identifier: traitmech:000049 label: host-associated definition: A habitat association in which an organism lives persistently on or in a plant or animal host (e.g. as a member of a host microbiome), spanning commensal, mutualistic, and pathogenic relationships. definition_source: DOI:10.1073/pnas.1218525110 trait_category: ECOLOGY term_kind: CLASS mapping_status: REVIEWED parent_traits: - traitmech:000047 evidence: - reference: DOI:10.1073/pnas.1218525110 notes: McFall-Ngai et al. document the ubiquity of host-associated microbial communities across the animal kingdom. - reference: DOI:10.1126/science.1104816 notes: Bäckhed et al. characterize the host-associated gut microbiota as a dense, coevolved community. canonical_examples: - taxon_id: NCBITaxon:562 taxon_label: Escherichia coli note: "gut commensal" reference: PMID:37038177 - taxon_id: NCBITaxon:818 taxon_label: Bacteroides thetaiotaomicron note: "gut symbiont" reference: PMID:41099497 causal_graphs: - graph_id: host_associated_microbiome title: Host association establishes persistent host microbiome membership description: Evidence-backed causal sketch linking host habitat to persistent membership in a host-associated microbial community. nodes: - node_id: host_associated_trait label: host-associated node_type: TRAIT grounding: traitmech:000049 description: Persistent life on or in a plant or animal host. - node_id: host_habitat label: host habitat node_type: ENVIRONMENTAL_FACTOR description: Plant or animal tissue surface or lumen. - node_id: host_colonization label: host colonization node_type: BIOLOGICAL_PROCESS description: Persistent establishment of microbes on or in a host. - node_id: mucin_o_glycans label: mucin O-glycans node_type: CHEMICAL description: Host mucus glycans degradable as a microbial nutrient source. - node_id: host_surface_adhesins label: cell appendages and adhesins node_type: GENE_OR_PROTEIN description: Flagella, pili, fimbriae, and adhesins including mucus-binding proteins. - node_id: host_surface_attachment label: attachment to host surfaces node_type: BIOLOGICAL_PROCESS description: Adhesion of microbes to host mucus or epithelial surfaces. - node_id: cyclic_di_gmp_camp label: c-di-GMP and cAMP second messengers node_type: CHEMICAL description: Second messengers regulating the attachment-to-biofilm transition. - node_id: biofilm_formation label: biofilm formation node_type: BIOLOGICAL_PROCESS description: Irreversible attachment with EPS and surface-protein production. grounding: GO:0042710 - node_id: root_exudates label: plant root exudates node_type: ENVIRONMENTAL_FACTOR description: Host-derived metabolites secreted from plant roots. - node_id: chemotaxis_to_host label: chemotaxis toward host node_type: BIOLOGICAL_PROCESS description: Directed motility toward host-derived chemical cues. - node_id: mucus_layer_niches label: mucus layer niches node_type: ENVIRONMENTAL_FACTOR description: Distinct inner (firm) and outer (loose) mucus colonization niches. edges: - subject: host_habitat predicate: enables object: host_colonization description: Host tissues provide the habitat in which the microbe colonizes. evidence: - reference: DOI:10.1073/pnas.1218525110 notes: McFall-Ngai et al. document ubiquitous host-associated microbial communities across animals. predicate_id: RO:0002327 - subject: host_colonization predicate: enables object: host_associated_trait description: Persistent host colonization realizes the host-associated lifestyle. evidence: - reference: DOI:10.1126/science.1104816 notes: Bäckhed et al. characterize host-associated microbiota as dense, coevolved communities. predicate_id: RO:0002327 - subject: mucin_o_glycans predicate: serves as nutrient source for object: host_colonization description: Mucin O-glycans are degraded and utilized as a nutrient source supporting colonization. evidence: - reference: DOI:10.1152/ajpgi.00261.2022 notes: Mucin O-glycans and glycan-derived sugars are degraded and utilized as a nutrient source by host-associated microbes. - subject: host_surface_adhesins predicate: enables object: host_surface_attachment description: Cell appendages and adhesins mediate attachment to host mucus and epithelia. evidence: - reference: DOI:10.1093/femsre/fuae008 notes: Cell appendages (flagella, pili, fimbriae) and adhesins mediate attachment to host mucus/epithelia. predicate_id: RO:0002327 - subject: host_surface_attachment predicate: enables object: host_colonization description: Attachment to host surfaces is a prerequisite step for persistent colonization. evidence: - reference: DOI:10.1093/femsre/fuae008 notes: Attachment to host surfaces underlies the transition to stable colonization. predicate_id: RO:0002327 - subject: cyclic_di_gmp_camp predicate: induces object: biofilm_formation description: c-di-GMP and cAMP trigger EPS and surface-protein production, driving irreversible attachment and biofilm. evidence: - reference: DOI:10.1093/femsre/fuae008 notes: cAMP and c-di-GMP regulate transition from reversible to irreversible attachment, triggering surface proteins and EPS leading to biofilm formation. - subject: biofilm_formation predicate: enables object: host_colonization description: Biofilm formation supports persistent microbial occupancy of host surfaces. evidence: - reference: DOI:10.1093/femsre/fuae008 notes: Biofilm formation following irreversible attachment supports persistent host colonization. predicate_id: RO:0002327 - subject: root_exudates predicate: activates object: chemotaxis_to_host description: Root exudates trigger chemotaxis via MCP/CheA/CheY signaling toward the host. evidence: - reference: DOI:10.3390/biology13020095 notes: Methyl-accepting chemotaxis proteins bind root exudates and trigger signal transduction (CheW/CheA/CheY), driving chemotaxis as the first colonization step. predicate_id: RO:0002213 - subject: chemotaxis_to_host predicate: enables object: host_colonization description: Chemotaxis toward host cues is an initial step enabling colonization. evidence: - reference: DOI:10.3390/biology13020095 notes: Chemotaxis is identified as the first step of host colonization. predicate_id: RO:0002327 - subject: root_exudates predicate: provides nutrient source for object: host_colonization description: Root exudates supply carbon and substrates supporting microbial growth and persistence. evidence: - reference: DOI:10.1093/femsre/fuad066 notes: Plants secrete 11-40% of photosynthate as exudates that supply carbon and substrates for rhizobacterial growth and persistence. - subject: mucus_layer_niches predicate: enables object: host_colonization description: Structured inner and outer mucus layers create distinct niches for microbial colonization. evidence: - reference: DOI:10.1128/ecosalplus.esp-0006-2023 notes: Structured inner (firm, sparsely colonized) versus outer (looser, microbe-colonized) mucus creates distinct colonization niches. predicate_id: RO:0002327 curation_history: - timestamp: '2026-06-02T00:00:00Z' curator: claude action: PROPOSED_FROM_RESEARCH changes: Proposed candidate ECOLOGY trait (host-associated); sub-variant of habitat association, parent of gut-associated. llm_assisted: true - timestamp: '2026-06-09T14:00:00Z' curator: claude action: CURATED_CAUSAL_GRAPH changes: Added evidence-backed causal graph (host-associated microbiome membership) with RO 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 (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 6 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327×5, RO:0002213×1). 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