Samples were collected from the University of California San Diego (UCSD) adult CF clinic during routine visits from patients. Sputum samples were expectorated into a sputum cup and transported back to the laboratory within 3 hours of collection. All samples were collected via the UCSD institutional review board–approved protocol for human subject research (project #160078). A total of 18 sputum samples were collected from CF patients for the pH experiments and another 19 for the oxygen experiments (table S1). In addition, six sputum samples were collected from healthy volunteers after saline mouth rinse and expectoration of airway mucus as a comparison for the pH experiments. Samples were split into four aliquots: one fresh for WinCF culturing and three aliquots frozen at −80°C for 16S ribosomal RNA (rRNA) gene sequencing and LC-MS/MS and GC-MS metabolomics.

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