Microbiomes without boundaries: cystic fibrosis 'pulmotype' classifications are dependent on algorithm choice and database size, and indicate continuous variation.

This dataset includes two CSV files containing genus-level relative abundance data from cystic fibrosis (CF) sputum microbiomes: Samples_Taxa_ppFEV1_Snapshot.csv: snapshot data representing the first microbiome sample per individual (n=1184), used for cross-sectional clustering analysis (DMM, PAM, k-means) and association with ppFEV1 lung function measurements. Samples_Taxa_ppFEV1_Longitudinal.csv: longitudinal microbiome samples (n=2842) from 427 individuals with CF used to assess transitions between pulmotypes over time. These data were used in the manuscript “Microbiomes without boundaries: cystic fibrosis ‘pulmotype’ classifications are dependent on algorithm choice and database size, and indicate continuous variation” by Zhao et al., 2025. All samples were processed with a standardized bioinformatics pipeline and represent a compilation of publicly available CF sputum microbiome studies (36 studies, 1184 individuals). Each row in the files corresponds to a sample, with metadata including subject ID, timepoint (where applicable), and ppFEV1 lung function data when available. The taxonomic data represent relative abundances at the genus level, filtered for common genera across studies.