mesophilic

METPO:1000615 · CLASS · REVIEWED

A temperature preference in which growth is favored at intermediate temperatures, typically ~20–45 °C.

Trait evidence (2)

DOI:10.1016/j.bpj.2013.06.029
Escherichia coli, a mesophilic bacterium

Organism example: Escherichia coli is described as mesophilic.
DOI:10.1146/annurev-micro-091313-103612
more unsaturated fatty acids

Membrane-adaptation review supports homoviscous membrane composition matched to ambient temperature as the basis of mesophile physiology.

Mesophilic growth with membrane and temperature-boundary support

DOI-backed nonmechanistic graph connecting mesophily to moderate temperature, balanced growth, homoviscous membrane fluidity, and cold- and heat-shock boundary-support branches.

NONMECHANISTIC · This record is an upper preference, broad tolerance, or central-range classification spanning multiple unrelated adaptations; contextual protein nodes are retained without assigning a misleading token UniProt example.

Edge evidence

moderate ambient temperature selects for mesophilic METPO:2007401
Moderate ambient temperatures select for mesophilic physiology.
- DOI:10.1016/j.bpj.2013.06.029 Escherichia coli, a mesophilic bacterium Supports a representative mesophile thriving at moderate temperatures.
homoviscous lipid composition regulates membrane fluidity RO:0002211
Homoviscous lipid composition maintains target membrane fluidity at mesophilic temperatures.
- DOI:10.1146/annurev-micro-091313-103612 more unsaturated fatty acids Supports homoviscous adaptation as the mechanism setting membrane fluidity.
mesophile enzyme repertoire enables balanced mesophilic growth RO:0002327
Mesophile enzyme repertoire enables balanced growth at intermediate temperatures.
- DOI:10.1016/s0300-9629(97)00003-0 energy transducing enzymes Supports temperature-tuned enzyme repertoires as the basis of adapted growth.
balanced mesophilic growth manifests as mesophilic METPO:2007400
Balanced growth at moderate temperatures manifests the mesophilic trait.
- DOI:10.1016/j.bpj.2013.06.029 Escherichia coli, a mesophilic bacterium Supports the trait endpoint in a representative organism.
temperature decrease increases unsaturated fatty acids RO:0002213
Temperature downshift increases membrane unsaturated fatty acid content through homeoviscous adaptation.
- DOI:10.1007/s42770-023-01057-4 production of double bonds in lipids Verified against the Ramón et al. cold-adaptation review; low-temperature adaptation includes membrane-composition remodeling through lipid double-bond production.
cold shock positively regulates CspA cold-shock protein RO:0002213
Cold shock strongly increases CspA cold-shock protein synthesis.
- DOI:10.1046/j.1365-2958.1999.01284.x more than 10% of the total cellular protein synthesis Verified against the open Molecular Microbiology full text; CspA is the major E. coli cold-shock protein and its synthesis rises sharply after temperature downshift.
CspA cold-shock protein promotes translation RO:0002213
CspA RNA chaperone activity destabilizes inhibitory mRNA secondary structures, promoting translation during cold shock.
- DOI:10.1046/j.1365-2958.1999.01284.x facilitates translation by destabilizing mRNA secondary structures Verified against the open Molecular Microbiology full text; CspA acts as an RNA chaperone that counters low-temperature mRNA secondary structure.
heat shock positively regulates sigma-32 (RpoH) RO:0002213
Heat shock transiently increases cellular sigma-32 (RpoH), the heat-shock sigma factor.
- DOI:10.1128/jb.183.18.5302-5310.2001 transient increase in the RpoH level observed upon heat shock Verified against the open Journal of Bacteriology full text; E. coli heat-shock induction is regulated by increased RpoH translation and transient sigma-32 stabilization.
sigma-32 (RpoH) positively regulates heat-shock response proteins RO:0002213
Sigma-32 (RpoH) positively regulates heat-shock response protein expression.
- DOI:10.1128/jb.183.18.5302-5310.2001 enhancing transcription of the heat shock genes Verified against the open Journal of Bacteriology full text; RpoH-dependent sigma-32 activity drives heat-shock-gene transcription.
DnaK chaperone negatively regulates sigma-32 (RpoH) RO:0002212
DnaK chaperone activity negatively regulates sigma-32 (RpoH) activity.
- DOI:10.1128/jb.183.18.5302-5310.2001 negative regulation of RpoH activity Verified against the open Journal of Bacteriology full text; the DnaK chaperone system participates in negative control of sigma-32 activity.
unsaturated fatty acids associated with homoviscous lipid composition biolink:associated_with
Unsaturated fatty-acid changes are associated with the homeoviscous lipid composition branch in this mesophilic temperature-response graph.
- DOI:10.1146/annurev-micro-091313-103612 incorporation of proportionally more unsaturated fatty acids Verified against the public Annual Review of Microbiology abstract; unsaturated fatty-acid incorporation is part of homeoviscous membrane remodeling as growth temperature decreases.
membrane fluidity associated with balanced mesophilic growth biolink:associated_with
Mesophilic balanced growth is associated with maintenance of target cytoplasmic-membrane fluidity.
- DOI:10.1146/annurev-micro-091313-103612 remodel the fluidity of their membrane bilayer Verified against the public Annual Review of Microbiology abstract; the connector links membrane-fluidity remodeling to growth-temperature acclimation without making a single lipid ratio define mesophily.
translation associated with balanced mesophilic growth biolink:associated_with
Cold-shock maintenance of translation is a lower-temperature boundary-support branch for balanced mesophilic growth.
- DOI:10.4161/rna.7.6.13482 facilitating transcription and translation at low temperature Verified against the open Phadtare and Severinov PMC abstract; the connector keeps CspA-family RNA chaperones as low-temperature translation context, not as a definition of mesophily.
heat-shock response proteins associated with balanced mesophilic growth biolink:associated_with
RpoH-regulated heat-shock response proteins form an upper-temperature boundary-support branch for balanced mesophilic growth.
- DOI:10.1128/mbio.02174-23 heat shock genes encoding chaperones, such as DnaK and GroEL Verified against the open Grunberger et al. PMC text; the connector keeps heat-shock chaperones as an upper-boundary proteostasis branch, not as a definition of mesophily.

