Oral microbiome alterations and sars-cov-2 saliva viral load in patients with covid-19

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

Research output: Contribution to journalArticlepeer-review

30 Scopus citations


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 SARSCoV- 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 SARSCoV- 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.

Original languageEnglish
Article numbere00055-21
JournalMicrobiology spectrum
Issue number2
StatePublished - Oct 2021
Externally publishedYes


  • COVID-19
  • Saliva microbiome
  • SARS-CoV-2
  • Viral load


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