Fig. 1

Study design. 121 healthy 1-week-old newborns were prospectively enrolled from different recruiting centres in Scotland (Aberdeen, Edinburgh) and England (Imperial College London, Queen Mary University London and Isle of Wight). Participants were sampled across two respiratory sites, the nostrils and oropharynx, for both bacterial and fungal targeted amplicon sequencing. An additional set of samples was acquired from the nostrils for host gene expression analyses. Resulting datasets and relevant metadata were integrated to address the impact of cross-kingdom associations on the developing respiratory immune system