Alteration of bacterial community composition with respiratory infection and linkage of taxa with bacterial pathogens in Saudi Arabia from the Arabian Peninsula

Background: The microbiome of the respiratory system functions as a gatekeeper of respiratory health and is influenced by respiratory diseases. The aim of this study was to identify changes in the respiratory bacterial community composition associated with respiratory infections and to explore their relationship with specific bacterial pathogens in the Saudi Arabian population. Methods: Nasopharyngeal samples were screened from 73 individuals, including 34 symptomatic respiratory tract infection patients, 10 asymptomatic participants, and 29 healthy controls. Respiratory pathogens were detected using real-time PCR, and the microbiota were characterized through 16S rRNA gene amplicon sequencing. Results: Alpha diversity analysis revealed a slight decrease in bacterial richness in patients and asymptomatic individuals compared to healthy controls. In beta diversity analysis, healthy controls clustered together, while most symptomatic patients clustered separately. Actinobacteria, known for maintaining microbial homeostasis and preventing pathogenic colonization, were abundant in asymptomatic and healthy controls (> 30 %) but were substantially reduced to < 20 % relative abundance in symptomatic patients. Several bacterial genera, including Abiotrophia, Capnocytophaga, Megasphaera, Campylobacter, Peptostreptococcus, Veillonella, Streptococcus, and Bulleidia, were positively correlated with respiratory infections. Corynebacterium, Dolosigranulum, and Lawsonella were more abundantly found in healthy and asymptomatic individuals. Patients harboring Streptococcus pneumoniae or methicillin-resistant Staphylococcus aureus (MRSA) exhibited distinct bacterial profiles. Genera such as Staphylococcus, Pseudomonas, and Peptoniphilus were correlated with MRSA infection, while samples positive for S. pneumoniae exhibited a relatively higher abundance of Neisseria and Prevotella. Notably, a substantial number of symptomatic patients tested negative for any of the screened pathogens by real-time PCR but still showed alterations in bacterial community composition. Conclusions: Specific bacterial taxa showed significant differences between healthy controls and symptomatically infected patients, suggesting that bacterial community structures and groups of taxa, rather than individual bacterial taxa, may play a role in regulating respiratory infections.