Improved gut microbiota features after the resolution of SARS‑CoV‑2 infection

Flavio De Maio, Gianluca Ianiro, Gaetano Coppola, Francesco Santopaolo, Valeria Abbate, Delia Mercedes Bianco, Fabio Del Zompo, Giuseppe De Matteis, Massimo Leo, Antonio Nesci, Alberto Nicoletti, Maurizio Pompili, Giovanni Cammarota, Brunella Posteraro, Maurizio Sanguinetti, Antonio Gasbarrini, Francesca Romana Ponziani

Research output: Contribution to journalLetterpeer-review


Background: The severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) has a tropism for the gastrointestinal tract and several studies have shown an alteration of the gut microbiota in hospitalized infected patients. However, long-term data on microbiota changes after recovery are lacking. Methods: We enrolled 30 patients hospitalized for SARS‑CoV‑2-related pneumonia. Their gut microbiota was analyzed within 48 h from the admission and compared with (1) that of other patients admitted for suspected bacterial pneumonia (control group) (2) that obtained from the same subject 6 months after nasopharyngeal swab negativization. Results: Gut microbiota alpha-diversity increased 6 months after the resolution of SARS-CoV-2 infection. Bacteroidetes relative abundance was higher (≈ 36.8%) in patients with SARS-CoV-2, and declined to 18.7% when SARS-CoV-2 infection resolved (p = 0.004). Conversely, Firmicutes were prevalent (≈ 75%) in controls and in samples collected after SARS-CoV-2 infection resolution (p = 0.001). Ruminococcaceae, Lachnospiraceae and Blautia increased after SARS-CoV-2 infection resolution, rebalancing the gut microbiota composition. Conclusion: SARS-CoV-2 infection is associated with changes in the gut microbiome, which tend to be reversed in long-term period.

Original languageEnglish
Article number62
JournalGut Pathogens
Issue number1
Publication statusPublished - Dec 2021


  • COVID-19
  • Gut microbiota
  • Pneumonia
  • SARS-CoV-2

ASJC Scopus subject areas

  • Parasitology
  • Microbiology
  • Gastroenterology
  • Virology
  • Infectious Diseases


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