Nasopharyngeal microbiome of COVID-19 patients revealed a distinct bacterial profile in deceased and recovered individuals

Abstract

The bacterial co-infections in SARS-CoV-2 patients remained the least explored subject of clinical manifestations that may also determine the disease severity. Nasopharyngeal microbial community structure within SARS-CoV-2 infected patients could reveal interesting microbiome dynamics that may influence the disease outcomes. Here, in this research study, we analyzed distinct nasopharyngeal microbiome profile in the deceased (n = 48) and recovered (n = 29) COVID-19 patients and compared it with control SARS-CoV-2 negative individuals (control) (n = 33). The nasal microbiome composition of the three groups varies significantly (PERMANOVA, p-value <0.001), where deceased patients showed higher species richness compared to the recovered and control groups. Pathogenic genera, including Corynebacterium (LDA score 5.51), Staphylococcus, Serratia, Klebsiella and their corresponding species were determined as biomarkers (p-value <0.05, LDA cutoff 4.0) in the deceased COVID-19 patients. Ochrobactrum (LDA score 5.79), and Burkholderia (LDA 5.29), were found in the recovered group which harbors ordinal bacteria (p-value <0.05, LDA-4.0) as biomarkers. Similarly, Pseudomonas (LDA score 6.19), and several healthy nasal cavity commensals including Veillonella, and Porphyromonas, were biomarkers for the control individuals. Healthy commensal bacteria may trigger the immune response and alter the viral infection susceptibility and thus, may play important role and possible recovery that needs to be further explored. This research finding provide vital information and have significant implications for understanding the microbial diversity of COVID-19 patients. However, additional studies are needed to address the microbiome-based therapeutics and diagnostics interventions.

Keywords: And SARS-CoV-2; Nasopharyngeal microbiome; Opportunistic pathogens.

Graphical abstract

Fig. 1

Alpha and Beta diversity plots (species level) for deceased, recovered and control patient group. (A) PCoA plot based on Bray-Curtis dissimilarity and with PERMANOVA statistics depicting significant differences (p-value <0.001). (B) NMDS plot based on Bray-Curtis dissimilarity and PERMANOVA statistics showing significant difference (p-value <0.001) among the three groups. (C), and (D), species richness estimated using Cho1, ACE index at the species level with Mann-Whitney/Kruskal-Walis statistical method. (E) Species richness and evenness estimated using Shannon index at species level with Mann-Whitney/Kruskal-Walis statistical method. No significant difference in the alpha diversity among the three groups.

Fig. 2

Comparison of microbial community between two groups. (A), (B), and (C) are the heat trees, depicting the significantly different genera between control vs deceased, control vs recovered and deceased vs recovered groups, respectively. Analysis was performed with non-parametric Wilcoxon Rank Sum test. The size and colour of nodes and edges are with the abundance (median) of organisms in each group. (D), (E), and (F), depicts the dot plots for Linear Discriminant Analysis (LDA) Effect Size (LEfSe) at the genus level for control vs deceased, control vs recovered and deceased vs recovered groups, respectively. LEfSe was performed with p-value cutoff 0.05 and Log LDA score cutoff 4.0.

Fig. 3

LEfSe analysis comparing three groups (deceased, recovered, and control). LEfSe analysis was performed at genus and species level with p-value cutoff 0.05 and Log LDA score cutoff 4.0 with and all the significant features i.e. 32 genera and 46 species are plotted. (A), and (C) depict the dot plots at genus and species level, respectively, and (B) and (D) depict bar plots at genus and species level, respectively.

Fig. 4

Box plots depicting log2 transformed abundance of important genera. (A)Corynebacterium, (B)Staphylococcus, (C)Serratia, (D)Micrococcus, (E)Klebsiella, (F)Ochrobactrum, (G) Unclassified betaproteobacteria, (H)Bulkhorderia, and (I)Pseudomonas. In the Box plot, each black dot represents a single sample, the bars on the Box represent upper and lower whiskers and the median value is shown as a horizontal line in the box.

Fig. 5

Depicting the results of Random Forest Classification where 1000 trees were grown. (A) shows the prediction of each sample in the respective group, class error and Out-of-bag (OOB), (B) classification performance, and (C) random forest plot for the importance of genera with their mean decrease accuracy, top 25 genera were plotted. The high value of mean decrease accuracy shows the importance of that genus in predicting the group.