FIGURE 4.

Microbiome community structure between sample sites. a) Nonmetric multidimensional scaling (NMDS) plots for individual babies for each sample site: i) tracheal aspirate fluid (TAF); ii) bronchoalveolar lavage (BAL); iii) nasopharyngeal aspirate (NPA); and iv) stool. Each coloured polygon joins all samples from an individual infant. b) α-diversity of observed genera/operational taxonomic units (OTUs) and Chao1 shown at i) genus and ii) operational taxonomic unit level. c) NMDS plot showing the relationship between the bacterial community between the anatomical sites. PERMANOVA showed significant differences between BAL versus TAF, BAL versus NPA, BAL versus stool, TAF versus NPA, TAF versus stool and NPA versus stool using Bonferroni correction (all p<0.01).