identifier: METPO:1000461 label: pH range mid1 definition: A pH range phenotype in which the growth-supporting external pH range spans approximately 6–7, characteristic of neutrophilic physiology. definition_source: DOI:10.1038/nrmicro2549 trait_category: ENVIRONMENT term_kind: CLASS mapping_status: REVIEWED parent_traits: - METPO:1000332 synonyms: - synonym_text: Alkali Tolerant synonym_type: EXACT_SYNONYM source: metpo.owl - synonym_text: Facultative acidophile synonym_type: EXACT_SYNONYM source: metpo.owl - synonym_text: Neutrophile synonym_type: EXACT_SYNONYM source: metpo.owl - synonym_text: pHR_6_to_7 synonym_type: RELATED_SYNONYM source: metpo.owl evidence: - reference: DOI:10.1038/nrmicro2549 snippet: cytoplasmic pH notes: pH-homeostasis review supports near-neutral cytoplasmic pH at near-neutral external pH as the neutrophilic regime. causal_graphs: - graph_id: ph_range_mid1_neutrophile_range title: pH-range-mid1 neutrophile range description: DOI-backed graph linking baseline pH-homeostasis at near-neutral external pH to a pH growth range of approximately 6–7. nodes: - node_id: ph_range_mid1_trait label: pH range mid1 node_type: TRAIT grounding: METPO:1000461 description: pH growth-supporting range approximately 6–7. - node_id: ph_range label: pH range node_type: TRAIT grounding: METPO:1000332 description: Span of external pH values supporting growth. - node_id: baseline_ph_homeostasis label: baseline pH homeostasis node_type: BIOLOGICAL_PROCESS description: Minimal proton-extrusion and buffering activity needed to maintain near-neutral cytoplasmic pH at near-neutral external pH. - node_id: proton_motive_force label: proton motive force node_type: BIOLOGICAL_PROCESS description: Electrochemical proton gradient (PMF) across the cytoplasmic membrane. - node_id: cytoplasmic_ph_homeostasis label: cytoplasmic pH homeostasis node_type: BIOLOGICAL_PROCESS description: Maintenance of near-neutral cytoplasmic pH (~7) across the external pH range. grounding: GO:0051453 - node_id: cation_proton_antiporters label: cation/proton antiporters node_type: GENE_OR_PROTEIN description: Membrane antiporters (e.g. Na+/H+) whose repertoire sets external-pH boundaries for maintaining cytoplasmic pH ~7. - node_id: acid_challenge label: acid challenge node_type: ENVIRONMENTAL_FACTOR description: Exposure to acidic external pH below the neutrophilic optimum. - node_id: respiratory_proton_pumping label: respiratory proton-pumping complexes node_type: GENE_OR_PROTEIN description: Respiratory chain complexes that extrude protons, upregulated under acid challenge. - node_id: alkaline_challenge label: alkaline challenge node_type: ENVIRONMENTAL_FACTOR description: Exposure to alkaline external pH above the neutrophilic optimum. edges: - subject: baseline_ph_homeostasis predicate: enables object: ph_range_mid1_trait description: Baseline pH-homeostasis enables growth across pH 6–7. evidence: - reference: DOI:10.1038/nrmicro2549 snippet: pH homeostasis notes: Supports baseline pH-homeostasis as the neutrophilic range mechanism. predicate_id: RO:0002327 - subject: ph_range_mid1_trait predicate: is a object: ph_range description: pH range mid1 is a quantitative bin of the pH-range phenotype. evidence: - reference: DOI:10.1038/nrmicro2549 snippet: external pH notes: Supports the pH 6–7 range as a value within the pH-range distribution. predicate_id: rdfs:subClassOf - subject: proton_motive_force predicate: enables object: cytoplasmic_ph_homeostasis description: PMF (membrane potential) is required to maintain cytoplasmic pH homeostasis. evidence: - reference: DOI:10.1103/PRXLife.2.043015 notes: 'Terradot et al. 2024: decreasing the PMF''s strength impairs the cells'' ability to maintain pH.' predicate_id: RO:0002327 - subject: cytoplasmic_ph_homeostasis predicate: enables object: ph_range_mid1_trait description: Maintaining near-neutral cytoplasmic pH supports the neutrophilic pH 6-7 growth range. evidence: - reference: DOI:10.1103/PRXLife.2.043015 notes: Cytoplasmic pH held near neutral underlies the neutralophile growth range. predicate_id: RO:0002327 - subject: cation_proton_antiporters predicate: determines object: cytoplasmic_ph_homeostasis description: Transporter repertoire (ClcA/NhaB/NhaA-like antiporters) sets the external-pH boundaries over which cytoplasmic pH ~7 is maintained. evidence: - reference: DOI:10.1103/PRXLife.2.043015 notes: 'Terradot et al. 2024: ClcA-like ~pHe 2-5, NhaB-like ~5-9, NhaA-like ~9-12 maintain pHi ~7.' - subject: acid_challenge predicate: positively regulates object: respiratory_proton_pumping description: Under acid challenge cells upregulate proton-pumping respiratory complexes (and downregulate ATP synthase) to support pH homeostasis. evidence: - reference: DOI:10.1038/nrmicro2549 notes: 'Krulwich et al. 2011: under acid challenge E. coli up-regulates proton-pumping respiratory complexes and down-regulates ATP synthase.' - subject: respiratory_proton_pumping predicate: enables object: baseline_ph_homeostasis description: Proton-pumping respiratory activity contributes to baseline pH homeostasis on the acidic side of the range. evidence: - reference: DOI:10.1038/nrmicro2549 notes: 'Krulwich et al. 2011: proton extrusion supports cytoplasmic pH maintenance under acid challenge.' predicate_id: RO:0002327 - subject: alkaline_challenge predicate: positively regulates object: cation_proton_antiporters description: Under alkaline challenge cells activate cation/proton antiporters and F1Fo-ATP synthase proton-capture to support pH homeostasis. evidence: - reference: DOI:10.1038/nrmicro2549 notes: 'Krulwich et al. 2011: under alkaline stress cells activate inward proton transport via cation/proton antiporters and increase ATP synthase expression.' curation_history: - timestamp: '2026-05-05T01:35:46.830444+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 baseline pH-homeostasis at near-neutral external pH to the neutrophilic pH-range-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 (RO:0002327×1, 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 (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 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327×3). llm_assisted: true - timestamp: '2026-06-24T17:21:17Z' curator: claude action: GROUND_CAUSAL_NODES changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0051453×1). llm_assisted: true