Statistics
Categorical and continuous metadata variables were compared by Fisher’s exact and Kruskal-Wallis test, respectively. Longitudinal analysis was restricted to one sample per timepoint per subject using first available where multiple samples existed. Alpha diversity was assessed by feature richness and Shannon diversity. Feature richness was calculated as the total number of individual features identified within a sample following normalisation. Beta diversity was assessed by weighted Bray-Curtis dissimilarity for bacterial communities and Canberra compositional dissimilarity for LC-MS and VOC metabolite datasets.Results of previous research by this group was used to determine which clinical variables to include in statistical models.