb/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml b/kb/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml index 334d7cba..d83bd3f2 100644 --- a/kb/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml +++ b/kb/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml @@ -133,6 +133,13 @@ ecological_interactions: term: id: GO:0015948 label: methanogenesis + downstream: + - target: Population Ratio Convergence During Growth + description: > + The thermodynamically required syntrophic coupling of butyrate oxidation to + hydrogenotrophic methanogenesis drives coordinated partner growth — cultures + inoculated at different initial cell ratios converge to a relatively constant + Syntrophomonas:Methanococcus ratio over time. evidence: - reference: PMID:34603271 supports: SUPPORT @@ -362,3 +369,29 @@ metal_relevance: NOT_APPLICABLE metal_notes: > No metal or rare earth element transformation role is curated for this methanogenic butyrate-oxidizing coculture. +discussions: +- discussion_id: kg-aggregation-and-diet-unverified + prompt: > + Does syntrophic aggregation / cell-to-cell attraction causally enhance + butyrate oxidation or methanogenesis in this coculture, and is direct + interspecies electron transfer (e.g. the reported carbon-nanotube methane + stimulation) involved rather than only H2/formate transfer? + kind: KNOWLEDGE_GAP + status: OPEN + attaches_to: + - ecological_interactions#Syntrophic Aggregation and Cell-to-Cell Attraction + rationale: > + Aggregation and disturbance-resistant cell-to-cell attraction are observed, + but no experiment demonstrates that aggregation increases butyrate oxidation or + methane production in this exact coculture, so no aggregation→enhancement + `downstream` edge was added. Likewise, carbon-nanotube acceleration of methane + production is reported, but DIET "does not always explain the enhancement of + methane production" and was not directly proven here, so a DIET mechanism is + not asserted. + evidence: + - reference: PMID:34603271 + supports: PARTIAL + evidence_source: IN_VITRO + snippet: suggesting the cell-to-cell attraction between Syntrophomonas and Methanococcus + explanation: Attraction/aggregation is observed, but its causal contribution to metabolic + performance is untested — the basis for the knowledge gap. diff --git a/kb/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml b/kb/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml index aff79d6c..3c906c16 100644 --- a/kb/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml +++ b/kb/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml @@ -199,6 +199,13 @@ ecological_interactions: term: id: GO:0044419 label: biological process involved in interspecies interaction between organisms + downstream: + - target: Fermenter-Stimulated Butyrate Oxidation and Methane Production + description: > + HYPOTHESIZED — ES5 co-aggregation with S. wolfei and M. hungatei may + spatially facilitate the improved butyrate oxidation and methane + production, but the aggregation is an observed correlate of the ES5 effect + and was NOT demonstrated to causally mediate the rate increases. evidence: - reference: PMID:35699440 supports: SUPPORT @@ -231,6 +238,14 @@ ecological_interactions: term: id: GO:0006635 label: fatty acid beta-oxidation + downstream: + - target: Fermenter-Stimulated Butyrate Oxidation and Methane Production + description: > + HYPOTHESIZED — the ES5-associated proteomic changes (activation of + additional butyryl-CoA dehydrogenase and electron-transfer flavoprotein in + S. wolfei; signal-transducing systems in M. hungatei) may underlie the + improved butyrate oxidation, but the proteome response is correlative and + was NOT shown to be the causal mediator of the improved performance. evidence: - reference: PMID:35699440 supports: SUPPORT @@ -416,3 +431,29 @@ metal_relevance: NOT_APPLICABLE metal_notes: > No metal or rare earth element transformation role is curated for this fermenter-stimulated methanogenic butyrate coculture. +discussions: +- discussion_id: kg-es5-mediation-mechanism-unresolved + prompt: > + Does T. flocculiformis ES5 improve the S. wolfei / M. hungatei syntrophy via + co-aggregation-based spatial bridging (possible DIET) or via the observed + proteomic changes, and is either mechanism causal rather than correlative? + kind: KNOWLEDGE_GAP + status: OPEN + attaches_to: + - ecological_interactions#Aggregation With Syntrophic Partners + - ecological_interactions#Proteome Response in the Syntrophic Partners + rationale: > + The ES5-driven increase in butyrate consumption (120%) and methane (150%) is + perturbation-supported, but the mediating mechanism is unresolved: aggregation + and the partner proteome response are observed correlates, not demonstrated + causal mediators (the two `downstream` edges here are flagged HYPOTHESIZED + accordingly). Direct interspecies electron transfer was not experimentally + demonstrated for this tri-culture, and the exact ES5 bridging role remains an + open question per the source. + evidence: + - reference: PMID:35699440 + supports: PARTIAL + evidence_source: IN_VITRO + snippet: T. flocculiformis ES5 to aggregate with the syntrophic partners + explanation: Aggregation is reported as an association accompanying the ES5 effect, without a + demonstrated causal-mediation or DIET mechanism — the basis for the knowledge gap.