Fig. 1

Alpha diversity measured by a) Faith’s Phylogenetic Diversity and b) Inverse Simpson metrics grouped by sample type. Alpha diversity values were calculated on CSS normalised and logged read counts. The p-values represent the difference between groups determined by Wilcoxon rank sum (case/control NPS) or Wilcoxon signed rank (MEF/MER and MEF/NPS) test where paired samples were from the same child