identifier: METPO:1000456 label: pH optimum mid1 definition: A pH optimum phenotype with the best-growth external pH between approximately 6 and 7, corresponding to neutrophilic physiology. definition_source: DOI:10.1038/nrmicro2549 trait_category: ENVIRONMENT term_kind: CLASS mapping_status: REVIEWED parent_traits: - METPO:1000331 synonyms: - synonym_text: Alkali Tolerant synonym_type: EXACT_SYNONYM source: metpo.owl - synonym_text: Neutrophile synonym_type: EXACT_SYNONYM source: metpo.owl - synonym_text: pHO_6_to_7 synonym_type: RELATED_SYNONYM source: metpo.owl evidence: - reference: DOI:10.1038/nrmicro2549 snippet: cytoplasmic pH notes: pH-homeostasis review supports a near-neutral external pH as the neutrophilic optimum, where cytoplasmic pH homeostasis operates with minimal load. causal_graphs: - graph_id: ph_optimum_mid1_neutrophile_setpoint title: pH-optimum-mid1 neutrophile setpoint description: DOI-backed graph linking minimal pH-homeostasis load at near-neutral external pH to a pH-optimum between 6 and 7 (neutrophile). nodes: - node_id: ph_optimum_mid1_trait label: pH optimum mid1 node_type: TRAIT grounding: METPO:1000456 description: pH optimum approximately 6–7. - node_id: ph_optimum label: pH optimum node_type: TRAIT grounding: METPO:1000331 description: External pH supporting maximal growth. - node_id: near_neutral_external_ph label: near-neutral external pH node_type: ENVIRONMENTAL_FACTOR description: External pH 6–7, typical of fresh-water and many host environments. grounding: PATO:0001428 - node_id: minimal_ph_homeostasis_load label: minimal pH-homeostasis load node_type: BIOLOGICAL_PROCESS description: Modest demand on proton extrusion and cytoplasmic buffering near a near-neutral cytoplasmic pH. - node_id: f0f1_atpase label: F0F1-ATPase node_type: GENE_OR_PROTEIN description: F-type ATP synthase/ATPase functioning as a proton pump. - node_id: proton label: proton (H+) node_type: CHEMICAL description: Hydrogen ion (H+), the determinant of pH. - node_id: amino_acid_decarboxylation label: amino-acid decarboxylation pathways node_type: PATHWAY description: Glutamate/lysine/arginine decarboxylase pathways that consume cytoplasmic protons. - node_id: gad_gaba_pathway label: glutamate decarboxylation / GABA pathway node_type: PATHWAY description: Glutamate decarboxylase / GABA shunt pathway consuming intracellular H+. - node_id: ammonia label: ammonia (NH3) node_type: CHEMICAL description: Ammonia, a base that scavenges protons. - node_id: ammonium label: ammonium (NH4+) node_type: CHEMICAL description: Ammonium ion formed when ammonia binds a proton. edges: - subject: near_neutral_external_ph predicate: imposes object: minimal_ph_homeostasis_load description: Near-neutral external pH imposes minimal pH-homeostasis demand on the cell. evidence: - reference: DOI:10.1038/nrmicro2549 snippet: cytoplasmic pH notes: Supports near-neutral external pH as the regime with the smallest cytoplasmic-pH gradient to maintain. - subject: minimal_ph_homeostasis_load predicate: produces object: ph_optimum_mid1_trait description: Minimal pH-homeostasis load yields a neutrophilic pH-optimum setpoint. evidence: - reference: DOI:10.1038/nrmicro2549 snippet: pH homeostasis notes: Supports a near-neutral optimum as the neutrophile outcome. predicate_id: METPO:2000202 - subject: ph_optimum_mid1_trait predicate: is a object: ph_optimum description: pH optimum mid1 is a quantitative bin of the pH-optimum phenotype. evidence: - reference: DOI:10.1016/j.tim.2007.02.005 snippet: proton motive force notes: Supports a near-neutral optimum as a value within the pH-optimum distribution. predicate_id: rdfs:subClassOf - subject: f0f1_atpase predicate: exports object: proton description: The F0F1-ATPase actively exports protons to maintain cytoplasmic pH. evidence: - reference: DOI:10.1371/journal.ppat.1011927 notes: actively exporting protons via proton pumps such as the F0F1-ATPase; classic pH-homeostasis mechanism. predicate_id: METPO:2000209 - subject: amino_acid_decarboxylation predicate: consumes object: proton description: Amino-acid decarboxylation pathways consume cytoplasmic protons, supporting pH homeostasis. evidence: - reference: DOI:10.1371/journal.ppat.1011927 notes: consume protons through amino-acid decarboxylation pathways (glutamate, lysine, arginine); general acid-resistance edge. predicate_id: biolink:consumes - subject: gad_gaba_pathway predicate: consumes object: proton description: The glutamate decarboxylation / GABA pathway consumes intracellular H+. evidence: - reference: DOI:10.1128/aem.00569-24 notes: glutamate-based systems and the GABA metabolic pathway consume H+. predicate_id: biolink:consumes - subject: ammonia predicate: binds object: proton description: Ammonia binds free protons, buffering against acidification. evidence: - reference: DOI:10.1128/aem.00569-24 notes: generated NH3 bind with intracellular free H+ to form NH4+; direct acid-buffering chemistry, generalizable. - subject: ammonia predicate: forms object: ammonium description: Ammonia combines with a proton to form ammonium, sequestering acid. evidence: - reference: DOI:10.1128/aem.00569-24 notes: generated NH3 bind with intracellular free H+ to form NH4+. predicate_id: biolink:produces - subject: f0f1_atpase predicate: contributes to object: minimal_ph_homeostasis_load description: Proton export by the F0F1-ATPase keeps the cytoplasmic-pH gradient small near neutral, contributing to minimal homeostasis load. evidence: - reference: DOI:10.1371/journal.ppat.1011927 notes: Proton pumping via F0F1-ATPase maintains cytosolic pH; near-neutral external pH minimizes the pumping demand. predicate_id: RO:0002326 curation_history: - timestamp: '2026-05-05T01:35:46.827192+00:00' curator: seed_from_metpo action: SEEDED_FROM_METPO changes: imported from data/raw/metpo.owl (CLASS) llm_assisted: false - timestamp: '2026-05-13T10:00:00-07:00' curator: claude action: CURATED_CAUSAL_GRAPH changes: Added DOI-backed definition and causal graph linking minimal pH-homeostasis load at near-neutral external pH to the neutrophilic pH-optimum-mid1 bin. llm_assisted: true - timestamp: '2026-05-20T03:35:30Z' curator: claude action: GROUND_CAUSAL_PREDICATES changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202×1, rdfs:subClassOf×1). llm_assisted: true - timestamp: '2026-05-24T08:14:32Z' curator: claude action: GROUND_CAUSAL_NODES changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (PATO:0001432×1). llm_assisted: true - timestamp: '2026-06-15T07:21:43Z' curator: claude action: FIX_NODE_GROUNDING_CURIE changes: Overwrote 1 pH causal-node grounding(s) to corrected PATO CURIEs (phase-2; verified vs OAK). llm_assisted: true - timestamp: '2026-06-23T00:00:00Z' curator: claude action: ENRICH_CAUSAL_GRAPH changes: Added 6 evidence-backed generic edges (6 new nodes) from the deep-research report. llm_assisted: true - timestamp: '2026-06-24T17:21:10Z' curator: claude action: GROUND_CAUSAL_PREDICATES changes: Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:consumes×2, METPO:2000209×1, biolink:produces×1, RO:0002326×1). llm_assisted: true