The Evolving Cystic Fibrosis Microbiome: A Comparative Cohort Study Spanning 16 Years

Area of Science:

• Microbiology
• Pulmonology
• Genomics

Background:

• Cystic fibrosis (CF) airways harbor a complex polymicrobial community.
• Understanding temporal shifts in the CF microbiome is crucial for disease management.
• Changes in CF pathogens parallel observed microbiome alterations.

Purpose of the Study:

• To investigate temporal changes in the CF airway microbiome.
• To correlate microbiome shifts with clinical status in young adults with CF.
• To identify alterations in microbial community composition and diversity over time.

Main Methods:

• Analysis of sputum samples from 45 adult CF patients across three successive cohorts (1997-2013).
• Utilized Illumina MiSeq sequencing of the 16S rDNA V3 region for microbial community assessment.
• Collected patient demographics, clinical data, and medication history via chart review.

Main Results:

• No significant differences in baseline demographics across cohorts.
• A trend towards improved health and increased use of disease-modifying therapies in later cohorts.
• Increased microbial diversity (Shannon diversity) and a decrease in Pseudomonas-dominated communities over time.
• An increase in Streptococcus prevalence was observed.
• Lung function remained the primary predictor of microbiome diversity, despite cohort-associated β-diversity.
• Core microbiome constituents were consistently preserved across all cohorts.

Conclusions:

• The CF airway microbiome in young adults undergoes modest compositional and structural changes over time.
• These microbiome shifts occurred concurrently with improvements in clinical status.
• Despite observed changes, the fundamental core microbiome constituents were preserved.