Provenance

Identifier source: METPO (2026-06-12)
Definition source: DOI:10.1016/j.bpj.2013.06.029

Parent traits (1)

temperature preference METPO:1000613

kg-microbe context

Matched 1 kg-microbe node via direct_metpo.

METPO:1000615 [+102.284, -178.453, -111.655, -113.199, …]

512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

Nearest neighbors in embedding space

Top-8 cosine-similar METPO traits from the 2026-04-25 deepwalk (512-D).

ecology human pathogen 0.360
ecology animal pathogen 0.330
environment aerobic 0.328
morphology motile 0.249
morphology swarming motility 0.249
morphology twitching motility 0.249
morphology bacillus shaped 0.241
morphology rod shaped 0.232

Deep research

Generated by just research-trait; source: research/traits/environment/mesophilic-deep-research-falcon.md

Unreviewed literature output — not curated TraitMech content Ontology identifiers suggested below have not been resolved against their ontologies, and some are known to be wrong. Check any CURIE against the source before using it.

# Curation report: microbial trait **mesophilic**

## Executive summary

**Trait:** `METPO:1000615`
**Category:** ENVIRONMENT
**Term kind:** CLASS
**Mapping status:** REVIEWED
**Parent:** `METPO:1000613`

Mesophily should be modeled as an **organism-level temperature preference in which the optimum or favored growth occurs at intermediate temperature**, operationally about **20–45 °C** under the supplied METPO definition. It is not equivalent to merely surviving at one temperature in that interval, having a broad growth range, or mounting a cold- or heat-shock response. Published boundaries are not perfectly uniform: one comparative study uses an optimal-growth-temperature range of 20–50 °C for mesophiles, illustrating why the measured optimum, complete growth curve, medium, pressure, pH, oxygen status, and acclimation history should accompany trait assertions (sen2022insightsonrigidity pages 1-3).

The strongest curation-ready mechanism is **homeoviscous adaptation**: temperature changes alter fatty-acid biosynthetic flux and membrane lipid composition, which counters temperature-driven changes in membrane viscosity. A 2024 quantitative study in *Escherichia coli* identified a fast, temperature-sensitive FabI/FabB metabolic valve plus slower FabR-mediated transcriptional feedback, restoring membrane composition within one generation after a temperature shift (hoogerland2024atemperaturesensitivemetabolic pages 9-10, hoogerland2024atemperaturesensitivemetabolic pages 5-6, hoogerland2024atemperaturesensitivemetabolic pages 1-2). Heat-shock and cold-shock systems are important **boundary-support mechanisms**, but they do not define mesophily.

