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black pigmented

METPO:1003022 · CLASS · REVIEWED

A pigmentation phenotype in which microbial colonies or cells appear black or very dark due to accumulation of dark pigments such as melanins.

Black pigmentation melanin polymer mechanism

Evidence-backed causal sketch linking black microbial pigmentation to phenolic precursors, oxidase-catalyzed melanin biosynthesis, dark melanin polymers, and visible black color.

Black pigmentation melanin polymer mechanism Interactive directed graph showing evidence-backed causal relationships for black pigmented.

Edge evidence

  • phenolic precursors feed into melanin biosynthesis

    Phenolic precursors feed oxidative melanin-forming pathways.

    • DOI:10.1007/s11274-020-02941-z oxidative polymerization of tyrosine derivatives Supports phenolic or tyrosine-derived precursors as melanin biosynthetic substrates.
  • tyrosinase/laccase oxidases catalyzes melanin biosynthesis biolink:catalyzes

    Oxidases catalyze precursor oxidation in melanin formation.

    • DOI:10.1016/j.biotechadv.2021.107773 biosynthesis ... oxidative polymerization Supports oxidative enzymatic routes for microbial melanin formation.
  • melanin biosynthesis has output black-brown melanin RO:0002234

    Melanin biosynthesis produces dark melanin polymers.

    • DOI:10.1016/j.biotechadv.2021.107773 Eumelanin and allomelanin impart black/brown color Supports black-brown melanins as microbial colorants.
  • black-brown melanin causes visible black color biolink:causes

    Dark melanin polymers cause visible black pigmentation when sufficiently accumulated.

    • DOI:10.1016/j.biotechadv.2021.107773 black/brown color Supports black color as an outcome of dark melanin accumulation.
  • visible black color manifests as black pigmented METPO:2007400

    Visible black color manifests the black-pigmented phenotype.

    • DOI:10.1016/j.biotechadv.2021.107773 black/brown color to the cells Supports the trait-level assignment.
  • tyrosinase catalyzes conversion of L-tyrosine

    Tyrosinase hydroxylates L-tyrosine to L-DOPA, initiating the DOPA-melanin pathway.

    • DOI:10.3390/ijms25053013 Tyrosinase first catalyzes the hydroxylation of L-tyrosine to L-DOPA.
  • dopaquinone/dihydroxyindole intermediates polymerizes into DOPA-melanin (eumelanin)

    Dopaquinone/dihydroxyindole intermediates polymerize into DOPA-melanin (eumelanin).

    • DOI:10.3390/jof9090891 Dopaquinone oxidized to dopachrome then dihydroxy-indoles which polymerize to form DOPA-melanins.
  • copper ion required cofactor for tyrosinase

    Copper ions are required cofactors for tyrosinase catalytic activity.

    • DOI:10.3390/microorganisms12071352 Tyrosinases are copper-dependent enzymes.
  • polyketide synthase (PKS) synthesizes precursor for DHN (1,8-dihydroxynaphthalene)

    Polyketide synthase forms tetrahydroxynaphthalene leading to DHN, precursor of DHN-melanin.

    • DOI:10.3390/microorganisms12071352 Polyketide synthase forms 1,3,6,8-tetrahydroxynaphthalene; polymerization of DHN leads to melanin.
  • DHN (1,8-dihydroxynaphthalene) polymerizes into DHN-melanin (allomelanin)

    DHN polymerizes into DHN-melanin (allomelanin), a dark pigment.

    • DOI:10.3390/microorganisms12071352 Polymerization of DHN leads to the formation of melanin.
  • HppD (4-hydroxyphenylpyruvate dioxygenase) converts 4-hydroxyphenylpyruvate

    HppD converts 4-hydroxyphenylpyruvate to homogentisic acid in the pyomelanin pathway.

    • DOI:10.1128/spectrum.00410-24 hppD codes for a protein responsible for conversion of 4-hydroxyphenylpyruvate to HGA.
  • HmgA (homogentisate 1,2-dioxygenase) converts homogentisic acid (HGA)

    HmgA (homogentisate 1,2-dioxygenase) converts HGA to maleylacetoacetate.

    • DOI:10.1128/spectrum.00410-24 Homogentisate 1,2-dioxygenase encoded by hmgA converts HGA to maleylacetoacetate.

Provenance

Source
METPO (2025-11-25)
Definition source
DOI:10.1016/j.biotechadv.2021.107773

Parent traits (1)

Synonyms (1)

  • Pigment_black RELATED_SYNONYM · metpo.owl

kg-microbe context

Matched 1 kg-microbe node via direct_metpo.

  • METPO:1003022 [-1.598, -1.748, -2.126, +1.386, …]

512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

Nearest neighbors in embedding space

Top-8 cosine-similar METPO traits from the 2026-04-25 deepwalk (512-D).

