Metabolomic and gut microbiome profiles across the spectrum of community-based COVID and non-COVID disease

Marc F. Österdahl*, Ronan Whiston, Carole H. Sudre, Francesco Asnicar, Nathan J. Cheetham, Aitor Blanco Miguez, Vicky Bowyer, Michela Antonelli, Olivia Snell, Liane dos Santos Canas, Christina Hu, Jonathan Wolf, Cristina Menni, Michael Malim, Deborah Hart, Tim Spector, Sarah Berry, Nicola Segata, Katie Doores, Sebastien OurselinEmma L. Duncan, Claire J. Steves

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


Whilst most individuals with SARS-CoV-2 infection have relatively mild disease, managed in the community, it was noted early in the pandemic that individuals with cardiovascular risk factors were more likely to experience severe acute disease, requiring hospitalisation. As the pandemic has progressed, increasing concern has also developed over long symptom duration in many individuals after SARS-CoV-2 infection, including among the majority who are managed acutely in the community. Risk factors for long symptom duration, including biological variables, are still poorly defined. Here, we examine post-illness metabolomic profiles, using nuclear magnetic resonance (Nightingale Health Oyj), and gut-microbiome profiles, using shotgun metagenomic sequencing (Illumina Inc), in 2561 community-dwelling participants with SARS-CoV-2. Illness duration ranged from asymptomatic (n = 307) to Post-COVID Syndrome (n = 180), and included participants with prolonged non-COVID-19 illnesses (n = 287). We also assess a pre-established metabolomic biomarker score, previously associated with hospitalisation for both acute pneumonia and severe acute COVID-19 illness, for its association with illness duration. We found an atherogenic-dyslipidaemic metabolic profile, including biomarkers such as fatty acids and cholesterol, was associated with longer duration of illness, both in individuals with and without SARS-CoV-2 infection. Greater values of a pre-existing metabolomic biomarker score also associated with longer duration of illness, regardless of SARS-CoV-2 infection. We found no association between illness duration and gut microbiome profiles in convalescence. This highlights the potential role of cardiometabolic dysfunction in relation to the experience of long duration symptoms after symptoms of acute infection, both COVID-19 as well as other illnesses.

Original languageEnglish
Article number10407
JournalScientific Reports
Issue number1
Early online date27 Jun 2023
Publication statusPublished - 27 Jun 2023


  • Humans
  • COVID-19
  • SARS-CoV-2
  • Gastrointestinal Microbiome
  • Pneumonia
  • Hospitalization


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