Gut Microbiota Diversity and C-Reactive Protein Are Predictors of Disease Severity in COVID-19 Patients

Abstract

The risk factors for coronavirus disease 2019 (COVID-19) severity are still poorly understood. Considering the pivotal role of the gut microbiota on host immune and inflammatory functions, we investigated the association between changes in the gut microbiota composition and the clinical severity of COVID-19. We conducted a multicenter cross-sectional study prospectively enrolling 115 COVID-19 patients categorized according to: (1) the WHO Clinical Progression Scale-mild, 19 (16.5%); moderate, 37 (32.2%); or severe, 59 (51.3%), and (2) the location of recovery from COVID-19-ambulatory, 14 (household isolation, 12.2%); hospitalized in ward, 40 (34.8%); or hospitalized in the intensive care unit, 61 (53.0%). Gut microbiota analysis was performed through 16S rRNA gene sequencing, and the data obtained were further related to the clinical parameters of COVID-19 patients. The risk factors for COVID-19 severity were identified by univariate and multivariable logistic regression models. In comparison to mild COVID-19 patients, the gut microbiota of moderate and severe patients have: (a) lower Firmicutes/Bacteroidetes ratio; (b) higher abundance of Proteobacteria; and (c) lower abundance of beneficial butyrate-producing bacteria such as the genera Roseburia and Lachnospira. Multivariable regression analysis showed that the Shannon diversity index [odds ratio (OR) = 2.85, 95% CI = 1.09-7.41, p = 0.032) and C-reactive protein (OR = 3.45, 95% CI = 1.33-8.91, p = 0.011) are risk factors for severe COVID-19 (a score of 6 or higher in the WHO Clinical Progression Scale). In conclusion, our results demonstrated that hospitalized patients with moderate and severe COVID-19 have microbial signatures of gut dysbiosis; for the first time, the gut microbiota diversity is pointed out as a prognostic biomarker of COVID-19 severity.

Keywords: COVID-19; Shannon—Weiner diversity index; WHO Clinical Progression Scale; dysbiosis; gut microbiota.

FIGURE 1

Comparison of coronavirus disease 2019 (COVID-19) gut microbiome with COVID-19 severity. Disease severity was determined according to the WHO Clinical Progression Scale: mild, moderate, and severe. (A) Heat tree visualization of the taxonomic differences between the COVID-19 severity groups based on the Log2 ratio median abundance (proportions), in which the terminal nodes correspond to bacterial genera. The identification of the nodes is shown in the bottom left image. Three comparisons were done: severe (blue green) vs. mild (orange); severe (blue green) vs. moderate (orange); and, ultimately, moderate (blue green) vs. mild (orange). The dominant color corresponds to a higher number of operational taxonomic units (OTUs). The Log2 ratio is 0 (gray) when the compared groups are similar. (B) The Shannon diversity index (mean + SEM) of the COVID-19 patients according to the WHO Clinical Progression Scale, from score 1 (asymptomatic, viral RNA detected) to score 9 (mechanical ventilation pO₂/FiO₂ < 150 and vasopressors, dialysis, or ECMO).

FIGURE 2

Fecal microbiota composition of coronavirus disease 2019 (COVID-19) patients according to patient location of recovery: ambulatory, hospitalized in ward, or hospitalized in ICU. (A) Fecal microbiota community alterations according to patient location in the NMDS2 (non-metric multidimensional scaling) plot based on the Bray–Curtis dissimilarity. (B) Main bacterial phyla in the fecal samples of COVID-19 patients according to patient location. (C) Box plot of the alpha diversity (measured by the Shannon diversity index) of the COVID-19 patients according to patient location.

FIGURE 3

Fecal microbiota composition of the coronavirus disease 2019 (COVID-19) patients according to the presence of SARS-CoV-2 in fecal samples. (A) Main bacterial phyla and (B) box plot of the alpha diversity (measured by the Shannon diversity index) of COVID-19 patients according to the presence of SARS-CoV-2 in fecal samples.

FIGURE 4

Schematic representation of the predictive microbial fingerprint for coronavirus disease 2019 (COVID-19) severity. Preexistent influences on the microbiota, such as lifestyle and environmental factors, and antibiotics can induce dysbiosis (red arrow), leading to increased inflammation (e.g., CRP levels). Hence, lower overall microbial diversity and abundance of beneficial commensal microorganisms (e.g., Roseburia), along with an increased abundance of Proteobacteria, are associated with high COVID-19 severity (a score of ≥ 6 in the WHO Clinical Progression Scale). CRP, C-reactive protein.