Progressive worsening of the respiratory and gut microbiome in children during the first two months of COVID-19

Abstract Background Children are less susceptible to COVID-19 and manifests lower morbidity and mortality after infection, for which a multitude of mechanisms may be proposed. Whether the normal development of gut-airway microbiome is affected by COVID-19 has not been evaluated. Results We demonstrate that COVID-19 alters the respiratory and gut microbiome of children. Alteration of the microbiome was divergent between the respiratory tract and gut, albeit the dysbiosis was dominated by genus Pseudomonas and sustained for up to 25–58 days in different individuals. The respiratory microbiome distortion persisted in 7/8 children for at least 19–24 days after discharge from the hospital. The gut microbiota showed early dysbiosis towards later restoration in some children, but not others. Conclusions Disturbed development of both gut and respiratory microbiomes, and prolonged respiratory dysbiosis in children imply possible long-term complications after clinical recovery from COVID-19, such as predisposition to an increased health risk in the post-COVID-19 era.