Nasopharyngeal Microbiome Profiles of SARS-CoV-2 RT-PCR Positive and Negative Outpatients in Guayaquil, Ecuador

The nasopharyngeal microbiome contributes to respiratory health and may influence host responses to respiratory viral infections, including SARS-CoV-2, yet its association with viral detection remains incompletely understood, particularly in outpatients from Latin America. In this cross-sectional study, adult outpatients undergoing SARS-CoV-2 RT-PCR testing in Guayaquil, Ecuador, were consecutively recruited between 2 and 7 June 2021, and their nasopharyngeal microbiome was characterized using 16S rRNA gene (V3–V4) sequencing. Microbiome diversity, taxonomic composition, differential abundance, and predicted functional profiles were compared between RT-PCR positive (n = 41) and RT-PCR negative (n = 17) individuals. Compositional analyses used 57 samples after taxon filtering (41 RT-PCR positive and 16 RT-PCR negative). No differences by RT-PCR status were detected in alpha or beta diversity, and no taxa or predicted pathways were differentially abundant; alpha- and beta-diversity results were unchanged after accounting for collection date. Both groups displayed similar microbial communities dominated by Corynebacterium sp. and Staphylococcus sp., which together with Cutibacterium sp. formed the core microbiome. These findings indicate that SARS-CoV-2 detection was not associated with major alterations in the taxonomic composition or predicted functional profiles of the nasopharyngeal microbiome in this outpatient Ecuadorian cohort, although smaller effects cannot be excluded given the size of the RT-PCR negative group.