## 1. Trait scope and boundary cases

### 1.1 Positive scope

The preferred representation is:

> A microbial phenotype in which growth rate, yield, or another validated growth measure is optimal or favored at intermediate temperature, typically approximately 20–45 °C.

An assay should ideally estimate an optimum from several temperatures rather than infer mesophily from growth at 30 or 37 °C alone. “Mesophilic” may describe an organism, community, reactor regime, enzyme, or process; only the **organism-level growth preference** directly instantiates `METPO:1000615`.

### 1.2 Distinctions from neighboring concepts

- **Psychrophile:** optimum near low temperature; cold-active macromolecules are evolutionarily tuned for activity and flexibility in the cold. Growth by a mesophile after acclimation at 10–15 °C does not make it psychrophilic.
- **Psychrotolerant/psychrotrophic:** can grow at low temperature but has a higher optimum. The 2023 review notes that most microorganisms multiply poorly below 4 °C, while some mesophilic pathogens can still proliferate at refrigeration temperatures; low-temperature growth alone is therefore insufficient for classification (ramon2023ageneraloverview pages 2-4).
- **Thermophile:** optimum above the mesophilic interval. A protein study uses `Topt >50 °C`, but classifications near 45–50 °C depend on the convention used (sen2022insightsonrigidity pages 1-3).
- **Thermotolerant:** withstands elevated temperature without having a thermophilic optimum.
- **Heat/cold shock:** acute response to a change relative to the organism’s previous or optimal temperature. In experimental bacterial literature, “cold shock” may mean a rapid shift such as 37→15 °C, followed by transient growth arrest and acclimation (horn2007structureandfunction pages 1-2).
- **Growth range versus optimum:** survival limits, minimum/maximum growth temperatures, and optimum growth temperature are separate phenotypes.
- **Mesophilic process condition:** “mesophilic anaerobic digestion at 35 °C” describes a reactor regime and community-level function; it does not prove every community member is a mesophile.

### 1.3 Mechanistic interpretation

Mesophily is probably an **emergent balance** rather than a single pathway: membranes must remain liquid-crystalline but sufficiently impermeable; proteins must retain both stability and catalytic dynamics; transcription, translation, transport, and central metabolism must remain coordinated. Reviews distinguish long-term genome evolution, which sets the viable temperature range, from short-term reversible regulation of gene expression and enzyme activity (siliakus2017adaptationsofarchaeal pages 3-5). Accordingly, causal edges from acute stress experiments should be annotated as acclimation or boundary support—not automatically as causes of the constitutive mesophilic optimum.

## 2. Candidate nodes grouped by type

Only identifiers that can be stated confidently are included. Labels should be retained without a CURIE when the exact accession has not been verified.

### 2.1 Trait, environmental, and experimental nodes

| Candidate node | Suggested grounding | Curation note |
|---|---|---|
| mesophilic | `METPO:1000615` | Target phenotype; quote identifier verbatim. |
| parent temperature-preference trait | `METPO:1000613` | Supplied parent. |
| intermediate growth temperature | label only | Represent measured temperature in °C as assay metadata. |
| temperature downshift / cold shock | label only | Experimental perturbation, not the trait itself. |
| temperature upshift / heat shock | label only | Experimental perturbation, not the trait itself. |
| optimal growth temperature | label only | Quantitative phenotype; do not collapse into growth range. |
| phosphate limitation | label only | Relevant modifier in 2024 *D. alkenivorans* lipidomics. |
| mesophilic anaerobic digestion | label only | Process/application node, generally around 35–40 °C. |

### 2.2 Organisms

| Organism | Grounding | Role |
|---|---|---|
| *Escherichia coli* | `NCBITaxon:562` | Principal mesophilic model for fatty-acid, cold-shock, and heat-shock mechanisms. |

Showing the first 60 of 264 lines of findings; the linked file also carries the run's front matter and the prompt it was given — read the full report.

