More than 100 trillion microbes inhabit the human body (Ursell et al, 2012). This vast assemblage of organisms, which is termed the microbiome, form distinct microbial communities that are now known to have an important role in maintaining health and modulating states of disease (Wypch et al, 2019; Pattaroni et al, 2018; Budden et al, 2017). In a healthy state, humans are widely assumed to be born sterile (de Goffau at el, 2019). Microbial colonisation usually commences from birth (Wypch et al, 2019) and matures in parallel with the neonatal immune system and other organs (Wypch et al, 2019). Lung microbiome research is limited by the invasiveness of lung sampling and reliance on sequence-analysis approaches. Consequently, the majority of lung bacteria remain uncultured, despite evidence they play an essential role in human health and disease (Lloyd-Price et al, 2017).
We aim to culture individual bacterial isolates from the nasopharynx and lung of neonates, infants and children and compare bacterial load and diversity between these anatomical sites. Non-bronchoscopic bronchoalveolar lavages and nasopharyngeal swabs were obtained from seven intubated neonates at Monash Children’s Hospital. Patients without a primary lung disease were included as controls (n=1). Samples were pooled in pairs for processing and respiratory bacteria was cultured on seven different media types. Thereafter, samples were sent for metagenomic sequencing to evaluate community diversity and relative species abundance. 990 isolates representing 21 distinct bacterial species were cultured. 16S rRNA gene sequencing revealed these 21 species grew on brain-infused heart, anaerobic, chocolate and Wilkin’s Chalgren media only. The ability to now culture distinct respiratory bacteria has provided an initial insight into bacterial load and diversity, thereby enabling functional validation of the respiratory bacteria to reveal their importance in health/disease.