identifier: METPO:1004004
label: human pathogen
definition: A pathogen that infects organisms of the species Homo sapiens.
definition_source: DOI:10.1146/annurev.micro.62.081307.162938
trait_category: ECOLOGY
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1004000
evidence:
- reference: DOI:10.1146/annurev.micro.62.081307.162938
  snippet: virulence factors
  notes: Virulence-factor review supports adaptation of bacterial virulence programs
    to the human host environment.
- reference: DOI:10.1038/nrmicro1592
  snippet: secretion systems
  notes: Secretion-systems review supports effector delivery as a major mechanism
    by which bacteria establish human infection.
canonical_examples:
- taxon_id: NCBITaxon:1280
  taxon_label: Staphylococcus aureus
  note: "major human pathogen"
  reference: PMID:30209034
- taxon_id: NCBITaxon:1773
  taxon_label: Mycobacterium tuberculosis
  note: "tuberculosis agent"
  reference: PMID:40588584
causal_graphs:
- graph_id: human_pathogen_anthropoid_adaptation
  title: Human-pathogen Homo sapiens host adaptation
  description: DOI-backed graph linking human-adapted virulence factors, body-temperature
    and tissue tropism, and human-specific immune evasion to the human-pathogen phenotype.
  nodes:
  - node_id: human_pathogen_trait
    label: human pathogen
    node_type: TRAIT
    grounding: METPO:1004004
    description: Pathogen of Homo sapiens.
  - node_id: human_virulence_factors
    label: human-adapted virulence factors
    node_type: GENE_OR_PROTEIN
    description: Virulence factors tuned to human-cell receptors and biology.
  - node_id: human_tropism
    label: human tissue tropism
    node_type: BIOLOGICAL_PROCESS
    description: Preferential adhesion and growth in human-specific tissues at body-core
      temperatures.
  - node_id: human_immune_evasion
    label: human immune evasion
    node_type: BIOLOGICAL_PROCESS
    description: Strategies evading human innate and adaptive immunity.
  - node_id: human_disease
    label: human disease
    node_type: BIOLOGICAL_PROCESS
    description: Pathology produced in a human host.
  - node_id: type_iv_secretion_system
    label: type IV secretion system
    node_type: GENE_OR_PROTEIN
    description: Multiprotein machine translocating protein effectors and toxins into
      host cells.
  - node_id: host_cell_manipulation
    label: host cell manipulation
    node_type: BIOLOGICAL_PROCESS
    description: Effector-driven subversion of host-cell processes promoting infection.
  - node_id: horizontal_gene_transfer
    label: horizontal gene transfer
    node_type: BIOLOGICAL_PROCESS
    description: Acquisition of genes via plasmids, transduction, transposons, and
      IS elements.
    grounding: GO:0009292
  - node_id: virulence_gene_acquisition
    label: acquisition of virulence/host-adaptation genes
    node_type: BIOLOGICAL_PROCESS
    description: Gain of one or more genes facilitating virulence and host-species
      tropism.
  - node_id: within_host_genetic_diversification
    label: within-host genetic diversification
    node_type: BIOLOGICAL_PROCESS
    description: Hypermutation, structural variation, and MGE/phage insertions generating
      diversity.
  - node_id: within_host_adaptation
    label: within-host adaptation and chronic infection
    node_type: BIOLOGICAL_PROCESS
    description: Adaptation to the host enabling increased pathogenicity and long-term
      persistence.
  - node_id: biofilm_formation
    label: biofilm formation
    node_type: BIOLOGICAL_PROCESS
    description: Surface-attached communities increasing treatment resistance and
      persistence.
    grounding: GO:0042710
  - node_id: treatment_resistance_persistence
    label: treatment resistance and persistence
    node_type: QUALITY
    description: Tolerance to antimicrobial treatment and persistent infection.
  edges:
  - subject: human_virulence_factors
    predicate: enables
    object: human_tropism
    description: Human-adapted virulence factors enable preferential adhesion and
      growth in human tissues.
    evidence:
    - reference: DOI:10.1146/annurev.micro.62.081307.162938
      snippet: virulence factors
      notes: Supports virulence factors as enablers of human tissue tropism.
    predicate_id: RO:0002327
  - subject: human_tropism
    predicate: enables
    object: human_disease
    description: Tissue tropism supports establishment of human disease at specific
      anatomical sites.
    evidence:
    - reference: DOI:10.1146/annurev.micro.62.081307.162938
      snippet: virulence factors
      notes: Supports tissue tropism as a determinant of human-disease pattern.
    predicate_id: RO:0002327
  - subject: human_immune_evasion
    predicate: enables
    object: human_disease
    description: Evasion of human immunity supports sustained infection and disease.
    evidence:
    - reference: DOI:10.1038/nrmicro1592
      snippet: secretion systems
      notes: Supports secretion-system-delivered effectors in human immune evasion.
    predicate_id: RO:0002327
  - subject: human_disease
    predicate: manifests as
    object: human_pathogen_trait
    description: Human disease manifests the human-pathogen trait.
