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

Abstract

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.

Alterations in microbiota of patients with COVID‐19: implications for therapeutic interventions

“…Analysis of nasopharyngeal microbiota abundance in hospitalized patients with COVID‐19 and healthy controls found that some gut microbiota and nasopharyngeal microbiota participate in the host immune response. 83 , 84 , 85 …”

Gut microbiota composition in recurrent acute otitis media: a cross-sectional observational study

“…Recent investigations into the interplay between microbiota and COVID-19 have significantly advanced this field of research, notably by elucidating microbial networks between throat and gut microbiota (Xu et al 2021). Studies have also highlighted disparities in the shared nasopharynxgut microbiota between COVID-19 patients and healthy individuals (Mancabelli et al 2023). However, it is worth noting that the study by Mancabelli et al focused on adult patients and reported distinct shared microbiota patterns compared to our findings.…”