Identity
Canonical name: Xylose 1
Known aliases: No aliases are reported in the source document. 1
Stable external identifier: No stable external identifier is reported in the source document. 1
Xylose is a compound proposed as a selective prebiotic substrate in a protective microbiome formulation for competitive exclusion of pseudomonas-aeruginosa. 1
Evidence from cf_formulation_design
The report identified xylose as a pathway-level metabolic opportunity because xylose utilization was complete in at least one core commensal species but absent in pseudomonas-aeruginosa PA14. 1
PA pathway completeness for xylose was 0%, and the corresponding selectivity value was 1.00. 1
The proposed prebiotic strategy predicts that xylose will support neisseria mucosa and gemella sanguinis more selectively than PA14. 1
This prediction was based on genomic pathway comparison rather than direct xylose growth experiments, because the 22-substrate carbon panel omitted the sugar alcohols and pentoses identified genomically. 1
The report found that PA14 outgrew the average commensal on every one of the 22 tested substrates, so xylose is a proposed alternative to amino-acid competition rather than a demonstrated commensal growth advantage. 1
Evidence from pseudomonas_carbon_ecology
The newer comparative analysis supports the genomic basis of the selectivity claim: xylose completeness was 0.0% in 7 Pseudomonas s.s. species and 74.4% in 189 Pseudomonas_E species, a difference of +74.4 percentage points. 2 This result refines the PA14-specific observation by placing xylose loss in the broader context of host-associated Pseudomonas s.s. versus the generally more environmentally associated Pseudomonas_E group; it does not directly test growth of PA14 or the proposed commensals. 2
Interpretation and limitations
Xylose therefore links metabolic-model-gapfilling with condition-specific-fitness: its proposed value comes from a metabolic gap between PA14 and candidate commensals that may shape condition-dependent competitive fitness. 1
The xylose prediction requires experimental validation before use in a formulation, including direct growth and competition assays with neisseria mucosa, gemella sanguinis, PA14, PAO1, and clinical PA isolates. 1
The new analysis supports retaining this validation requirement: carbon-pathway profiles showed ecological structure, but xylose alone was not established as a fine-grained environment discriminator, and the analysis did not provide direct competition evidence. 2
The result also contributes to multi-omics-integration and pangenome-integration, because the proposed substrate was identified by combining pathway comparisons with patient metatranscriptomics and pangenome data. 1
Source
- Rational Design of Protective Microbiome Formulations for Competitive Exclusion of *Pseudomonas aeruginosa* in Cystic Fibrosis Airways — formulation-design report integrating metabolic assays, patient omics, interaction data, and pangenome analysis. 1
- Carbon Source Utilization Predicts Ecology and Lifestyle in Pseudomonas — comparative Pseudomonas carbon-pathway analysis contextualizing xylose pathway loss. 2