Longitudinal Weekly Surveillance of Respiratory Viruses and the Nasal Microbiome in Children Under Five (MINNE-LOVE Study)

Early childhood is a critical period for both nasal microbiome development and susceptibility to respiratory viral infections. While prior cross-sectional and limited longitudinal studies suggest that the nasal microbiome is shaped by both host and environmental factors, high-frequency longitudinal data linking microbial dynamics and respiratory viral disease in young children remain sparse. MethodsWe conducted the MINNE-LOVE prospective longitudinal cohort study of children under 5 years of age with weekly symptom surveillance and parent-collected anterior nasal swabs. Total nucleic acid was extracted and analyzed for nasal microbiome composition by 16S rRNA sequencing on short- and long-read platforms and viral pathogen detection by target-enriched metagenomic sequencing. Microbiome diversity, community structure, viral detection patterns, and correlations among dominant bacterial taxa were assessed over time. ResultsWithin individuals, microbiome composition was relatively stable over time, with acute shifts observed. We detected a broad array of respiratory viruses, including frequent viral co-detections and prolonged detection of select viruses across multiple weeks. ConclusionIn this longitudinal cohort of young children undergoing high-frequency sampling, we demonstrated the feasibility of multiomic assessment of nasal microbial communities. Key bacterial ecological relationships described in prior cross-sectional studies were recapitulated using dense temporal sampling. Target-enriched sequencing enhanced the range of viral pathogen detection, including co-infections and prolonged viral shedding. Full-length 16S long-read sequencing enabled clinically relevant species-level resolution not achievable with short-read approaches. These findings highlight the value of intensive longitudinal cohort designs for defining host-virus-microbiome interactions in early childhood and informing future mechanistic and interventional studies. Key pointsWe conducted weekly symptom assessment, nasal microbiome profiling, and respiratory virus detection by target-enrichment metagenomics in four Minnesota preschool children. We demonstrated high symptom and viral burden, intraindividual microbiome stability, and improved taxonomic resolution with long-read 16S gene sequencing.