Microbiome in the nasopharynx: Insights into the impact of COVID-19 severity

Abstract

Background: The respiratory tract harbors a variety of microbiota, whose composition and abundance depend on specific site factors, interaction with external factors, and disease. The aim of this study was to investigate the relationship between COVID-19 severity and the nasopharyngeal microbiome.

Methods: We conducted a prospective cohort study in Mexico City, collecting nasopharyngeal swabs from 30 COVID-19 patients and 14 healthy volunteers. Microbiome profiling was performed using 16S rRNA gene analysis. Taxonomic assignment, classification, diversity analysis, core microbiome analysis, and statistical analysis were conducted using R packages.

Results: The microbiome data analysis revealed taxonomic shifts within the nasopharyngeal microbiome in severe COVID-19. Particularly, we observed a significant reduction in the relative abundance of Lawsonella and Cutibacterium genera in critically ill COVID-19 patients (p < 0.001). In contrast, these patients exhibited a marked enrichment of Streptococcus, Actinomyces, Peptostreptococcus, Atopobium, Granulicatella, Mogibacterium, Veillonella, Prevotella_7, Rothia, Gemella, Alloprevotella, and Solobacterium genera (p < 0.01). Analysis of the core microbiome across all samples consistently identified the presence of Staphylococcus, Corynebacterium, and Streptococcus.

Conclusions: Our study suggests that the disruption of physicochemical conditions and barriers resulting from inflammatory processes and the intubation procedure in critically ill COVID-19 patients may facilitate the colonization and invasion of the nasopharynx by oral microorganisms.

Keywords: COVID-19; Corynebacterium; Cutibacterium Core microbiome; Intubation; Lawsonella; Nasopharyngeal microbiome; Nasopharynx; Staphylococcus; Streptococcus.

Fig. 1

Richness and alpha diversity indices. a) Richness Chao1 index, b) Fisher index showing no significant differences. c) Shannon index revealing a significant difference between the control and critical COVID-19 (p = 0.03). d) Beta diversity of the nasopharyngeal microbiome among different severity groups of COVID-19. Significance was determined using Kruskal-Wallis test with Dunn's multiple comparison with a 95 % confidence interval. The NMDS plot is based on Bray-Curtis dissimilarity, and PERMANOVA statistics indicate a significant difference among the three groups. Each color represents a specific analyzed group. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 2

a) Taxonomy bar plot showing the top 20 microbiome profiles at the genus level, ranked by relative abundance, in control, severe, and critical patients. b) and c) Violin plot displaying the relative abundance of Staphylococcus and Corynebacterium genera. No significant differences were observed between severity groups. c) and d) Decrease in the relative abundance of Lawsonella and Cutibacterium genera in critical COVID-19 patients. Significance was determined using the Kruskal-Wallis test with Dunn's multiple comparison, 95 % confidence interval, where ∗ p ≤ 0.05, ∗∗ p ≤ 0.01, and ∗∗∗ p ≤ 0.001.

Fig. 3

Genera with increased relative abundance in critical COVID-19 patients. Significance was determined using the Kruskal-Wallis test with Dunn's multiple comparison 95 % confidence interval, where ∗ p ≤ 0.05, ∗∗ p ≤ 0.01, and ∗∗∗ p ≤ 0.001.

Fig. 4

Nasopharyngeal Core Microbiome. Microorganisms shared across communities, are present in at least 60 % of the samples with 0.001 % of relative abundance.