Alterations of the fecal microbiota in relation to acute COVID-19 infection and recovery

Abstract

People with acute COVID-19 due to SARS-CoV-2 infection experience a range of symptoms, but major factors contributing to severe clinical outcomes remain to be understood. Emerging evidence suggests associations between the gut microbiome and the severity and progression of COVID-19. To better understand the host-microbiota interactions in acute COVID-19, we characterized the intestinal microbiome of patients with active SARS-CoV-2 infection in comparison to recovered patients and uninfected healthy controls. We performed 16S rRNA sequencing of stool samples collected between May 2020 and January 2021 from 20 COVID-19-positive patients, 20 COVID-19-recovered subjects and 20 healthy controls. COVID-19-positive patients had altered microbiome community characteristics compared to the recovered and control subjects, as assessed by both α- and β-diversity differences. In COVID-19-positive patients, we observed depletion of Bacteroidaceae, Ruminococcaceae, and Lachnospiraceae, as well as decreased relative abundances of the genera Faecalibacterium, Adlercreutzia, and the Eubacterium brachy group. The enrichment of Prevotellaceae with COVID-19 infection continued after viral clearance; antibiotic use induced further gut microbiota perturbations in COVID-19-positive patients. In conclusion, we present evidence that acute COVID-19 induces gut microbiota dysbiosis with depletion of particular populations of commensal bacteria, a phenomenon heightened by antibiotic exposure, but the general effects do not persist post-recovery.

Metformin Therapy Changes Gut Microbiota Alpha-Diversity in COVID-19 Patients with Type 2 Diabetes: The Role of SARS-CoV-2 Variants and Antibiotic Treatment

“…Therefore, the observed differences in alpha-diversity between the two groups of patients may have important clinical implications. Our findings are consistent with those reported by other researchers who have investigated the impact of antibiotics on gut microbiota diversity in various patient populations, including COVID-19 patients [14][15][16][17][18].…”

High Incidence of Candidemia in Critically Ill COVID-19 Patients Supported by Veno-Venous Extracorporeal Membrane Oxygenation: A Retrospective Study

“…Moreover, an overall gastrointestinal dysbiosis was reported as largely affecting SARSCoV2 infected patients and possibly related with the severity of the related disease [ 29 ]. In particular, SARSCoV2 infection induces gut microbiota dysbiosis with depletion of specific populations of commensal bacteria such as Bacteroidaceae, Lachnospiraceae and Ruminococcaceae [ 30 , 31 ]. Interestingly, gut dysbiosis was found to be associated with significant alterations in fecal mycobiomes of SARSCoV2 infected subjects.…”

Mechanisms of gastrointestinal barrier dysfunction in COVID-19 patients

“…A study by Sun et al [ 38 ] using metagenomic and metaproteomic methods showed significant changes in the composition of the gut microbiome in COVID-19 patients, characterized by a decrease in commensal species and an increase in opportunistic pathogenic species. Moreover, other studies have shown that the microbiota of COVID-19 patients is enriched with opportunistic pathogens, compared with healthy individuals[ 64 , 67 - 69 ]. Furthermore, the plasma concentration of the gut permeability marker FABP2 and gut microbial antigens PGN and LPS were significantly elevated in COVID-19 patients in comparison to healthy controls[ 70 ].…”