Background and objective: Bacterial colonisation of the nasopharynx during infancy can significantly impact future respiratory health. We have previously shown that the predictable succession of the nasopharyngeal microbiota during the first year of life appears to be largely independent of external exposures, suggesting that interactions between bacterial species are likely to be key determinants of this succession. Here, we aimed to elucidate the role of bacterial-bacterial interactions in temporal patterns of bacterial carriage using in-silico analysis of longitudinal nasopharyngeal microbiota profiles.
Methods: We implemented V4 16S rRNA gene sequencing to study the nasopharyngeal bacteriome of 103 South African infants, sampled monthly over the first year of life. We inferred correlations from nasopharyngeal microbiota data using five network correlation methods, including sparse correlations for compositional data networks (SparCC), correlation inference for compositional data through lasso (CCLasso), Spearman correlation coefficient, Pearson correlation coefficient and compositionality corrected by renormalization and permutation (CCREPE). We identified correlations between pairs of bacterial taxa independently at genus- and amplicon sequence variant (ASV)-levels, using a cut-off correlation coefficient of r>0.3.
Results and conclusions: Bacterial-bacterial interactions were identified in 1,358 nasopharyngeal specimens from 103 healthy infants. Both positive and negative correlations were observed between healthy commensals and opportunistic pathogens. A consistently positive correlation was identified between Dolosigranulum and Corynebacterium, at both genus- and ASV-level. In contrast, strong negative correlations were observed between Corynebacterium and Haemophilus, and between Dolosigranulum and Haemophilus at both levels. Additionally, a negative correlation was found between the two dominant taxa Haemophilus and Moraxella. Overall, our findings indicate that strong bacterial interactions may influence patterns of colonisation of the nasopharynx during early life. An improved understanding of these interactions may offer the opportunity for diagnostic or therapeutic interventions to improve respiratory health.