Fig 1.
Comparison of the gut microbiota composition before and after surgical resection.
(A, C) Boxplots, with median (centrelines), first and third quartiles (box limits) and 1.5x interquartile range (whiskers), showing alpha diversity Shannon, Simpson, and Chao1 indices at (A) bacterial species and (C) bacterial MetaCyc pathways. Gray lines connect samples of the same patient from before and after surgical resection. (B, D) Principal Coordinate Analysis plot based on Bray-Curtis distances before and after surgical resection at (B) bacterial species and (D) bacterial MetaCyc pathways. Gray lines connect the measurement of a patient before and after surgical resection.
Fig 2.
Taxonomic analysis of the gut microbiome in response to surgical resection.
(A) Heatmap of differentially abundant bacterial species (P<0.05, Wilcoxon signed-rank test) before and after surgical resection. Red and blue in the far-left column indicates increased and decreased relative abundance, respectively. (B) Co-abundance network of bacterial species using SparCC [30]. Only correlations between differentially abundant bacterial species (P<0.05, Wilcoxon signed-rank test) that changed direction were used for network construction. The nodes are coloured based on their affiliated phyla. Edge colour indicates either correlations that changed from positive to negative (blue) or from negative to positive (red).
Fig 3.
Functional analysis of the gut microbiome in response to surgical resection.
Heatmaps of the top 20 increased (top) and decreased (bottom) differentially abundant bacterial MetaCyc pathways (P<0.05, Wilcoxon signed-rank test). Histogram (left panel) shows the pathways ranked by variation (log2 fold-change after surgical resection).
Fig 4.
Correlations between taxonomic and functional profiles and CPET.
(A) Heatmap of partial Spearman’s rank correlation analysis between bacterial species and bacterial MetaCyc pathways versus lung function parameters adjusting for COPD and cancer type. Only differentially abundant species and pathways (P<0.05, Wilcoxon signed-rank test) were used. (B) Heatmap of partial Spearman’s rank correlation analysis between fungal species versus lung function parameters adjusting for COPD and cancer type. (A, B) Cell colour indicates either negative correlation (blue) or positive correlation (red). Only species and pathways with significant correlations ((A) P<0.05; (B) P<0.05, absolute correlation coefficient > 0.65) are shown (*P<0.05, **P<0.01, ***P<0.001).