The Nasopharyngeal and Gut Microbiota in Children in a Pediatric Otolaryngology Practice

Background: The human microbiome evolves rapidly in early life with contributions from various factors such as diet, delivery mode, medical history, antibiotics exposure, genetics, immunomodulators and the environment. A high use of antibiotics in pediatric outpatient settings has been well documented, and improvement in antibiotic selection is required to reduce the risks of antibiotic resistance and disruption of the microbiome. Methods: We performed an exploratory study using 16S rRNA gene-based sequencing to characterize the gut and nasopharyngeal microbiome of children (n = 50) age 1-6 years of age in a pediatric otolaryngology practice. Results: Relative abundance ofHaemophilusandMoraxellawere higher in nasopharyngeal swabs, whilePrevotella, Bacteroides, PorphyromonasandFaecalibacteriumwere highly abundant in rectal swabs. The gut microbiome composition in children BacteroidesandAkkermansia. The nasopharyngeal microbiome differed between children who received antibiotics in the 3 months before sample collection compared with those that did not.Haemophilusspp. was highly abundant in children who received antibiotics 3 months before sampling. Conclusions: The pediatric nasopharyngeal and rectal microbiomes differ in bacterial composition and diversity. The increased abundance ofHaemophilusspp. in the nasopharyngeal microbiome of children who received antibiotics during the 3 months before sampling suggests a potential impact of antibiotics in colonization with the otopathogen and may be relevant to clinical practice.