Fig. 4: Stool and gastric residuals microbiome.

Principal coordinate analysis (PCoA) of stool and GR samples, colored by sample type (A) and S.epidermidis (B), K.pneumoniae (C), and E.coli (D) relative abundance. Each sample is represented as a dot on the plot. E Comparison by sample type of average microbial dissimilarity across two consecutive samples. Each dot represents the estimated subject-specific average daily Bray-Curtis dissimilarity derived from pairs of consecutive samples, divided by the number of days between them. Measurements (dots) from the same infant are connected with a dashed line. p-value was calculated using a two-sided paired Wilcoxon test (n = 15 sample pairs). Boxes show the median and represent the 25% and 75% quantiles, whiskers extend to 1.5 times the interquartile range from box edges. F, G, H Strain-level analysis of key taxa across all stool (n = 199) and GR (n = 69) samples. Phylogenetic trees of S.epidermidis (F), K.pneumoniae (G), and E.coli (H). Each leaf (dots) represents a single sample. The phylogenetic distance between dominant strains of two samples is the sum of the distances on the x-axis (branches of the tree). Samples are colored by the subject from which the sample was taken, and  shaped according to the sample type.