Signatures of COVID-19 Severity and Immune Response in the Respiratory Tract Microbiome
Carter Merenstein, Guanxiang Liang, Samantha A. Whiteside, Ana G. Cobián-Güemes, Madeline S. Merlino, Louis J. Taylor, Abigail Glascock, Kyle Bittinger, Ceylan Tanes, Jevon Graham-Wooten, Layla A. Khatib, Ayannah S. Fitzgerald, Shantan Reddy, Amy E. Baxter, Josephine R. Giles, Derek A. Oldridge, Nuala J. Meyer, E. John Wherry, John E. McGinniss, Frederic D. Bushman, Ronald G. Collman
Abstract
COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection of the respiratory tract, results in highly variable outcomes ranging from minimal illness to death, but the reasons for this are not well understood. We investigated the respiratory tract bacterial microbiome and small commensal DNA viruses in hospitalized COVID-19 patients and found that each was markedly abnormal compared to that in healthy people and differed from that in critically ill patients without COVID-19. Early airway samples tracked with the level of COVID-19 illness reached during hospitalization, and the airway microbiome also correlated with immune parameters in blood. These findings raise questions about the mechanisms linking SARS-CoV-2 infection and other microbial inhabitants of the airway, including whether the microbiome might regulate severity of COVID-19 disease and/or whether early microbiome features might serve as biomarkers to discriminate disease severity.