Pneumocystis sp. is a pivotal ecological driver contributing to shifts in microbial equilibrium during the early-life lower airway microbiome assembly

Background. Early life gut microbiota is being increasingly recognized as a major contributor to short and/or long-term human health and diseases. However, little is known about these early-life events in the human microbiome of the lower respiratory tract. Objective. To explore fungal and bacterial colonization in the lower airways over the first year of life using lung tissue from autopsied infants. Method. The fungal and bacterial communities of lung tissue samples from 54 autopsied infants were characterized by NGS of ITS and 16S rRNA genes respectively. Results. Our study highlights a high degree of inter-individual variability in both fungal and bacterial communities inhabiting the infant lung, providing insights into the diverse nature of the lower respiratory tract microbiome. Mainly transient microorganisms composed the lower respiratory tract microbiota, but some genera were identified as inhabiting the lung, indicating their potential role in lung physiology or disease. At 3-4 months of age, important dynamic changes to the microbial community were observed, which might correspond to a transitional time period in the maturation of the lung microbiome. This timeframe represents a susceptibility period for the colonization of pathogens such as Pneumocystis. The asymptomatic colonization of Pneumocystis was associated with changes in the fungal and bacterial communities. Conclusions. These findings suggest that the period of 2-4 months of age is a “critical window” early in life. Pneumocystis sp. could be a pivotal ecological driver contributing to shifts in microbial equilibrium during the early-life lower airway microbiome assembly, and to the future health of children.