Deep research

Generated by just research-trait; source: research/traits/morphology/black_pigmented-deep-research-falcon.md

Unreviewed literature output — not curated TraitMech content Ontology identifiers suggested below have not been resolved against their ontologies, and some are known to be wrong. Check any CURIE against the source before using it. 
# Curation report: microbial **black pigmented**

## Trait record and scope

- **Trait:** black pigmented
- **Identifier:** **METPO:1003022**
- **Category / kind:** MORPHOLOGY / CLASS
- **Parent:** METPO:1003021
- **Synonym:** Pigment_black
- **Recommended operational meaning:** an observed colony-, cell-, spore-, biofilm-, or extracellular-material phenotype that is black or sufficiently dark brown/green-black to be scored as black under a stated assay or culture condition.

The phenotype is **not equivalent to “melanin production.”** Three melanin-associated modules commonly produce black-to-dark material: fungal DHN/allomelanin, DOPA-derived eumelanin, and homogentisate-derived pyomelanin. However, pigment identity, concentration, localization, medium, colony age, illumination, and scoring method all influence apparent color. Recent work on *Lomentospora prolificans*, for example, found medium- and age-dependent pigmentation and evidence for simultaneous DHN-, DOPA-, and pyomelanin-like material, so a black phenotype need not map to one exclusive pathway (liporagilopes2024newinsightsinto pages 15-18, liporagilopes2024newinsightsinto pages 12-15).

A critical boundary case is the “black-pigmented” oral anaerobes. *Porphyromonas gingivalis* produces green-black surface deposits of Fe(III) μ-oxo bisheme, and *Prevotella intermedia* produces brown-black monomeric Fe(III) protoporphyrin IX deposits. These are **heme pigments, not melanins** (olczak2024hemophorelikeproteinsof pages 5-7, olczak2024hemophorelikeproteinsof pages 2-5). Accordingly, the existing `black_pigmented_melanin_polymer` graph is appropriate as one mechanistic branch, but it should not be treated as an exhaustive definition of **METPO:1003022**.

### Recommended inclusion and exclusion rules

**Include** a strain-level assertion when a source directly reports black, green-black, black-brown, or very dark cells/colonies/material under specified conditions. Record the culture medium, age, precursor supplementation, oxygen/light conditions, and localization where available.

**Do not infer the trait solely from:**

1. Presence of a melanin-pathway gene without an observed dark phenotype.
2. UV resistance, virulence, antioxidant activity, or metal binding without color evidence.
3. A purified pigment described only as brown unless the organism itself is reported as black/very dark.
4. The name “black fungus,” “black mold,” or “black-pigmented anaerobe” without phenotype-level evidence.
5. Heme accumulation as evidence of melanin production.

## Candidate graph architecture

A robust TraitMech representation should use a **convergent graph** rather than a single linear pathway:

1. **DHN-melanin branch** → dark polymer → cell-wall/conidial deposition → black or very dark phenotype.
2. **DOPA/eumelanin branch** → DHI/DHICA-rich polymer → wall or extracellular deposition → dark phenotype.
3. **Pyomelanin branch** → extracellular HGA polymer → brown-black phenotype when abundance and assay conditions are sufficient.
4. **Heme-PPIX branch** → surface ferriheme/μ-oxo bisheme accumulation → brown-black or green-black phenotype; explicitly non-melanin.
5. Optional organism-specific branches for chemically distinct pigments, such as 5-deoxybostrycoidin-derived black perithecial pigment, only after primary evidence is curated (yin2026researchprogresson pages 20-20).

## Candidate nodes grouped by type

### Trait and phenotype nodes

- **black pigmented** — **METPO:1003022**
- black/dark colony pigmentation — label-only assay phenotype
- black/dark conidial pigmentation — label-only
- extracellular brown-black pigment — label-only; requires a color threshold/context qualifier
- green-black surface pigment — label-only; appropriate for *P. gingivalis*
- reduced/light pigmentation — label-only contrast phenotype

### Pathways and metabolic modules

- DHN-melanin biosynthesis
- DOPA-melanin/eumelanin biosynthesis
- tyrosine degradation/pyomelanin biosynthesis
- oxidative polymerization of phenolic or indolic precursors
- melanin granule trafficking and cell-wall anchoring
- heme acquisition and ferriheme surface accumulation
- cAMP/PKA regulation; HOG/MAPK regulation — organism-specific regulatory modules

### Genes, proteins, and enzymes

Showing the first 60 of 263 lines of findings; the linked file also carries the run's front matter and the prompt it was given — read the full report.

Curation history

  1. · SEEDED_FROM_METPO · seed_from_metpo

    imported from data/raw/metpo.owl (CLASS)

  2. · CURATED_WITH_LITERATURE · codex

    Added DOI-backed definition and causal graph for phenolic precursors, oxidative melanin biosynthesis, black-brown melanin polymers, and visible black color.

  3. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202×1).

  4. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:catalyzes×1, biolink:causes×1).

  5. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400×1).

  6. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0042438×1).

  7. · ENRICH_CAUSAL_GRAPH · claude

    Added 7 evidence-backed generic edges (12 new nodes) from the deep-research report.

  8. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:36242×1).

  9. · GROUND_CAUSAL_NODES · claude

    Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:Q5Y9G5×1, UniProtKB:A0A023Y3L4×1).

  10. · RETRACT_DEAD_UNIPROT_GROUNDINGS · claude

    Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)

  11. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0004503×1).

  12. · MIGRATE_MICROBE_DOMAIN_EDGES · claude

    Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.