Nasopharyngeal Microbiome Signature in COVID-19 Positive Patients: Can We Definitively Get a Role to Fusobacterium periodonticum?

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the pandemic Coronavirus Disease 2019 (COVID-19). This virus is highly transmissible among individuals through both droplets and aerosol leading to determine severe pneumonia. Among the various factors that can influence both the onset of disease and the severity of its complications, the microbiome composition has also been investigated. Recent evidence showed the possible relationship between gut, lung, nasopharyngeal, or oral microbiome and COVID-19, but very little is known about it. Therefore, we aimed to verify the relationships between nasopharyngeal microbiome and the development of either COVID-19 or the severity of symptoms. To this purpose, we analyzed, by next generation sequencing, the hypervariable V1-V2-V3 regions of the bacterial 16S rRNA in nasopharyngeal swabs from SARS-CoV-2 infected patients (n=18) and control (CO) individuals (n=12) using Microbiota solution A (Arrow Diagnostics). We found a significant lower abundance of Proteobacteria and Fusobacteria in COVID-19 patients in respect to CO (p=0.003 and p<0.0001, respectively) from the phylum up to the genus (p<0.001). The Fusobacterium periodonticum (FP) resulted as the most significantly reduced species in COVID-19 patients respect to CO. FP is reported as being able to perform the surface sialylation. Noteworthy, some sialic acids residues on the cell surface could work as additional S protein of SARS-CoV-2 receptors. Consequently, SARS-CoV-2 could use sialic acids as receptors to bind to the epithelium of the respiratory tract, promoting its clustering and the disease development. We can therefore speculate that the significant reduction of FP in COVID-19 patients could be directly or indirectly linked to the modulation of sialic acid metabolism. Finally, viral or environmental factors capable of interfering with sialic metabolism could determine a fall in the individual protection from SARS-CoV-2. Further studies are necessary to clarify the precise role of FP in COVID-19.

Association between the nasopharyngeal microbiome and metabolome in patients with COVID-19

“…Recently, a Chinese team from Wuhan institute of virology published a metagenomic sequencing study that reveals the potential linkages between pharyngeal microbiota and COVID-19 [ 15 ]. Our study is a novel metagenomic study to reveal the nasopharyngeal microbiome features of COVID-19 patients in China, which also have been reported by other studies in USA [ 14 ] and Italy [ 27 ].…”

Nasopharyngeal Microbiota in SARS-CoV-2 Positive and Negative Patients

“…Recent cross-sectional studies have attempted to distinguish nasal microbial profiles collected from COVID-19-positive and negative subjects using nasopharyngeal swab [ 5 – 8 ]. Of the four prior studies using nasopharyngeal swabs, our results are most similar to those of Mostafa et al [ 7 ].…”

“…, Meisel et al [ 26 ]), Propionibacterium were not well represented and no direct comparison with the results of Mostafa et al could be made. Elsewhere, Nardelli and colleagues targeted the V1-V3 variable regions of 16S rRNA genes using amplicon sequencing [ 8 ], while De Maio et al targeted the V5-V6 variable regions [ 5 ]. Differences in PCR conditions can make direct comparison of results generated with different primer sets challenging, as PCR conditions can introduce substantial bias into observed microbial communities.…”

“…However, few studies have examined the nasopharyngeal microbiota in COVID-19 patients. To date, two studies found no significant differences in microbial diversity between COVID-19-positive and negative patients [ 5 , 6 ] whereas two studies did note differences in community structure [ 7 , 8 ]. One of these studies reports a significant decrease in microbial diversity, differences between microbial communities, and a higher abundance of Propionibacteriaceae and a reduction in Corynebacterium accolens in COVID-19-positive relative to -negative patients [ 7 ].…”

“…One of these studies reports a significant decrease in microbial diversity, differences between microbial communities, and a higher abundance of Propionibacteriaceae and a reduction in Corynebacterium accolens in COVID-19-positive relative to -negative patients [ 7 ]. The other study observed differences between microbial communities, with a significantly lower abundance of Fusobacterium periodonticum in COVID-19 positive compared to negative patients [ 8 ]. These mixed results highlight the critical need for more information.…”