Profiling of Oral Microbiota and Cytokines in COVID-19 Patients.

Valerio Iebba,Roberto Luzzati,Marco Confalonieri,Nunzia Zanotta,Verena Zerbato,Anna Teresa Palamara,Manola Comar,Giuseppina Campisciano,Carolina Cason,Stefano Di Bella

doi:10.3389/fmicb.2021.671813

Abstract

The presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been recently demonstrated in the sputum or saliva, suggesting how the shedding of viral RNA outlasts the end of symptoms. Recent data from transcriptome analysis show that the oral cavity mucosa harbors high levels of angiotensin-converting enzyme 2 (ACE2) and transmembrane protease, serine 2 (TMPRSS2), highlighting its role as a double-edged sword for SARS-CoV-2 body entrance or interpersonal transmission. Here, we studied the oral microbiota structure and inflammatory profile of 26 naive severe coronavirus disease 2019 (COVID-19) patients and 15 controls by 16S rRNA V2 automated targeted sequencing and magnetic bead-based multiplex immunoassays, respectively. A significant diminution in species richness was observed in COVID-19 patients, along with a marked difference in beta-diversity. Species such as Prevotella salivae and Veillonella infantium were distinctive for COVID-19 patients, while Neisseria perflava and Rothia mucilaginosa were predominant in controls. Interestingly, these two groups of oral species oppositely clustered within the bacterial network, defining two distinct Species Interacting Groups (SIGs). COVID-19-related pro-inflammatory cytokines were found in both oral and serum samples, along with a specific bacterial consortium able to counteract them. We introduced a new parameter, named CytoCOV, able to predict COVID-19 susceptibility for an unknown subject at 71% of power with an Area Under Curve (AUC) equal to 0.995. This pilot study evidenced a distinctive oral microbiota composition in COVID-19 subjects, with a definite structural network in relation to secreted cytokines. Our results would be usable in clinics against COVID-19, using bacterial consortia as biomarkers or to reduce local inflammation.

Highlights

Coronavirus disease 2019 (COVID-19) is a global pandemic established at the end of 2019, whose etiological agent is severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a member of betacoronaviruses (Li et al, 2020)
The unsupervised algorithm of Principal Coordinate Analysis (PCoA) visually represented a significant separation of COVID-19 oral samples from controls (p < 1∗10−3) (Figure 1B), meaning a different oral microbiota composition assessed with two different measures of beta-diversity (ANOSIM and PERMANOVA)
In order to find a pattern of bacterial species able to describe the changes in microbiota composition of COVID-19 samples, we used the supervised algorithm of Partial Least Square Discriminant Analysis (PLS-DA), which generated a Variable Importance Plot (VIP) showing the most important species able to separate the two cohorts (Figure 1C)

Summary

Introduction

Coronavirus disease 2019 (COVID-19) is a global pandemic established at the end of 2019, whose etiological agent is severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a member of betacoronaviruses (Li et al, 2020). Transcriptome analysis found that angiotensin-converting enzyme 2 (ACE2) and transmembrane protease, serine 2 (TMPRSS2) receptors, employed by SARS-CoV-2 to enter cells, were highly expressed in salivary glands and epithelial cells, showing the potential vulnerability risk for oral cavity for lung or gut involvement (Herrera et al, 2020) From these data, virus–host interplay within the oral cavity seems to be a promising feature of COVID19 pathogenesis, forming the basis of disease severity and spread. We characterized the interplay of oral microbiota and inflammatory cytokines in COVID-19 patients

Methods

Results

Conclusion