identifier: traitmech:000040 label: symbiosis definition: An ecological lifestyle in which a microorganism lives in persistent physical association with a host or partner organism. It encompasses mutualism, commensalism, and parasitism, which form an evolutionary continuum. definition_source: DOI:10.1073/pnas.1218525110 trait_category: ECOLOGY term_kind: CLASS mapping_status: REVIEWED parent_traits: - METPO:1000059 synonyms: - synonym_text: symbiotic synonym_type: RELATED_SYNONYM source: DOI:10.1073/pnas.1218525110 evidence: - reference: DOI:10.1073/pnas.1218525110 notes: McFall-Ngai et al., "Animals in a bacterial world", supports persistent host-microbe association (symbiosis) as a pervasive microbial lifestyle; parent of the mutualism/commensalism/parasitism sub-variants. - reference: DOI:10.1038/s41579-021-00550-7 notes: Drew et al. frame symbioses as a parasite-mutualist continuum, supporting symbiosis as the umbrella lifestyle for these interaction modes. canonical_examples: - taxon_id: NCBITaxon:9 taxon_label: Buchnera aphidicola note: "obligate aphid endosymbiont" reference: PMID:19909925 - taxon_id: NCBITaxon:382 taxon_label: Sinorhizobium meliloti note: "legume root-nodule symbiont" reference: PMID:12620125 causal_graphs: - graph_id: symbiosis_host_interaction title: Symbiosis as persistent host-microbe interaction description: Evidence-backed causal sketch linking host-microbe interaction to persistent symbiotic association along the parasite-mutualist continuum. nodes: - node_id: symbiosis_trait label: symbiosis node_type: TRAIT grounding: traitmech:000040 description: Persistent physical association with a host or partner. - node_id: host_organism label: host organism node_type: ENVIRONMENTAL_FACTOR description: Eukaryotic or microbial partner with which the focal microbe persistently interacts. - node_id: symbiotic_interaction label: biological process involved in symbiotic interaction node_type: BIOLOGICAL_PROCESS grounding: GO:0044403 description: Persistent biological interaction between organisms living together. - node_id: host_metabolites label: host metabolites / exudates node_type: CHEMICAL description: Host-produced primary and specialized metabolites that act as chemoattractants and nutrients. - node_id: chemotaxis_machinery label: chemotaxis machinery node_type: PATHWAY description: Bacterial chemosensing and chemotaxis system that senses and follows host-derived gradients. - node_id: host_colonization label: host colonization node_type: BIOLOGICAL_PROCESS description: Establishment of bacteria on or within host tissues, broadly required across mutualists and pathogens. - node_id: biofilm_formation label: biofilm formation node_type: BIOLOGICAL_PROCESS description: Aggregated surface-associated bacterial community that protects from host stresses and supports persistence. grounding: GO:0042710 - node_id: o_antigen label: O-antigen node_type: CHEMICAL description: LPS O-antigen polysaccharide that cloaks MAMPs at the cell envelope. - node_id: immune_evasion label: immune evasion node_type: BIOLOGICAL_PROCESS description: Avoidance of host innate immune detection during host association. - node_id: host_cues label: host-associated cues node_type: ENVIRONMENTAL_FACTOR description: Host-niche signals such as iron, acidic pH, cationic peptides, divalent metals, and oxygen depletion. - node_id: two_component_systems label: two-component systems node_type: PATHWAY description: Sensor-regulator signaling systems that detect host-associated cues and trigger gene regulatory programs. - node_id: outer_membrane_modification label: outer-membrane modification node_type: BIOLOGICAL_PROCESS description: Remodeling of the bacterial cell envelope in response to host-associated cues. - node_id: adhesins label: adhesins node_type: GENE_OR_PROTEIN description: Bacterial surface adhesins binding host receptors, a prerequisite for long-term colonization. edges: - subject: host_organism predicate: causes object: symbiotic_interaction description: Presence of a host or partner organism establishes the symbiotic interaction. evidence: - reference: DOI:10.1073/pnas.1218525110 notes: McFall-Ngai et al. document host-microbe association as a pervasive feature of animal biology. predicate_id: biolink:causes - subject: symbiotic_interaction predicate: enables object: symbiosis_trait description: Sustained symbiotic interaction realizes the symbiotic lifestyle. evidence: - reference: DOI:10.1038/s41579-021-00550-7 notes: Drew et al. frame symbioses as a parasite-mutualist continuum of persistent interactions. predicate_id: RO:0002327 - subject: host_metabolites predicate: sensed by object: chemotaxis_machinery