Tracking upper respiratory microbiome dynamics in patients admitted to intensive care unit: insights from a pilot study

Patients in intensive care units (ICUs) are highly susceptible to nosocomial infections, yet data on respiratory microbiome dynamics in non-ventilated patients with respiratory failure remain limited. In this pilot study, upper respiratory tract (URT) microbiota in 21 ICU patients was examined at three stages: prior to antibiotic-initiation, early-treatment, and late-treatment. Oropharyngeal swabs underwent 16 S rRNA amplicon sequencing followed by taxonomic, functional prediction, and network analyses. Microbial diversity declined progressively following ICU admission through the course of ICU treatment, including antibiotic therapy, accompanied by depletion of commensal genera such as Neisseria , Haemophilus , and Rothia , alongside enrichment of opportunistic pathogens, including Acinetobacter , Klebsiella and Staphylococcus . Predicted functional profiling indicated stress-associated functional changes and enrichment of resistance-associated pathways, while network analysis suggested ecological destabilization and increasing pathogen centrality over time. These findings demonstrate rapid URT dysbiosis during ICU hospitalization and highlight the value of longitudinal, non-invasive microbiome profiling for monitoring pathogen-associated dysbiosis in critically ill patients, with potential relevance to future infection-risk assessment.