identifier: METPO:1000457 label: pH optimum mid2 definition: A pH optimum phenotype with the best-growth external pH between approximately 7 and 8, corresponding to neutrophilic or moderately alkaliphilic 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: Alkaliphile synonym_type: EXACT_SYNONYM source: metpo.owl - synonym_text: Neutrophile synonym_type: EXACT_SYNONYM source: metpo.owl - synonym_text: pHO_7_to_8 synonym_type: RELATED_SYNONYM source: metpo.owl evidence: - reference: DOI:10.1038/nrmicro2549 snippet: pH homeostasis notes: pH-homeostasis review supports the 7–8 external-pH range as the common neutrophile / moderately alkaline-tolerant optimum. causal_graphs: - graph_id: ph_optimum_mid2_alkaline_tolerant_setpoint title: pH-optimum-mid2 alkaline-tolerant setpoint description: DOI-backed graph linking modest alkaline pH-homeostasis at slightly basic external pH to a pH-optimum between 7 and 8. nodes: - node_id: ph_optimum_mid2_trait label: pH optimum mid2 node_type: TRAIT grounding: METPO:1000457 description: pH optimum approximately 7–8. - node_id: ph_optimum label: pH optimum node_type: TRAIT grounding: METPO:1000331 description: External pH supporting maximal growth. - node_id: slightly_alkaline_external_ph label: slightly alkaline external pH node_type: ENVIRONMENTAL_FACTOR description: External pH 7–8, typical of seawater and many host body fluids. - node_id: modest_alkaline_homeostasis label: modest alkaline pH homeostasis node_type: BIOLOGICAL_PROCESS description: Mild K+/H+ antiport and cytoplasmic acidification activity maintaining cytoplasmic pH at slightly basic external pH. - node_id: cytoplasmic_buffering_capacity label: cytoplasmic buffering capacity node_type: BIOLOGICAL_PROCESS description: Buffering of the cytoplasm (e.g. phosphate pools) absorbing pH fluctuations. - node_id: intracellular_ph_homeostasis label: intracellular pH homeostasis node_type: BIOLOGICAL_PROCESS description: Regulation maintaining cytoplasmic pH near neutral. - node_id: na_h_antiporters label: Na+/H+ antiporters node_type: GENE_OR_PROTEIN description: Sodium:proton antiporters that acidify the cytoplasm when internal pH is too high. - node_id: k_h_antiporters label: K+/H+ antiporters node_type: GENE_OR_PROTEIN description: Potassium:proton antiporters regulating bacterial internal pH. grounding: UniProtKB:A0A1Z4VR00 - node_id: respiratory_proton_pumping label: proton-pumping respiratory chain components node_type: PATHWAY description: Respiratory electron transport chain components that pump protons. - node_id: metabolite_decarboxylation label: metabolite decarboxylation pathways node_type: PATHWAY description: Decarboxylation reactions whose free-energy change can be stored as PMF. - node_id: proton_motive_force label: proton motive force node_type: BIOLOGICAL_PROCESS description: Electrochemical proton gradient (ΔpH + Δψ) across the membrane. - node_id: f0f1_atp_synthase label: F0F1-ATP synthase node_type: GENE_OR_PROTEIN description: Proton-transporting ATP synthase complex that makes ATP from PMF. edges: - subject: slightly_alkaline_external_ph predicate: engages object: modest_alkaline_homeostasis description: Slightly alkaline external pH engages modest alkaline pH-homeostasis. evidence: - reference: DOI:10.1016/j.tim.2007.02.005 snippet: proton motive force notes: Supports balanced proton motive force at slightly alkaline pH as the energetic setting of this regime. - subject: modest_alkaline_homeostasis predicate: produces object: ph_optimum_mid2_trait description: Modest alkaline pH-homeostasis yields a neutrophile / alkaline-tolerant pH-optimum setpoint. evidence: - reference: DOI:10.1038/nrmicro2549 snippet: pH homeostasis notes: Supports the 7–8 optimum as the neutrophile / mild-alkaliphile outcome. predicate_id: METPO:2000202 - subject: ph_optimum_mid2_trait predicate: is a object: ph_optimum description: pH optimum mid2 is a quantitative bin of the pH-optimum phenotype. evidence: - reference: DOI:10.1038/nrmicro2549 snippet: cytoplasmic pH notes: Supports the 7–8 optimum as a value within the pH-optimum distribution. predicate_id: rdfs:subClassOf - subject: cytoplasmic_buffering_capacity predicate: stabilizes object: intracellular_ph_homeostasis description: Cytoplasmic buffering capacity stabilizes intracellular pH against fluctuations. evidence: - reference: DOI:10.1093/femsre/fuad033 notes: Buffering capacity of the cytoplasm absorbs pH fluctuations; broad bacterial mechanism supporting near-neutral pHi at external pH 7-8. - subject: na_h_antiporters predicate: maintains object: intracellular_ph_homeostasis description: Na+/H+ antiporters acidify the cytoplasm when pHi is too high, maintaining pH homeostasis. evidence: - reference: DOI:10.1093/femsre/fuad033 notes: Proton-sensing antiporters acidify the cytoplasm by exporting Na+ for protons when internal pH gets too high; general mechanism relevant at external pH 7-8. - subject: k_h_antiporters predicate: regulates object: intracellular_ph_homeostasis description: K+/H+ antiporters are key regulators of bacterial internal pH. evidence: - reference: DOI:10.1093/femsre/fuad033 notes: Na+/H+ and K+/H+ antiporters are key regulators of bacterial pH homeostasis; general regulator. predicate_id: RO:0002211 - subject: respiratory_proton_pumping predicate: maintains object: intracellular_ph_homeostasis description: Proton-pumping respiratory chain components prevent the internal pH from becoming too low. evidence: - reference: DOI:10.1093/femsre/fuad033 notes: Activation of proton-pumping respiratory chains prevents internal pH becoming too low; broad statement across respiratory bacteria. - subject: metabolite_decarboxylation predicate: generates object: proton_motive_force description: Metabolite decarboxylation pathways store free energy as proton motive force. evidence: - reference: DOI:10.1093/femsre/fuad033 notes: The free energy change from decarboxylation reactions can be stored as a proton motive force; general, not taxon-specific. predicate_id: biolink:produces - subject: proton_motive_force predicate: powers object: f0f1_atp_synthase description: Proton motive force powers F0F1-ATP synthase ATP synthesis. evidence: - reference: DOI:10.1093/femsre/fuad033 notes: The proton motive force can be used by F0F1-ATP synthase to make ATP; strong general bioenergetic edge. curation_history: - timestamp: '2026-05-05T01:35:46.827757+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 modest alkaline pH-homeostasis to the neutrophile / mild-alkaliphile pH-optimum-mid2 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: '2026-06-23T00:00:00Z' curator: claude action: ENRICH_CAUSAL_GRAPH changes: Added 6 evidence-backed generic edges (8 new nodes) from the deep-research report. llm_assisted: true - timestamp: '2026-06-24T17:21:10Z' curator: claude action: GROUND_CAUSAL_PREDICATES changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211×1, biolink:produces×1). llm_assisted: true - timestamp: '2026-06-26T07:15:17Z' curator: claude action: GROUND_CAUSAL_NODES changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A1Z4VR00×1). llm_assisted: true