Design and Development of a Model to Study the Effect of Supplemental Oxygen on the Cystic Fibrosis Airway Microbiome

Supplemental Oxygen Alters the Airway Microbiome in Cystic Fibrosis

“…It is well known that canonical CF pathogens such as Pseudomonas aeruginosa exhibit a different phenotype when studied in isolation than when studied in the presence of a broader microbial community ( 52 , 53 ). We used artificial sputum formulated to mimic the composition of sputum for pwCF ( 27 ) rather than using rich medium more typically used in clinical microbiology laboratories. We have previously shown that sputum cultured under the 21% oxygen condition in our model recapitulates microbial communities of uncultured sputum when assessed by metagenomic sequencing ( 27 ).…”

“…We used artificial sputum formulated to mimic the composition of sputum for pwCF ( 27 ) rather than using rich medium more typically used in clinical microbiology laboratories. We have previously shown that sputum cultured under the 21% oxygen condition in our model recapitulates microbial communities of uncultured sputum when assessed by metagenomic sequencing ( 27 ). We evaluated changes in absolute rather than relative abundance in our taxonomic profiles with the use of spike-in controls prior to nucleic acid extraction, although we did not verify the derived absolute abundance estimates.…”

“…There are limitations to this study approach that must be considered in evaluating these findings. First, we employed an ex vivo model for culture that we have previously shown can recapitulate uncultured airway microbial communities from pwCF ( 27 ). However, while useful, all models have inherent limitations, and the exact effects in vivo may differ somewhat from those observed in our ex vivo approach.…”

“…Figure S3 provides details on the observed microbes that were and were not able to be cultured, as well as the oxygen tolerance capability and Gram stain result for each species. Full details on the validation of this culture approach, including justification for the composition of artificial sputum medium and oxygen sparging protocol, have been previously described ( 27 ).…”

“…In this study, we tested our hypothesis that supplemental oxygen alters the airway microbiome in pwCF. Our approach used a previously validated method ( 27 ) for culturing sputum from pwCF in artificial sputum medium under various oxygen conditions. We performed taxonomic, predicted functional, antimicrobial resistance, and mobile genetic element profiling using shotgun metagenomic sequencing, with the use of spike-in bacteria to determine absolute microbial abundance.…”