Open AccessHigh-Resolution Longitudinal Dynamics of the Cystic Fibrosis Sputum Microbiome and Metabolome through Antibiotic Therapy
Author(s) -
Ruma Raghuvanshi,
Karla Vasco,
Yoshiki Vázquez-Baeza,
Lingjing Jiang,
James T. Morton,
Danxun Li,
Antonio González,
Lindsay DeRight Goldasich,
Gregory Humphrey,
Gail Ackermann,
Austin D. Swafford,
Douglas Conrad,
Rob Knight,
Pieter C. Dorrestein,
Robert A. Quinn
Publication year - 2020
Publication title -
msystems
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.931
H-Index - 39
ISSN - 2379-5077
DOI - 10.1128/msystems.00292-20
Subject(s) - metabolome , microbiome , biology , unifrac , cystic fibrosis , sputum , pseudomonas aeruginosa , alpha diversity , microbiology and biotechnology , metabolomics , medicine , bacteria , bioinformatics , pathology , genetics , ecology , 16s ribosomal rna , tuberculosis , habitat
Subjects with cystic fibrosis battle polymicrobial lung infections throughout their lifetime. Although antibiotic therapy is a principal treatment for CF lung disease, we have little understanding of how antibiotics affect the CF lung microbiome and metabolome and how much the community changes on daily timescales. By analyzing 594 longitudinal CF sputum samples from six adult subjects, we show that the sputum microbiome and metabolome are dynamic. Significant changes occur during times of stability and also through pulmonary exacerbations (CFPEs). Microbiome alpha-diversity increased as a CFPE developed and then decreased during treatment in a manner corresponding to the reduction in the log ratio of anaerobic bacteria to classic pathogens. Levels of metabolites from the pathogen P. aeruginosa were also highly variable through time and were negatively associated with anaerobes. The microbial dynamics observed in this study may have a significant impact on the outcome of antibiotic therapy for CFPEs and overall subject health.