title: 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.
authors.affiliation: Department of Biology, San Diego State University, San Diego, CA, USA.|Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA, USA.
authors.forename: Robert A
authors.initials: RA
authors.lastname: Quinn
authors.affiliation: Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA, USA.
authors.forename: Vanessa V
authors.initials: VV
authors.lastname: Phelan
authors.affiliation: Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, USA.
authors.forename: Katrine L
authors.initials: KL
authors.lastname: Whiteson
authors.affiliation: Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA, USA.
authors.forename: Neha
authors.initials: N
authors.lastname: Garg
authors.affiliation: Department of Mathematics and Statistics, San Diego State University, San Diego, CA, USA.
authors.forename: Barbara A
authors.initials: BA
authors.lastname: Bailey
authors.affiliation: Department of Biology, San Diego State University, San Diego, CA, USA.
authors.forename: Yan Wei
authors.initials: YW
authors.lastname: Lim
authors.affiliation: Department of Medicine, University of California at San Diego, La Jolla, CA, USA.
authors.forename: Douglas J
authors.initials: DJ
authors.lastname: Conrad
authors.affiliation: Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA, USA.
authors.forename: Pieter C
authors.initials: PC
authors.lastname: Dorrestein
authors.affiliation: Department of Biology, San Diego State University, San Diego, CA, USA.
authors.forename: Forest L
authors.initials: FL
authors.lastname: Rohwer
mesh_terms: D000293:Adolescent; D002518:Ceramides / Q000737:chemistry; D003550:Cystic Fibrosis / Q000382:microbiology*; D006801:Humans; D008168:Lung / Q000382:microbiology; D055442:Metabolome; D064307:Microbiota; D011552:Pseudomonas Infections / Q000382:microbiology*; D011550:Pseudomonas aeruginosa / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D015363:Quinolones / Q000737:chemistry*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D013183:Sputum / Q000737:chemistry / Q000382:microbiology; D015262:Xenobiotics / Q000737:chemistry*
chemical_list: C407944:2-heptyl-3-hydroxy-4-quinolone; D002518:Ceramides; D015363:Quinolones; D012336:RNA, Ribosomal, 16S; D015262:Xenobiotics