    evidence:
    - reference: DOI:10.1146/annurev.micro.62.081307.162938
      snippet: virulence factors
      notes: Supports the trait endpoint.
    predicate_id: METPO:2007400
  - subject: type_iv_secretion_system
    predicate: enables
    object: host_cell_manipulation
    description: Type IV secretion systems translocate protein effectors and toxins
      that manipulate host cells during infection.
    evidence:
    - reference: DOI:10.1038/s41579-023-00974-3
      notes: T4SSs function as protein effector translocators delivering effectors
        or toxins; viable targets to thwart infection by pathogens.
    predicate_id: RO:0002327
  - subject: host_cell_manipulation
    predicate: enables
    object: human_disease
    description: Effector-driven host cell manipulation supports establishment of
      human infection and disease.
    evidence:
    - reference: DOI:10.1038/s41579-023-00974-3
      notes: Effector translocation enables host cell manipulation and infection by
        pathogens.
    predicate_id: RO:0002327
  - subject: horizontal_gene_transfer
    predicate: enables
    object: virulence_gene_acquisition
    description: HGT via plasmids, transduction, transposons, and IS elements enables
      acquisition of virulence and host-adaptation genes.
    evidence:
    - reference: DOI:10.1093/femsre/fuae019
      notes: HGT via conjugation, transduction, transposons, IS elements can be associated
        with gain of genes facilitating host tropism and virulence factors.
    predicate_id: RO:0002327
  - subject: virulence_gene_acquisition
    predicate: enables
    object: human_virulence_factors
    description: Acquired genes contribute the human-adapted virulence factor repertoire
      underlying human pathogenicity.
    evidence:
    - reference: DOI:10.1093/femsre/fuae019
      notes: Gene acquisition facilitates changes in host species tropism, including
        virulence factors enabling human-pathogenic lineages.
    predicate_id: RO:0002327
  - subject: within_host_genetic_diversification
    predicate: enables
    object: within_host_adaptation
    description: Hypermutation, structural variation, and MGE/phage insertions generate
      diversity driving within-host adaptation.
    evidence:
    - reference: DOI:10.1146/annurev-pathmechdis-051122-111408
      notes: Secondary mechanisms including hypermutation, structural variation, and
        MGE/phage insertions can increase pathogenicity and facilitate long-term persistence.
    predicate_id: RO:0002327
  - subject: within_host_adaptation
    predicate: enables
    object: human_disease
    description: Within-host adaptation increases pathogenicity and supports chronic
      human infection.
    evidence:
    - reference: DOI:10.1146/annurev-pathmechdis-051122-111408
      notes: Within-host evolution can increase pathogenicity and facilitate long-term
        persistence in the host.
    predicate_id: RO:0002327
  - subject: biofilm_formation
    predicate: enables
    object: treatment_resistance_persistence
    description: Biofilm formation makes bacteria resistant to treatment and supports
      persistence.
    evidence:
    - reference: DOI:10.3389/fmicb.2024.1370818
      notes: Bacteria can form biofilms, making them resistant to treatment.
    predicate_id: RO:0002327
  - subject: treatment_resistance_persistence
    predicate: enables
    object: human_disease
    description: Treatment resistance and persistence exacerbate the severity and
      duration of human infection.
    evidence:
    - reference: DOI:10.3389/fmicb.2024.1370818
      notes: Biofilm-associated resistance to treatment contributes to infection severity
        and persistence.
    predicate_id: RO:0002327
curation_history:
- timestamp: '2026-05-05T01:35:46.949749+00:00'
  curator: seed_from_metpo
  action: SEEDED_FROM_METPO
  changes: imported from data/raw/metpo.owl (CLASS)
  llm_assisted: false
- timestamp: '2026-05-11T23:15:00-07:00'
  curator: claude
  action: CURATED_CAUSAL_GRAPH
  changes: Added DOI-backed causal graph linking human-adapted virulence factors,
    tissue tropism, immune evasion, and disease to the human-pathogen trait.
  llm_assisted: true
- timestamp: '2026-05-20T03:35:29Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002327×1).
  llm_assisted: true
- timestamp: '2026-05-23T21:30:06Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2007400×1).
  llm_assisted: true
- timestamp: '2026-05-24T04:13:18Z'
  curator: claude
  action: RENAME_PREDICATE_LABELS
  changes: 'Renamed 2 causal-edge predicate label(s) to align with existing groundings:
    supports → enables ×2.'
  llm_assisted: true
- timestamp: '2026-05-24T04:13:20Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002327×2).
  llm_assisted: true
- timestamp: '2026-06-17T04:09:43Z'
  curator: claude
  action: REMOVE_REDUNDANT_SYNONYM
  changes: Removed 1 synonym(s) whose text duplicated the label (seeder redundancy;
    no information lost).
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 8 evidence-backed generic edges (8 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:09Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 8 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002327×8).
  llm_assisted: true
- timestamp: '2026-06-24T17:21:16Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (GO:0009292×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:23:29Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (GO:0042710×1).
  llm_assisted: true