A Pro-Inflammatory Gut Microbiome Characterizes SARS-CoV-2 Infected Patients and a Reduction in the Connectivity of an Anti-Inflammatory Bacterial Network Associates With Severe COVID-19

Abstract

The gut microbiota contributes to maintaining human health and regulating immune responses. Severe COVID-19 illness is associated with a dysregulated pro-inflammatory immune response. The effect of SARS-CoV-2 on altering the gut microbiome and the relevance of the gut microbiome on COVID-19 severity needs to be clarified. In this prospective study, we analyzed the gut microbiome of 212 patients of a tertiary care hospital (117 patients infected with SARS-CoV-2 and 95 SARS-CoV-2 negative patients) using 16S rRNA gene sequencing of the V3-V4 region. Inflammatory markers and immune cells were quantified from blood. The gut microbiome in SARS-CoV-2 infected patients was characterized by a lower bacterial richness and distinct differences in the gut microbiome composition, including an enrichment of the phyla Proteobacteria and Bacteroidetes and a decrease of Actinobacteria compared to SARS-CoV-2 negative patients. The relative abundance of several genera including Bifidobacterium, Streptococcus and Collinsella was lower in SARS-CoV-2 positive patients while the abundance of Bacteroides and Enterobacteriaceae was increased. Higher pro-inflammatory blood markers and a lower CD8⁺ T cell number characterized patients with severe COVID-19 illness. The gut microbiome of patients with severe/critical COVID-19 exhibited a lower abundance of butyrate-producing genera Faecalibacterium and Roseburia and a reduction in the connectivity of a distinct network of anti-inflammatory genera that was observed in patients with mild COVID-19 illness and in SARS-CoV-2 negative patients. Dysbiosis of the gut microbiome associated with a pro-inflammatory signature may contribute to the hyperinflammatory immune response characterizing severe COVID-19 illness.

Keywords: COVID-19; SARS-CoV-2; intestinal microbiota; microbiome; severity.

Figure 1

SARS-CoV-2 infected patients exhibit distinct differences in the gut microbiome (A) Bacterial richness in SARS-CoV-2 positive and negative patients determined by observed features (amplicon sequence variants [ASV]). Kruskal-Wallis test was used to test for significant differences among groups. * FDR-P < .05; ** FDR-P < .01¸*** FDR-P < .001 (B) Principal Coordinates Analysis (PCoA) of SARS-CoV-2 positive performed with of Binary Jaccard distance matrix. PERMANOVA multivariate analysis was used to test for significant differences. (C) Differences in the relative abundance of bacterial phyla linked to SARS-CoV-2 infection. (D) Illustration of the differences in the relative abundance of bacterial genera linked to SARS-CoV-2 infection. (E) Linear discriminant effect size (LEfSe) analysis identified several bacterial taxa enriched in SARS-CoV-2 positive (green) and SARS-CoV-2 negative patients (red) (F) Cladogram reports the taxa showing different abundance values (LDA>3.5) according to LEfSe. Colors are presented in the color of the most abundant group (SARS-CoV-2 positive in green, SARS-CoV-2 negative in red).

Figure 2

(A) Serum levels of pro-inflammatory markers interleukin 6 (IL-6), C-reactive protein (CRP) and soluble IL-2 receptor (sIL2R) and (B) total number of CD3⁺ T cells, CD8⁺ T cells and CD4⁺ T cells in COVID-19 patients according to disease severity. *P <.05; **P < .01¸***P < .001 (C) Relative abundance of bacterial genera Faecalibacterium and Roseburia in patients with non-severe and severe/critical COVID-19 according to the WHO classification. *P < .05 (D) Gut microbiota co-occurrence networks are visualized for SARS-CoV-2 negative patients, patients with mild, moderate and severe COVID-19 severity illness. Nodes represent bacterial genera. The size of each node indicates the average relative abundance of the genus in the corresponding group and each node is colored based on the degree of the node (number of edges). Labels are scaled with the size of the nodes. The intensity of the red color of the nodes increases according to the number of the genera’s edges. Genera without a significant co-occurrence are colored in gray in the group that lacks a co-occurrence partner. The width of the edges are weighted based on the absolute value of the co-occurrences and colored red for positive and blue for negative correlations.

Figure 3

Schematic summary of differences of the gut microbiome linked to SARS-CoV-2 infection and COVID-19 severity illness.