| name | dom-biosurfactant |
| description | Route dissolved organic matter (DOM) / glycan substrate capacity, biosurfactant production, and hydrocarbon/plastic biodegradation annotation for shotgun metagenomics. Covers “like-dissolves-like” solubility-related microbial functions: CAZyme–glycan (dbCAN), biosurfactants + HC degradation (HADEG, BioSurfDB), and related BGC context (antiSMASH). Child skills: hadeg, biosurfdb; also dbcan, antismash, dram. Route via microbial-mining.
|
| license | MIT |
| category | orchestration |
| tags | ["DOM","biosurfactant","hydrocarbon","biodegradation","CAZyme","solubility","HADEG"] |
| stage | mining |
DOM / biosurfactant / biodegradation
Genetic potential for dissolving, emulsifying, and degrading organic matter
— CAZymes against complex glycans (DOM-relevant polymers), biosurfactants,
and hydrocarbon / plastic degradation. Not measured concentrations or CMC.
What to claim (pin tool)
| Claim | Prefer | Notes |
|---|
| Complex carbohydrate / glycan DOM processing | dbcan (dbCAN3 substrates / CGC) | Cellulose, xylan, pectin, mucin, … |
| Biosurfactant production genes | hadeg · biosurfdb | Lipopeptide/glycolipid pathways as covered |
| Alkane / alkene / aromatic HC degradation | hadeg · biosurfdb | Aerobic markers; pin DB release |
| Plastic polymer degradation genes | hadeg | Experimental-evidence set |
| Surfactant-related BGCs (NRPS lipopeptides, …) | antismash | Cluster ≠ purified surfactant |
| Broad metabolic distillate | dram | Complements, does not replace HADEG |
Analytical thinking
Hard rules:
- Name substrate class (glycan vs HC vs plastic vs surfactant) and DB version
- Do not merge CAZyme tables, HADEG hits, and antiSMASH regions unlabeled
- Hits ≠ emulsification assay or degradation rate
- Filter low-quality MAGs (
mag-qc) before community-level claims
Decision tree
Organic solubility / DOM / surfactant / HC need?
│
├─ Glycan / polymer DOM (CAZymes, PUL/CGC substrates) → dbcan
├─ Biosurfactant + HC/plastic curated genes → hadeg
├─ BioSurfDB pathways / portal BLAST → biosurfdb
├─ Lipopeptide / glycolipid BGCs → antismash
├─ Broad metabolism sheets → dram
└─ Unsure → this hub + microbial-mining
Related skills
hadeg · biosurfdb · dbcan · antismash · dram · element-cycling ·
qsap · microbial-mining · tool-selection
