IMR Press / FBL / Volume 29 / Issue 2 / DOI: 10.31083/j.fbl2902059
Open Access Original Research
SARS-CoV-2 Infection is Associated with Age- and Gender-Specific Changes in the Nasopharyngeal Microbiome
Show Less
1 Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy
2 CISM Mass Spectrometry Center, University of Florence, 50139 Firenze, Italy
*Correspondence: (Claudio Costantini)
These authors contributed equally.
Front. Biosci. (Landmark Ed) 2024, 29(2), 59;
Submitted: 17 July 2023 | Revised: 4 December 2023 | Accepted: 20 December 2023 | Published: 6 February 2024
(This article belongs to the Special Issue Immunology in COVID-19 Disease)
Copyright: © 2024 The Author(s). Published by IMR Press.
This is an open access article under the CC BY 4.0 license.

Background: The recent Coronavirus Disease 2019 (COVID-19) pandemic has dramatically exposed our gap in understanding the pathogenesis of airborne infections. Within such a context, it is increasingly clear that the nasal cavity represents a critical checkpoint not only in the initial colonization phase but also in shaping any infectious sequelae. This is particularly relevant to COVID-19 in that the nasal cavity is characterized by high-level expression of the Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) receptor, Angiotensin-Converting Enzyme 2 (ACE2), all along the respiratory tract. As part of the nasal mucosa, commensal microbes harbored by the nasal cavity likely are far more than just innocent bystanders in the interaction between SARS-CoV-2 and the local microenvironment. Yet the role of the qualitative composition of the nasal microbiome is unclear, as is its function, whether protective or not. Methods: In this study, individuals undergoing SARS-CoV-2 molecular testing at the Hospital of Perugia (Italy) were recruited, with their residual material from the nasopharyngeal swabs being collected for microbiome composition analysis and short-chain fatty acid (SCFA) measurements (by 16S rRNA sequencing and gas chromatography-mass spectrometry), respectively. Results: After stratification by age, gender, and viral load, the composition of the nasopharyngeal microbiome appeared to be influenced by age and gender, and SARS-CoV-2 infection further determined compositional changes. Notwithstanding this variability, a restricted analysis of female subjects—once SARS-CoV-2–infected—unraveled a shared expansion of Lachnospirales-Lachnospiraceae, irrespective of the viral load and age. This was associated with a reduction in the branched SCFA isobutanoic acid, as well as in the SCFAs with longer chains. Conclusions: Our results indicate that the nasopharyngeal microbiome is influenced by age, gender, and viral load, with consistent patterns of microbiome changes being present across specific groups. This may help in designing a personalized medicine approach in COVID-19 patients with specific patterns of nasal microbial communities.

nasopharyngeal microbiome
short-chain fatty acids
19645 (2020.0425)/Fondazione Perugia
847507/European Union’s Horizon 2020 research and innovation program
Fig. 1.
Back to top