The Gut Microbiota of Critically Ill Patients With COVID-19

Abstract

The SARS-CoV-2-associated COVID-19 pandemic has shaken the global healthcare system. Although the best-known symptoms are dry cough and pneumonia, viral RNA has been detected in the stool and about half of COVID-19 patients exhibit gastrointestinal upset. In this scenario, special attention is being paid to the possible role of the gut microbiota (GM). Fecal samples from 69 COVID-19 patients from three different hospitals of Bologna (Italy) were analyzed by 16S rRNA gene-based sequencing. The GM profile was compared with the publicly available one of healthy age- and gender-matched Italians, as well as with that of other critically ill non-COVID-19 patients. The GM of COVID-19 patients appeared severely dysbiotic, with reduced diversity, loss of health-associated microorganisms and enrichment of potential pathogens, particularly Enterococcus. This genus was far overrepresented in patients developing bloodstream infections (BSI) and admitted to the intensive care unit, while almost absent in other critically ill non-COVID-19 patients. Interestingly, the percentage of patients with BSI due to Enterococcus spp. was significantly higher during the COVID-19 pandemic than in the previous 3 years. Monitoring the GM of critically ill COVID-19 patients could help clinical management, by predicting the onset of medical complications such as difficult-to-treat secondary infections.

Dissecting the Role of the Human Microbiome in COVID-19 via Metagenome-assembled Genomes

“…We identified multiple species with highly similar genomes from those permissive nrMAGs ( Fig.5b ), including Enterocloster bolteae (3 nrMAGs), Anaeroglobus micronuciformis, Hungatella effluvii (3 nrMAGs), and Enterococcus B faecium . Consistent with previous reports that the gut microbiome of COVID-19 patients showed significant higher abundance of Enterococcus faecium compared to health controls 46 . Among the 63 protective nrMAGs, the dominant species were Blautia A obeum (13 nrMAGs), Bariatricus comes (9 nrMAGs), Faecalibacterium prausnitzii D (6 nrMAGs), Blautia A wexlerae (6 nrMAGs), Faecalibacterium sp900539945 (4 nrMAGs), Dorea longicatena B (3 nrMAGs), Blautia A sp003480185 (3 nrMAGs), Blautia A sp003471165 (3 nrMAGs), Dorea formicigenerans (2 nrMAGs), Fusicatenibacter saccharivorans (2 nrMAGs), and GCA-900066135 sp900543575 (2 nrMAGs).…”

Diagnostic, Prognostic, and Therapeutic Roles of Gut Microbiota in COVID-19: A Comprehensive Systematic Review

“…We found that the dysbiosis of gut microbiota may be a determinant factor in the clinical severity of COVID-19. Increase of the dominant Enterococcus and reduction of Ruminococcaceae and Lachnospiraceae are reported in severe cases of COVID-19 who were admitted to the medical intensive unit (MICU) (Gaibani et al, 2021).…”

“…Lachnospiraceae, which is known as SCFA-producing bacteria, decreases in patients with COVID-19 (d'Ettorre et al, 2020;Gu et al, 2020b;Zuo et al, 2020a;Cao et al, 2021;Gaibani et al, 2021;Gautier et al, 2021;Zuo et al, 2021a). It may be attributed common use of azithromycin and other antibiotics in the management of COVID-19 (Segal et al, 2020).…”

Inflammatory Bowel Disease and COVID-19: How Microbiomics and Metabolomics Depict Two Sides of the Same Coin

“…When compared with non-infected individuals, gut dysbiosis in patients with COVID-19 is marked by the depletion of C. leptum (cluster IV) group, F. prausnitzii , and E. rectale species, Ruminococcaceae , and Lachnospiraceae families, in conjunction with the overgrowth of Enterococcus genus, Veillonellaceae , and Enterobacteriaceae families ( Tang et al, 2020 ; Tao et al, 2020 ; Zuo et al, 2020 , 2021 ; Gaibani et al, 2021 ; He et al, 2021 ; Wu et al, 2021 ; Yeoh et al, 2021 ). The abundance of Coprobacillus , C. ramosum , C. hathewayi ( Zuo et al, 2020 ), and Enterococcus ( Gaibani et al, 2021 ) was found positively correlated with COVID-19 severity; conversely, an inverse correlation was observed between the disease severity and the abundance of C. leptum (cluster IV) group, Lactobacillus , Bifidobacterium , C. butyricum ( Tang et al, 2020 ), Bilophila , Citrobacter ( Tao et al, 2020 ), Bacteroides ( Gaibani et al, 2021 ), F. prausnitzii , E. rectale ( Tang et al, 2020 ; Yeoh et al, 2021 ), B. bifidum , and B. adolescentis ( Yeoh et al, 2021 ). In addition, the abundance of some microbial taxa, including Erysipelotrichaceae bacterium 2_2_44A ( Zuo et al, 2020 ), P. copri , E. dolichum ( Wu et al, 2021 ), C. aerofaciens , C. tanakaei , S. infantis ( Zuo et al, 2021 ) positively correlates with the fecal SARS-CoV-2 load.…”