16S rRNA gene sequencing of rectal swab in patients affected by COVID-19

Abstract

COronaVIrus Disease-2019 (COVID-19) is a pandemic respiratory infection caused by a new betacoronavirus, the Severe Acute Respiratory Syndrome-CoronaVirus-2 (SARS-CoV-2). Few data are reported on the gut microbiota in COVID-19 patients. 16S rRNA gene sequencing was performed to reveal an altered composition of the gut microbiota in patients with COVID-19 pneumonia admitted in intensive care unit (ICU) (i-COVID19), or in infectious disease wards (w-COVID19) as compared to controls (CTRL). i-COVID19 patients showed a decrease of Chao1 index as compared to CTRL and w-COVID19 patients indicating that patients in ICU displayed a lower microbial richness while no change was observed as for Shannon Index. At the phylum level, an increase of Proteobacteria was detected in w-COVID19 patients as compared to CTRL. A decrease of Fusobacteria and Spirochetes has been found, with the latter decreased in i-COVID19 patients as compared to CTRL. Significant changes in gut microbial communities in patients with COVID-19 pneumonia with different disease severity compared to CTRL have been identified. Our preliminary data may provide valuable information and promising biomarkers for the diagnosis of the disease and, when validated in larger cohort, it could facilitate the stratification of patients based on the microbial signature.

Fig 1

Box-plots of Chao1 index of species richness (A) and Shannon index of species diversity (B) in w-COVID19, i-COVID19 patients and CTRL. Triangles indicate the medians and Q1 and Q3 are reported.

Fig 2. Principal coordinates plot (PCoA) based on Bray-Curtis distances at family level showing a clustering pattern among samples obtained from controls (red), w-COVID19 (green) and i-COVID19 (blue).

Fig 3. Microbiota composition of w-COVID19, i-COVID19 patients and CTRL, at the phylum level.

The mean value of all the detected taxa is represented.

Fig 4. Microbiota composition of w-COVID19, i-COVID19 patients and CTRL, at the family level.

The mean value of all the detected taxa is represented.

Fig 5. Taxonomy bar plot showing the individual microbiota profile at phylum levels.

Fig 6. Taxonomy bar plot showing the individual microbiota profile at family levels.

Fig 7. Heatmap of one-way hierarchical clustering of differentially abundant families among the three cohorts.

A dual-color code counts for species up- (red) and down-represented (blue), respectively.

Fig 8

Venn diagrams showing the number of distinct and shared families (A), genera (B) and species (C) up and decreased between subjects grouped by w-COVID19, i-COVID19 patients as compared to CTRL used as referenced.