Gut microbiota composition reflects disease severity and dysfunctional immune responses in patients with COVID-19

Abstract

Objective: Although COVID-19 is primarily a respiratory illness, there is mounting evidence suggesting that the GI tract is involved in this disease. We investigated whether the gut microbiome is linked to disease severity in patients with COVID-19, and whether perturbations in microbiome composition, if any, resolve with clearance of the SARS-CoV-2 virus.

Methods: In this two-hospital cohort study, we obtained blood, stool and patient records from 100 patients with laboratory-confirmed SARS-CoV-2 infection. Serial stool samples were collected from 27 of the 100 patients up to 30 days after clearance of SARS-CoV-2. Gut microbiome compositions were characterised by shotgun sequencing total DNA extracted from stools. Concentrations of inflammatory cytokines and blood markers were measured from plasma.

Results: Gut microbiome composition was significantly altered in patients with COVID-19 compared with non-COVID-19 individuals irrespective of whether patients had received medication (p<0.01). Several gut commensals with known immunomodulatory potential such as Faecalibacterium prausnitzii, Eubacterium rectale and bifidobacteria were underrepresented in patients and remained low in samples collected up to 30 days after disease resolution. Moreover, this perturbed composition exhibited stratification with disease severity concordant with elevated concentrations of inflammatory cytokines and blood markers such as C reactive protein, lactate dehydrogenase, aspartate aminotransferase and gamma-glutamyl transferase.

Conclusion: Associations between gut microbiota composition, levels of cytokines and inflammatory markers in patients with COVID-19 suggest that the gut microbiome is involved in the magnitude of COVID-19 severity possibly via modulating host immune responses. Furthermore, the gut microbiota dysbiosis after disease resolution could contribute to persistent symptoms, highlighting a need to understand how gut microorganisms are involved in inflammation and COVID-19.

Keywords: colonic bacteria; colonic microflora; inflammation.

Figure 1

Compositional differences in gut microbiota between patients with COVID-19 and non-COVID-19 subjects. (A) Average relative abundances of microbial phyla detected in stools from in-hospital patients with COVID-19, patients discharged after negative RT-qPCR for viral RNA in nasopharyngeal swabs, and non-COVID-19 individuals. (B) Principal component analysis of gut microbiota composition of patients with COVID-19 with and without antibiotics compared with non-COVID-19 subjects. Filled circles represent the first stool samples (if serial samples are available) of in-hospital patients whereas crosses represent non-COVID-19 subjects. Group centroids are indicated by the group labels.

Figure 2

Associations between gut microbiota composition of in-hospital patients with COVID-19 and plasma concentrations of inflammatory cytokines and blood inflammation markers. (A) Principal component analysis (PCA) of gut microbiota composition and association with plasma concentrations of cytokines/chemokines. (B) PCA of gut microbiota composition and association with blood inflammation markers. Statistical correlations were determined using Procrustes tests. Only cytokines and inflammation markers significantly correlated with gut microbiota composition are shown. Red arrows represent gradients of the corresponding cytokines/inflammation marker concentrations and point to the direction of greatest increase in these measures. Colour of the circles represents disease severity groups, and ellipses represent SD of the group centroid. Group centroids are indicated by the group labels. AST, aspartate aminotransferase; CRP, C-reactive protein; ESR, erythrocyte sedimentation rate; GGT, gamma-glutamyl transferase; LDH, lactate dehydrogenase; NT-proBNP, N-terminal-pro-brain natriuretic peptide; TNF, tumour necrosis factor.

Figure 3

Correlations between COVID-19 enriched/depleted gut microbial taxa and plasma concentrations of (A) CXCL10, (B) IL-10, (C) TNF-α, (D) CCL2, (E) CXCL8, (F) IL-1β and (G) IL-6. Only statistically significant correlations are shown. Linear regression lines are shown in each scatter plot in blue, and shaded regions represent 95% CIs. CCL, C-C motif ligand; CXCL, C-X-C motif ligand; TNF, tumour necrosis factor.

Figure 4

Principal component analysis of gut microbiota composition in recovered patients with COVID-19 who had or had not received antibiotics compared with non-COVID-19 subjects. Patients were considered recovered following negative quantitative reverse transcription PCR (RT-qPCR) tests for SARS-CoV-2 RNA in nasopharyngeal swabs. Filled circles represent all stools collected after discharge from hospital whereas crosses represent non-COVID-19 subjects.