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Introduction: While bronchiolitis is regarded as a viral lower respiratory tract infection, there is some evidence for the perturbation of the airway microbiota in infants with bronchiolitis. Little is known about the lower airway microbiota in children with bronchiolitis due to difficulty obtaining samples. Aim: To describe the lower airway microbiota in comparison with upper airway microbiota in infants with severe bronchiolitis needing intubation and ventilation. Methods: Infants intubated with bronchiolitis in the paediatric intensive care unit were recruited and nasal swabs and non-bronchoscopic lavage were performed. Bacterial DNA was extracted and the V3-V4 region of the 16S rRNA gene was amplified and sequenced using Illumina MiSeq. The relative abundance of taxa and alpha diversity were calculated. Results: Ten infants (median age of 3 months) were sampled. Five children had RSV bronchiolitis and five had Rhinovirus bronchiolitis. Proteobacteria were the most abundant taxa in both upper and lower airway samples. In the lower airway samples, Haemophilus was the most abundant genus (mean relative abundance 67.7%), followed by Streptococcus (15.1%) and Moraxella (5.1%). This was very similar to the upper airway samples (mean relative abundance Haemophilus 42.2% followed by Streptococcus 18.1%, Prevotella 10.5% and Moraxella 6.7%). Conclusion: In infants with severe bronchiolitis, the lower and upper airway microbiota are largely similar in bacterial composition with dominance of Proteobacteria at the Phylum level and Haemophilus at the genus level.