The salivary and nasopharyngeal microbiomes are associated with SARS‐CoV‐2 infection and disease severity

• Published in: Journal of medical virology Vol. 95; no. 2; pp. e28445 - n/a
• Main Authors: Kim, Josh G., Zhang, Ai, Rauseo, Adriana M., Goss, Charles W., Mudd, Philip A., O'Halloran, Jane A., Wang, Leyao
• Format: Journal Article
• Language: English
• Published: United States Wiley Subscription Services, Inc 01.02.2023
• Subjects: 16S rRNA gene sequencing; Abundance; airway microbiome; Bifidobacterium; Biomarkers; Coronaviruses; COVID-19; Depletion; Diarrhea; Gene sequencing; Humans; Immune response; Infections; Interleukins; Lactobacillus; Microbiomes; Microbiota; Microorganisms; Monocyte chemoattractant protein; Monocytes; Nasopharynx; oral microbiome; Patient Acuity; Relative abundance; Respiratory diseases; rRNA 16S; Saliva; SARS-CoV-2; Severe acute respiratory syndrome; Severe acute respiratory syndrome coronavirus 2; Signs and symptoms; symptom severity; Viral diseases; Virology; COVID-19; oral microbiome; symptom severity; 16S rRNA gene sequencing; airway microbiome
• ISSN: 0146-6615; 1096-9071; 1096-9071
• DOI: 10.1002/jmv.28445

Emerging evidence suggests the oral and upper respiratory microbiota may play important roles in modulating host immune responses to viral infection. As the host microbiome may be involved in the pathophysiology of coronavirus disease 2019 (COVID‐19), we investigated associations between the oral and nasopharyngeal microbiome and COVID‐19 severity. We collected saliva (n = 78) and nasopharyngeal swab (n = 66) samples from a COVID‐19 cohort and characterized the microbiomes using 16S ribosomal RNA gene sequencing. We also examined associations between the salivary and nasopharyngeal microbiome and age, COVID‐19 symptoms, and blood cytokines. Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection status, but not COVID‐19 severity, was associated with community‐level differences in the oral and nasopharyngeal microbiomes. Salivary and nasopharyngeal microbiome alpha diversity negatively correlated with age and were associated with fever and diarrhea. Oral Bifidobacterium, Lactobacillus, and Solobacterium were depleted in patients with severe COVID‐19. Nasopharyngeal Paracoccus was depleted while nasopharyngeal Proteus, Cupravidus, and Lactobacillus were increased in patients with severe COVID‐19. Further analysis revealed that the abundance of oral Bifidobacterium was negatively associated with plasma concentrations of known COVID‐19 biomarkers interleukin 17F and monocyte chemoattractant protein‐1. Our results suggest COVID‐19 disease severity is associated with the relative abundance of certain bacterial taxa.