What this entity is
Canonical name: Pseudomonas fluorescens. 1
Known aliases: P. fluorescens; Pseudomonas_E fluorescens/protegens is the broad GTDB-reclassified clade label used for aggregated records and is not a direct synonym for every strain. 1
Stable external identifier: No stable external identifier was reported in the document. 1
The document uses P. fluorescens as the species-level reference for comparing FW300-N2E3 exometabolite production with bacdive utilization phenotypes. 1
The ENIGMA analysis refines this species-level framing: all ENIGMA Pseudomonas belonged to the environmental Pseudomonas_E fluorescens/protegens clade, whereas globally sampled Pseudomonas was 37.8% clinical, 12.9% soil/plant, and 9.4% aquatic. 2 The ENIGMA-linked environmental profile therefore should not be treated as representative of the full global genus distribution; the 14 ENIGMA genera occurred in 4,086–288,686 of 464,000 global 16S samples, with Pseudomonas occurring in 206K samples. 2
The carbon-ecology analysis further refines the clade-level context: its Pseudomonas_E comparison included 189 species, including the P. fluorescens/putida group, rather than measuring P. fluorescens alone. 3 Across the comparison, 43 of 62 GapMind carbon pathways differed significantly between 7 Pseudomonas s.s. species and those 189 Pseudomonas_E species after Benjamini-Hochberg false-discovery-rate correction, with the largest Pseudomonas_E advantages involving xylose (74.4% versus 0.0%), ribose (92.0% versus 27.9%), arabinose (62.6% versus 0.0%), and myo-inositol (58.8% versus 0.0%). 3 This supports pathway-rich environmental specialization in the broader Pseudomonas_E clade but does not establish these values for every P. fluorescens strain. 3
Key facts from fw300_metabolic_consistency
pseudomonas-fw300-n2e3 was analyzed against species-level P. fluorescens utilization data from bacdive, but the report cautions that the BacDive aggregation spans a broad clade under GTDB reclassification and may not represent the FW300-N2E3 strain specifically. 1
Among WoM-produced metabolites, P. fluorescens BacDive utilization was positive for 3 of 7 matched metabolites (43%), compared with an overall P. fluorescens baseline of 22 of 80 (27.5%); the binomial comparison gave p = 0.40. 1
For tryptophan, 0 of 50 P. fluorescens strains utilized the compound as a carbon source, with n = 50 and pct_positive = 0.0 under the report’s per-strain consensus procedure. 1
For trehalose, 1 of 6 P. fluorescens strains was positive; for lysine, 0 of 3 were positive; and for glycine, 0 of 1 was positive. 1
The report treats tryptophan as the strongest production-versus-utilization discordance because FW300-N2E3 increased tryptophan in WoM, showed 231 significant Fitness Browser gene effects when grown on tryptophan, and had a complete GapMind tryptophan-biosynthesis prediction, whereas 0 of 50 P. fluorescens strains utilized tryptophan. 1
The trehalose result is interpreted as potentially strain-variable and more consistent with an osmoprotectant role than a carbon-source role, while the lysine result has a small sample and the glycine result is insufficient for a firm conclusion. 1
Three metabolites showed strong BacDive utilization among the matched data: malate was utilized by 49 of 49 P. fluorescens strains (100%), arginine by 40 of 48 strains (83%), and valine by 1 of 1 strain. 1
BacDive utilization values were calculated after applying majority voting among duplicate records for each strain, and the report emphasizes that compound coverage ranged from 1 to 51 strains. 1
The carbon analysis supports the distinction between broad clade-level capability and strain physiology: within Pseudomonas_E, plant-associated species averaged 56.7 complete pathways, free-living species 56.1, and host-associated species 55.2, while lifestyle categories substantially overlapped. 3 Among 54 free-living and plant-associated species, carbon profiles nevertheless showed a significant but modest environment association (999-permutation p = 0.006); a four-class Random Forest achieved balanced accuracy of 0.408 +/- 0.169 against a 0.250 chance baseline. 3 Thus, these results refine the environmental interpretation: carbon profiles contain ecological signal, but are insufficient alone for fine-grained environment prediction. 3
The ENIGMA analysis supports retaining this caution: strain-name collisions caused 12 of 32 genus-level pangenome mismatches, and GTDB-Tk genus checks reduced verified linkages from 32 to 20 while eliminating all false matches. 2 Thus, the report uses P. fluorescens utilization data as a species- and clade-level comparison for pseudomonas-fw300-n2e3, not as a direct measurement of FW300-N2E3 physiology. 1
The carbon study also notes that its 62 GapMind pathways omit genus-specific aromatic capabilities, including toluene, naphthalene, and benzoate degradation, which may be important to P. putida and related environmental ecotypes. 3 It proposes within-species analysis of P. fluorescens and P. putida ecotypes and experimental comparison with RB-TnSeq fitness data from kescience-fitnessbrowser. 3
Related pages
- Metabolic Consistency of Pseudomonas FW300-N2E3 Across Four KBase Data Lakehouse Databases — source summary containing the cross-database analysis. 1
- Genotype × Condition to Phenotype Prediction from ENIGMA Growth Curves — integrated genotype–condition–phenotype analysis and environmental context. 2
- Carbon Source Utilization Predicts Ecology and Lifestyle in Pseudomonas — GapMind carbon-pathway analysis across Pseudomonas species and environments. 3
- bacdive — database supplying the species-level utilization phenotypes. 1
- pseudomonas-fw300-n2e3 — FW300-N2E3 isolate analyzed in the report. 1
- multi-omics-integration — cross-database integration of metabolomics, fitness, phenotype, and pathway evidence. 1
- metabolic-model-gapfilling — interpretation of GapMind pathway predictions alongside utilization data. 1