Investigation of Nasal/Oropharyngeal Microbial Community of COVID-19 Patients by 16S rDNA Sequencing

Abstract

Since December 2019, SARS-CoV-2 infection has been still rapidly spreading, resulting in a pandemic, followed by an increasing number of cases in countries throughout the world. The severity of the disease depends on the patient's overall medical condition but no appropriate markers are available to establish the prognosis of the patients. We performed a 16S rRNA gene sequencing, revealing an altered composition of the nasal/oropharyngeal (NOP) microbiota in 21 patients affected by COVID-19, paucisymptomatic or in an Intensive Care Unit (ICU), as compared to 10 controls negative for COVID-19 or eight affected by a different Human Coronavirus (HKU, NL63 and OC43). A significant decrease in Chao1 index was observed when patients affected by COVID-19 (in ICU) were compared to paucisymptomatic. Furthermore, patients who were in ICU, paucisymptomatic or affected by other Coronaviruses all displayed a decrease in the Chao1 index when compared to controls, while Shannon index significantly decreased only in patients under ICU as compared to controls and paucisymptomatic patients. At the phylum level, Deinococcus-Thermus was present only in controls as compared to SARS-CoV-2 patients admitted to ICU, paucisymptomatic or affected by other coronaviruses. Candidatus Saccharibacteria (formerly known as TM7) was strongly increased in negative controls and SARS-CoV-2 paucisymptomatic patients as compared to SARS-CoV-2 ICU patients. Other modifications were observed at a lower taxonomy level. Complete depletion of Bifidobacterium and Clostridium was exclusively observed in ICU SARS-CoV-2 patients, which was the only group characterized by the presence of Salmonella, Scardovia, Serratia and Pectobacteriaceae. In conclusion, our preliminary results showed that nasal/oropharyngeal microbiota profiles of patients affected with SARS-CoV-2 may provide valuable information in order to facilitate the stratification of patients and may open the way to new interventional strategies in order to ameliorate the outcome of the patients.

Keywords: Nasal/Oropharyngeal; SARS-CoV2; microbiota.

Figure 1

Boxplots of age (A), Chao1 index of species richness (B) and Shannon index of species diversity (C) in healthy subjects (Neg Controls), patients infected with other human coronaviruses (Other HCoVs), paucisymptomatic patients (SARS-CoV-2 Pauci) and patients in Intensive Care Units (SARS-CoV-2 ICU). (## = p < 0.10; * = p < 0.05; ** = p < 0.01; *** = p < 0.005). (D) Multidimensional Scaling plot from Principal Coordinates Analysis (PCoA) based on Bray–Curtis distances at genus level showing a clustering pattern among samples obtained from Neg controls (red), other HCoVs (green), SARS-CoV-2 Pauci (blue) and SARS-CoV-2 ICU (violet).

Figure 2

Microbiota composition of Neg Controls, Other HCoVs, SARS-CoV-2 Pauci and SARS-CoV-2 ICU at the phylum level. The mean value of all the detected taxa is represented.

Figure 3

Microbiota composition of Neg Controls, Other HCoVs, SARS-CoV-2 Pauci and SARS-CoV-2 ICU at the family level. The mean value of all the detected taxa is represented.

Figure 4

Microbiota composition of Neg Controls, Other HCoVs, SARS-CoV-2 Pauci and SARS-CoV-2 ICU at the genus level. The mean value of all the detected taxa is represented.

Figure 5

Venn diagrams showing the number of distinct and shared families (A) and genera (B) up and downregulated between subjects grouped by Neg Controls, other HCoVs, SARS-CoV-2 Pauci and SARS-CoV-2 ICU.