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Disentangling the interactions between nasopharyngeal and gut microbiome and their involvement in the modulation of COVID-19 infection

Microbiology Spectrum, ISSN: 2165-0497, Vol: 11, Issue: 5, Page: e0219423
2023
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Article Description

The human organism is inhabited by trillions of microorganisms, known as microbiota, which are considered to exploit a pivotal role in the regulation of host health and immunity. Recent investigations have suggested a relationship between the composition of the human microbiota and COVID-19 infection, highlighting a possible role of bacterial communities in the modulation of the disease severity. In this study, we performed a shotgun metagenomics analysis to explore and compare the nasopharyngeal microbiota of 38 hospitalized Italian patients with and without COVID-19 infection during the third and fourth pandemic waves. In detail, the metagenomic analysis combined with specific correlation analyses suggested a positive association of several microbial species, such as S. parasanguinis and P. melaninogenica, with the severity of COVID-19 infection. Furthermore, the comparison of the microbiota composition between the nasopharyngeal and their respective fecal samples highlighted an association between these different compartments represented by a sharing of several bacterial species. Additionally, lipidomic and deep-shotgun functional analyses of the fecal samples suggested a metabolic impact of the microbiome on the host’s immune response, indicating the presence of key metabolic compounds in COVID-19 patients, such as lipid oxidation end products, potentially related to the inflammatory state. Conversely, the patients without COVID-19 displayed enzymatic patterns associated with the biosynthesis and degradation of specific compounds like lysine (synthesis) and phenylalanine (degradation) that could positively impact disease severity and contribute to modulating COVID-19 infection. IMPORTANCE The human microbiota is reported to play a major role in the regulation of host health and immunity, suggesting a possible impact on the severity of COVID-19 disease. This preliminary study investigated the possible correlation between nasopharyngeal microbiota and COVID-19 infection. In detail, the analysis of the nasopharyngeal microbiota of hospitalized Italian patients with and without COVID-19 infection suggested a positive association of several microbial species with the severity of the disease and highlighted a sharing of several bacteria species with the respective fecal samples. Moreover, the metabolic analyses suggested a possible impact of the microbiome on the host's immune response and the disease severity.

Bibliographic Details

Leonardo Mancabelli; Giuseppe Taurino; Andrea Ticinesi; Tecla Ciociola; Federica Vacondio; Christian Milani; Federico Fontana; Gabriele Andrea Lugli; Chiara Tarracchini; Giulia Alessandri; Alice Viappiani; Massimiliano Bianchi; Antonio Nouvenne; Alfredo Antonio Chetta; Francesca Turroni; Tiziana Meschi; Marco Mor; Ovidio Bussolati; Marco Ventura; Paolo Visca

American Society for Microbiology

Biochemistry, Genetics and Molecular Biology; Environmental Science; Immunology and Microbiology; Medicine

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