Canonical examples (1)

Organisms cited as exemplars of this trait. Taxon ids are NCBITaxon and link out to the NCBI record.

Escherichia coli NCBITaxon:562 DOI:10.1021/acsomega.2c04786 Canonical mesophile and universal model organism (optimum ~37 C).

Curation history

2026-05-05T01:35:46.857659+00:00 · SEEDED_FROM_METPO · seed_from_metpo
imported from data/raw/metpo.owl (CLASS)
2026-05-06T14:58:45-07:00 · CURATED_WITH_ORGANISM_EXAMPLE · codex
Added Escherichia coli organism example with PMID-backed evidence.
2026-05-13T11:30:00-07:00 · CURATED_CAUSAL_GRAPH · claude
Added DOI-backed causal graph linking moderate ambient temperature, homoviscous membrane composition, mesophile enzyme repertoire, and balanced growth to the mesophilic trait.
2026-05-13T22:45:00-07:00 · IMPROVED_CAUSAL_GRAPH_EVIDENCE · codex
Replaced Escherichia coli mesophile PMID fallback with the article DOI in definition, record evidence, and CausalEdge evidence.
2026-05-20T03:35:29Z · GROUND_CAUSAL_PREDICATES · claude
Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327×1).
2026-05-23T21:30:06Z · GROUND_CAUSAL_PREDICATES · claude
Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007401×1, METPO:2007400×1).
2026-05-24T04:13:18Z · RENAME_PREDICATE_LABELS · claude
Renamed 1 causal-edge predicate label(s) to align with existing groundings: maintains → regulates ×1.
2026-05-24T04:13:21Z · GROUND_CAUSAL_PREDICATES · claude
Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211×1).
2026-05-24T04:41:03Z · GROUND_CAUSAL_NODES · claude
Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007505×1).
2026-05-26T02:30:12Z · RETYPE_CAUSAL_NODES · claude
Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: membrane fluidity: BIOLOGICAL_PROCESS → QUALITY ×1.
2026-06-17T04:09:43Z · REMOVE_REDUNDANT_SYNONYM · claude
Removed 1 synonym(s) whose text duplicated the label (seeder redundancy; no information lost).
2026-06-23T00:00:00Z · ENRICH_CAUSAL_GRAPH · claude
Added 6 evidence-backed generic edges (9 new nodes) from the deep-research report.
2026-06-24T17:21:10Z · GROUND_CAUSAL_PREDICATES · claude
Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213×2).
2026-06-24T17:23:30Z · GROUND_CAUSAL_NODES · claude
Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:27208×1, GO:0006412×1).
2026-08-04T03:08:12Z · GROUND_CAUSAL_PREDICATES · claude
Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212×1).
2026-08-26T03:23:00Z · REVIEW_GRAPH_PROTEIN_TAXON · claude
Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope mesophilic_homoviscous_adaptation=NONMECHANISTIC with scope_notes; marked 5 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (mesophile_enzyme_repertoire, cspa, rpoh_sigma32, heat_shock_proteins, dnak); added 1 node(s) and 1 edge(s) (heat_shock_proteins); removed 1 node(s) and 1 edge(s) together with their evidence (heat_shock_genes).
2026-09-04T00:40:00Z · REVIEW_CAUSAL_EVIDENCE · codex
Reviewed the broad mesophilic_homoviscous_adaptation graph for issue #183: added snippets to 6 edge-level evidence items and regrounded 3 heat/cold shock response edges from legacy free-text predicates to RO:0002213 positive regulation. No paid research service was called.
2026-09-04T13:00:00Z · CONNECT_CAUSAL_GRAPH_COMPONENTS · codex
Resolved issue #183 graph fragmentation (5 components to 1) by adding 4 source- and verbatim-snippet-backed association connectors among the homoviscous membrane, cold-shock RNA, and heat-shock boundary branches. No paid research service was called.
2026-09-06T13:30:00Z · ADVERSARIAL_REVIEW_REPAIR · codex
Addressed PR #664 adversarial review issue #665: replaced two sigma-32 snippets with exact RpoH wording from the Journal of Bacteriology source.
2026-09-06T17:10:00Z · ADVERSARIAL_REVIEW_REPAIR · codex
Addressed PR #664 adversarial review: replaced copied nonmechanistic bridge snippets with independent exact source snippets while preserving the existing connector edge scope.