Metagenomic assessment of gut microbial communities and risk of severe COVID-19

Abstract

The gut microbiome is a critical modulator of host immunity and is linked to the immune response to respiratory viral infections. However, few studies have gone beyond describing broad compositional alterations in severe COVID-19, defined as acute respiratory or other organ failure. We profiled 127 hospitalized patients with COVID-19 (n=79 with severe COVID-19 and 48 with moderate) who collectively provided 241 stool samples from April 2020 to May 2021 to identify links between COVID-19 severity and gut microbial taxa, their biochemical pathways, and stool metabolites. 48 species were associated with severe disease after accounting for antibiotic use, age, sex, and various comorbidities. These included significant in-hospital depletions of Fusicatenibacter saccharivorans and Roseburia hominis, each previously linked to post-acute COVID syndrome or “long COVID”, suggesting these microbes may serve as early biomarkers for the eventual development of long COVID. A random forest classifier achieved excellent performance when tasked with predicting whether stool was obtained from patients with severe vs. moderate COVID-19. Dedicated network analyses demonstrated fragile microbial ecology in severe disease, characterized by fracturing of clusters and reduced negative selection. We also observed shifts in predicted stool metabolite pools, implicating perturbed bile acid metabolism in severe disease. Here, we show that the gut microbiome differentiates individuals with a more severe disease course after infection with COVID-19 and offer several tractable and biologically plausible mechanisms through which gut microbial communities may influence COVID-19 disease course. Further studies are needed to validate these observations to better leverage the gut microbiome as a potential biomarker for disease severity and as a target for therapeutic intervention.

Gut microbial profiling of COVID-19 patients in Uganda

“…Distinct microbial signatures were identified, with the prevalence of specific OTUs in COVID-19 patients and a particular abundance of Prevotella in severe cases. This was similar to findings from a recent study [30] which highlighted a protective role of the Prevotella genus in the long-term recovery process while other investigations [31,32] reported varied results. The variation could be attributed to various factors like sample collection methods, patient demographics, or even geographic variations in microbial populations.…”

SARS-CoV-2 infection elucidates unique features of pregnancy-specific immunity

“…Growing evidence suggests that gut microbiota composition dictates the duration and magnitude of host immune responses upon respiratory infection 83 . Additionally, recent data indicate that SARS-CoV-2 infection induces changes in the gut microbiota 84 and these changes may affect the disease course 85 . We performed shotgun metagenomic sequencing analyses with pregnant women’s stool samples [Pregnant controls (n = 29), Pregnant COVID-19 (n = 27) (13 mild, 6 moderate, 8 severe/critical), Non-pregnant COVID-19 (n = 13)] collected from SARS-CoV-2 negative and SARS-CoV-2-infected groups.…”