Add Saccharomyces-Acinetobacter lignocellulose detox coculture community#65
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Curate a new community YAML (CommunityMech:000263) from the orphan cache PMID:38711153 (Salusjarvi et al. 2024 Biotechnol Biofuels, "Enhanced upgrading of lignocellulosic substrates by coculture of Saccharomyces cerevisiae and Acinetobacter baylyi ADP1"). Defined two-member synthetic coculture, well-supported by a single PMID with a complete abstract. Members: - engineered Saccharomyces cerevisiae (NCBITaxon:4932, PRIMARY_DEGRADER) - lactic acid producer. - engineered Acinetobacter baylyi ADP1 (NCBITaxon:202950, CROSS_FEEDER) - furan-aldehyde detoxifier and wax-ester producer from S. cerevisiae byproducts. Interactions: - Furan Aldehyde Detoxification Cross-Protection (COMMENSALISM): A. baylyi bioconverts furfural and 5-HMF without competing for substrates, raising S. cerevisiae lactic acid productivity ~1.5x over monoculture (to 0.41 +/- 0.08 g/L/h). - Carbon Diversion to Wax Esters (CROSS_FEEDING): residual carbon and byproducts from S. cerevisiae are diverted by A. baylyi into wax ester biosynthesis. Environmental factor: furan aldehyde inhibitors (furfural and 5-HMF) in synthetic lignocellulosic hydrolysate. All snippets are verbatim substrings of the cached PubMed abstract. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Pull request overview
Adds a new curated CommunityMech knowledge-base entry (CommunityMech:000263) describing an engineered, two-member Saccharomyces cerevisiae + Acinetobacter baylyi ADP1 coculture for lignocellulosic hydrolysate detoxification and product formation, backed by PMID:38711153.
Changes:
- Introduces a new community YAML with engineering design metadata, member taxonomy, and evidence-backed interactions.
- Encodes two ecological interactions (detoxification cross-protection; carbon diversion to wax esters) plus an inhibitor environmental factor.
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- S. cerevisiae functional_role: PRIMARY_DEGRADER -> SECONDARY_FERMENTER. Per the schema, PRIMARY_DEGRADER is "degrades complex substrates"; in this system the yeast produces lactic acid from already- hydrolysed sugars (fermentative role), so SECONDARY_FERMENTER fits. - biological_processes term label fix: GO:0009410 is actually "response to xenobiotic stimulus" (confirmed via QuickGO and OLS), not "response to toxic substance". My preferred_term already had the right text; I had the label wrong. Aligned the label to match. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Summary
Curate a new community YAML (`CommunityMech:000263`) from the orphan cache PMID:38711153 (Salusjärvi et al. 2024 Biotechnol Biofuels, "Enhanced upgrading of lignocellulosic substrates by coculture of Saccharomyces cerevisiae and Acinetobacter baylyi ADP1").
Defined two-member synthetic coculture, well-supported by the single source paper.
Members:
Interactions:
Plus one environmental factor: furan aldehyde inhibitors (furfural and 5-HMF) in synthetic lignocellulosic hydrolysate.
Test plan
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