A systematic review of gut microbiota profile in COVID-19 patients and among those who have recovered from COVID-19

Daniel Martin Simadibrata, Elvira Lesmana, Jeffri Gunawan, Eamonn Martin Quigley, Marcellus Simadibrata

Research output: Contribution to journalReview articlepeer-review

1 Scopus citations


Objectives: Given the scale and persistence of coronavirus disease 2019 (COVID-19), significant attention has been devoted to understanding the relationship between human gut microbiota and COVID-19. In this systematic review we aimed to comprehensively assess the gut microbiota composition in patients infected with COVID-19 and those recovered from COVID-19 in comparison to healthy controls (HCs). Methods: Peer-reviewed articles and preprints published up to September 1, 2022, were searched in Ovid MEDLINE, Ovid EMBASE, and SCOPUS. Observational studies reporting the gut microbiota profile in adult (≥18 years) COVID-19 patients or those recovered from COVID-19 compared to HCs were eligible for inclusion in this systematic review. The quality assessment of studies was performed using the Newcastle-Ottawa scale. Results: We identified 27 studies comprising 18 studies that compared COVID-19 patients and six that compared recovered COVID-19 patients to HCs, while the other three studies compared both COVID-19 and recovered COVID-19 patients to HCs. Compared to HCs, decreased gut microbial diversity and richness and a distinctive microbial composition were reported in COVID-19 patients and recovered COVID-19 patients. In COVID-19 patients, Bacteroidetes were found to be enriched, and Firmicutes depleted. Decreased short-chain fatty acid (SCFA)-producing bacteria, such as Faecalibacterium, Ruminococcus, and Bifidobacterium, among others, were also observed in COVID-19 patients, which were not restored to normal levels in those who recovered. Conclusion: Gut dysbiosis was evident in COVID-19, and available data suggested that dysbiosis persisted even in recovered COVID-19 patients, with decreased Firmicutes and SCFA-producing bacteria.

Original languageEnglish (US)
Pages (from-to)244-261
Number of pages18
JournalJournal of Digestive Diseases
Issue number4
StatePublished - Apr 2023


  • COVID-19
  • dysbiosis
  • gastrointestinal microbiome
  • post-acute COVID-19 syndrome
  • systematic review
  • Bifidobacterium
  • Humans
  • Gastrointestinal Microbiome
  • Dysbiosis/complications
  • Fatty Acids, Volatile
  • Feces/microbiology
  • Adult
  • Bacteria

ASJC Scopus subject areas

  • Gastroenterology


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