Lower respiratory infections (LRIs) rank among the leading causes of mortality worldwide. Many microorganisms responsible for LRIs, such as Streptococcus pneumoniae and respiratory viruses, exhibit variable behavior: they can exist as asymptomatic colonizers, cause mild disease, or lead to severe invasive infections. Various factors influence the clinical manifestations and severity of LRIs. Emerging evidence suggests that the nasopharyngeal microbiota (NM) plays a crucial role in these processes. This study aims to identify microbiota profiles associated with respiratory health and disease.

A prospective case-control study was conducted between February 2021 and September 2022. NM samples were collected from adults with pneumococcal pneumonia (PPn), COVID-19 pneumonia (CPn), and healthy controls (HC). Samples were analyzed using 16S rRNA gene sequencing. Participants were matched for age and gender. Random Forest modeling was applied to microbiota data to distinguish pneumococcal pneumonia from viral community-acquired pneumonia (CAP).

A total of 129 samples were analyzed, including 38 from PPn cases, 54 from CPn cases, and 37 from HC. While age and sex distributions were similar across groups, comorbidities, immunosuppression, and prior infections were more common among cases. Alpha-diversity analysis revealed no significant differences in species richness or evenness across groups. However, beta-diversity analysis showed distinct microbial compositions: Corynebacterium was predominant in CPn patients, whereas Streptococcus was more abundant in PPn patients compared to HC.

The nasopharyngeal microbiota differs significantly in adults with pneumococcal pneumonia compared to those with COVID-19 pneumonia and healthy controls. These associations highlight the potential relevance of specific bacterial genera in disease susceptibility. A deeper understanding of healthy nasopharyngeal microbiota profiles could contribute to future strategies for the prevention and management of respiratory infections.