description: Host-produced metabolites diffuse to create concentration gradients sensed by bacterial chemotaxis machinery. evidence: - reference: DOI:10.1093/femsre/fuac048 notes: Host-produced metabolites act as chemoattractants; diffusion creates concentration gradients that bacteria sense and follow. Broad cross-system review (Wiesmann et al. 2023). - subject: chemotaxis_machinery predicate: promotes object: host_colonization description: Chemotaxis and motility direct bacteria toward host surfaces, promoting colonization across lifestyles. evidence: - reference: DOI:10.1093/femsre/fuac048 notes: Chemotaxis and motility are broadly required across mutualists and pathogens; general edge spanning pathogenic, commensal, and mutualist lifestyles. predicate_id: RO:0002213 - subject: adhesins predicate: required for object: host_colonization description: Binding of bacterial adhesins to host receptors is a prerequisite for long-term host colonization. evidence: - reference: DOI:10.3390/microorganisms12051026 notes: Binding of bacterial adhesins to host receptors is a prerequisite for the long-term colonization of bacteria; broad colonization review (Lin et al. 2024). Curated as a general adhesin node per report warning. - subject: biofilm_formation predicate: supports object: symbiotic_interaction description: Biofilm formation protects bacteria from host-secreted antimicrobials and stresses, supporting persistent host association. evidence: - reference: DOI:10.1093/femsre/fuac048 notes: After colonization, biofilm formation protects bacteria from host-secreted antimicrobial peptides and other stresses, supporting persistence. Strong conserved persistence edge. - subject: o_antigen predicate: contributes to object: immune_evasion description: O-antigen presence contributes to immune evasion, partly by cloaking MAMPs from host recognition. evidence: - reference: DOI:10.1093/femsre/fuac048 notes: O-antigen presence contributes to immune evasion, partly by cloaking MAMPs; strong envelope-modification edge across host systems. predicate_id: RO:0002326 - subject: immune_evasion predicate: promotes object: host_colonization description: Evading host innate immune detection enables sustained colonization. evidence: - reference: DOI:10.1093/femsre/fuac048 notes: Loss of O-antigen induces TLR4 activation and ROS bursts, impairing colonization; conversely immune evasion supports colonization (Wiesmann et al. 2023). predicate_id: RO:0002213 - subject: host_cues predicate: sensed by object: two_component_systems description: Two-component systems sense host-associated cues such as iron, acidic pH, cationic peptides, and oxygen depletion. evidence: - reference: DOI:10.1093/femsre/fuac048 notes: Two-component systems sense host-associated cues (iron, acidic pH, cationic peptides, divalent metals, oxygen depletion). Strong regulatory edge with generic node. - subject: two_component_systems predicate: triggers object: outer_membrane_modification description: Two-component systems trigger gene regulatory programs leading to outer-membrane modification and biofilm formation. evidence: - reference: DOI:10.1093/femsre/fuac048 notes: TCSs trigger gene regulatory programs that causally lead to specialized metabolism, outer-membrane modification, and biofilm formation. High-level mechanistic umbrella edge. - subject: two_component_systems predicate: triggers object: biofilm_formation description: Two-component system signaling promotes biofilm formation as part of host-cue-triggered programs. evidence: - reference: DOI:10.1093/femsre/fuac048 notes: TCSs trigger gene regulatory programs that causally lead to outer-membrane modification and biofilm formation. curation_history: - timestamp: '2026-06-02T00:00:00Z' curator: claude action: PROPOSED_FROM_RESEARCH changes: Proposed candidate ECOLOGY axis class (symbiosis) from literature research to fill the host-interaction lifestyle gap; parent of mutualism, commensalism, parasitism, and endosymbiosis. llm_assisted: true - timestamp: '2026-06-09T14:00:00Z' curator: claude action: CURATED_CAUSAL_GRAPH changes: Added evidence-backed causal graph (host-microbe symbiotic interaction) with GO node grounding and RO/biolink predicate groundings; promoted PROPOSED to REVIEWED. llm_assisted: true - timestamp: '2026-06-23T00:00:00Z' curator: claude action: ENRICH_CAUSAL_GRAPH changes: Added 9 evidence-backed generic edges (10 new nodes) from the deep-research report. llm_assisted: true - timestamp: '2026-06-24T17:21:09Z' curator: claude action: GROUND_CAUSAL_PREDICATES changes: Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213×2, RO:0002326×1). 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