Supplementary Materials

The PDF file includes:

  • Fig. S1. Schematic of the experimental design with the WinCF system modified for the pH experiments and the oxygen experiments.
  • Fig. S2. Actual measurement versus predicted value from RF machine learning algorithm on the microbiome and metabolome data through pH, gas production, and depth variables.
  • Fig. S3. Niche partitioning of CF lung microbiota in the pH and oxygen experiments.
  • Fig. S4. O2 microenvironment (% air saturation) through the WinCF vertical depth gradient after incubation with sputum from two patients compared to a noninoculated control.
  • Fig. S5. Microbiome profiles of individual patients in the pH and oxygen experiments.
  • Fig. S6. Molecular network of rhamnolipids and quinolones detected in the LC-MS/MS data.
  • Fig. S7. GLMM results for different bacterial genera on a per patient basis.
  • Fig. S8. Mean abundance of tobramycin by ion count in the WinCF columns after incubation.
  • Fig. S9. Tobramycin and N-propionyl tobramycin identification from polar LC-MS/MS data.
  • Fig. S10. A. fumigatus metabolites in tobramycin-treated WinCF columns.
  • Fig. S11. Mean abundance of pooled anaerobes in the WinCF columns after the different treatments.
  • Fig. S12. WinCF model equations.
  • Fig. S13. Principle co-ordinate analysis (PCoA) plots of metabolome and microbiome data from all samples.
  • Legends for Tables S1 to S7
  • Supplementary Methods
  • References (46–51)

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Other Supplementary Material for this manuscript includes the following:

  • Table S1 (Microsoft Excel format). Patient samples and information collected in this study.
  • Table S2 (Microsoft Excel format). ANOVA of qualitative and quantitative variables measured during the WinCF pH gradient experiments.
  • Table S3 (Microsoft Excel format). Metabolites that most changed with the WinCF gas production gradient according to an RF variable importance plot from the untreated samples.
  • Table S4 (Microsoft Excel format). Mean abundance through the depth gradient (1 to 10 mm) of P. aeruginosa virulence factor metabolites detected in the WinCF depth experiments and the corresponding Pearson’s correlation (r).
  • Table S5 (Microsoft Excel format). Deblurred OTUs and their sequences that most changed with the WinCF depth gradient according to an RF variable importance plot from the untreated samples.
  • Table S6 (Microsoft Excel format). Results of the assessment of bias in WinCF system.
  • Table S7 (Microsoft Excel format). Confusion matrix and out-of-bag error from an RF classification of the pH experiment metabolomics data based on patient source.

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