Oral Microbiome Alterations and SARS-CoV-2 Saliva Viral Load in Patients with COVID-19

Miller, Emily Happy; Annavajhala, Medini K; Chong, Alexander M; Park, Heekuk; Nobel, Yael R; Soroush, Ali; Blackett, John W; Krigel, Anna; Phipps, Meaghan M; Freedberg, Daniel E; Zucker, Jason; Sano, Ellen D; Uhlemann, Anne-Catrin; Abrams, Julian A

Bacterial-viral interactions in saliva have been associated with morbidity and mortality for respiratory viruses such as influenza and SARS-CoV. However, such transkingdom relationships during SARS-CoV-2 infection are currently unknown. Here, we aimed to elucidate the relationship between saliva microbiota and SARS-CoV-2 in a cohort of newly hospitalized COVID-19 patients and controls. We used 16S rRNA sequencing to compare microbiome diversity and taxonomic composition between COVID-19 patients (n = 53) and controls (n = 59) and based on saliva SARS-CoV-2 viral load as measured using reverse transcription PCR (RT-PCR). The saliva microbiome did not differ markedly between COVID-19 patients and controls. However, we identified significant differential abundance of numerous taxa based on saliva SARS-CoV-2 viral load, including multiple species within Streptococcus and Prevotella. IMPORTANCE Alterations to the saliva microbiome based on SARS-CoV-2 viral load indicate potential biologically relevant bacterial-viral relationships which may affect clinical outcomes in COVID-19 disease.