Fig. 4

Cross-kingdom microbial interactions in the nasal and oropharyngeal respiratory niches and effect of perinatal factors on nasal and oropharyngeal microbiota composition. a Nasal habitat interaction network inferred with SPIEC-EASI for bacteria only (left panel), fungi only (middle panel) and both kingdoms (right panel) on 5% prevalence filtered ASVs. Connecting edges represent significant interactions with node size proportional to ASV average abundance in total samples set and nodes are colored by Kingdom (red color for bacterial ASVs, green color for fungal ASVs) with opacity increasing with closeness centrality. b Number of intra- and inter-kingdom edges for each network (bacteria-bacteria in red color, fungi-fungi in green color and bacteria-fungi in salmon color). c Frequency of node degrees for each network (red color for bacterial networks, green color for fungal networks, salmon color for multi-kingdom networks). d–f Corresponding figures for the oropharyngeal cavity. g Bacterial taxa associated with breastfeeding or its absence in the oropharyngeal cavity and normalised relative abundance of the top 2 bacterial taxa associated with feeding mode. Boxplots represent the median and interquartile range with whiskers determined by Tukey’s method. h Corresponding fungi data. i Fungal taxa associated with country factor in the nasal habitat. Sample sizes for the networks are n = 51 for nasal and n = 39 for oropharynx networks, respectively. Sample sizes are n = 78 for nasal habitat bacterial data, n = 105 for oropharyngeal habitat bacterial data, n = 68 for nasal habitat fungal data and n = 44 for oropharyngeal habitat fungal data differential abundance testing