Microbial, host and xenobiotic diversity in the cystic fibrosis sputum metabolome

Abstract

Cystic fibrosis (CF) lungs are filled with thick mucus that obstructs airways and facilitates chronic infections. Pseudomonas aeruginosa is a significant pathogen of this disease that produces a variety of toxic small molecules. We used molecular networking-based metabolomics to investigate the chemistry of CF sputa and assess how the microbial molecules detected reflect the microbiome and clinical culture history of the patients. Metabolites detected included xenobiotics, P. aeruginosa specialized metabolites and host sphingolipids. The clinical culture and microbiome profiles did not correspond to the detection of P. aeruginosa metabolites in the same samples. The P. aeruginosa molecules that were detected in sputum did not match those from laboratory cultures. The pseudomonas quinolone signal (PQS) was readily detectable from cultured strains, but absent from sputum, even when its precursor molecules were present. The lack of PQS production in vivo is potentially due to the chemical nature of the CF lung environment, indicating that culture-based studies of this pathogen may not explain its behavior in the lung. The most differentially abundant molecules between CF and non-CF sputum were sphingolipids, including sphingomyelins, ceramides and lactosylceramide. As these highly abundant molecules contain the inflammatory mediator ceramide, they may have a significant role in CF hyperinflammation. This study demonstrates that the chemical makeup of CF sputum is a complex milieu of microbial, host and xenobiotic molecules. Detection of a bacterium by clinical culturing and 16S rRNA gene profiling do not necessarily reflect the active production of metabolites from that bacterium in a sputum sample.

Metabolomic responses to lumacaftor/ivacaftor in cystic fibrosis

“…We found that amino acid and lipid metabolites, and phospholipids and sphingolipids in particular, were significantly altered by Lumacaftor/Ivacaftor initiation. This data corroborates metabolomics work by Quinn and colleagues who demonstrated that the most differentially abundant molecules between CF and non‐CF sputum were sphingolipids . A portion of our findings may be explained if increased levels and/or more active CFTR are causing increased insertion of PC and PE into cell membranes.…”

Natural products as mediators of disease

“…147 A recent study compared the repertoire of P. aeruginosa quinolones produced in laboratory cultures to sputum samples from CF patients. 148 The predominant culture produced quinolone, pseudomonas quinolone signal ( 9 , PQS), was not detected in sputum samples.…”

Metabolomics‐based chemotaxonomy of root endophytic fungi for natural products discovery

“…This step, however, only provided an overall direct and indirect (‘level‐two’) dereplication of 307 metabolites, representing a total of 3.8% of those in a spectral family. This annotation rate is similar to those achieved in studies from bacterial and human sources (Floros et al ., ; Quinn et al ., ), which achieved annotations for 2.5%–3.5% of all metabolites using the same workflow, and it did not increase noticeably when using high resolution MS/MS spectra, indicating that the precision of measurements is not a major factor affecting identifications. Altogether, the relatively low annotation rate highlights an insufficient coverage of fungal chemistries in GNPS libraries rather than an actual lack of knowledge on fungal natural products.…”