SARS-CoV-2 infection reduces human nasopharyngeal commensal microbiome with inclusion of pathobionts

M Nazmul Hoque,Md Murshed Hasan Sarkar,Asish Kumar Ghosh,M Shaminur Rahman,Keith A Crandall,Iffat Jahan,Abu Sayeed Mohammad Mahmud,Mahmuda Yeasmin,Md Maruf Ahmed Molla ,Shafiqul Alam ,Barna Goswami,Shahina Akter,A K Mohammad Shamsuzzaman ,Tofazzal Islam,Md Saddam Hossain ,Tanjina Akhtar Banu,Tasnim Nafisa,Mohammad Samir Uzzaman,Md Ahashan Habib ,Eshrar Osman,Mala Khan

doi:10.1038/s41598-021-03245-4

Abstract

The microbiota of the nasopharyngeal tract (NT) play a role in host immunity against respiratory infectious diseases. However, scant information is available on interactions of SARS-CoV-2 with the nasopharyngeal microbiome. This study characterizes the effects of SARS-CoV-2 infection on human nasopharyngeal microbiomes and their relevant metabolic functions. Twenty-two (n = 22) nasopharyngeal swab samples (including COVID-19 patients = 8, recovered humans = 7, and healthy people = 7) were collected, and underwent to RNAseq-based metagenomic investigation. Our RNAseq data mapped to 2281 bacterial species (including 1477, 919 and 676 in healthy, COVID-19 and recovered metagenomes, respectively) indicating a distinct microbiome dysbiosis. The COVID-19 and recovered samples included 67% and 77% opportunistic bacterial species, respectively compared to healthy controls. Notably, 79% commensal bacterial species found in healthy controls were not detected in COVID-19 and recovered people. Similar dysbiosis was also found in viral and archaeal fraction of the nasopharyngeal microbiomes. We also detected several altered metabolic pathways and functional genes in the progression and pathophysiology of COVID-19. The nasopharyngeal microbiome dysbiosis and their genomic features determined by our RNAseq analyses shed light on early interactions of SARS-CoV-2 with the nasopharyngeal resident microbiota that might be helpful for developing microbiome-based diagnostics and therapeutics for this novel pandemic disease.

Highlights

The microbiota of the nasopharyngeal tract (NT) play a role in host immunity against respiratory infectious diseases
We demonstrated a remarkable shift in the diversity and composition of the nasopharyngeal microbiomes of COVID-19 and Recovered people compared to the Healthy humans through the state-of-the-art RNAseq technology
The identifiable changes in the microbiome diversity, composition and associated genomic features demonstrated in this study might be associated with the development, treatment, and resolution of COVID-19

Summary

Introduction

The microbiota of the nasopharyngeal tract (NT) play a role in host immunity against respiratory infectious diseases. Several lines of evidence suggest that development of COVID-19 disease modulates the population and diversity of resident commensal microbiota of humans, little is known about the outcome of the interactions of SARS-CoV-2 with nasal commensal microbiome which is thought to be critical for transmission, modulation, and progression of COVID-1919,20. To shed light on the effects and consequences of SARS-CoV-2 infection on the NT microbiome, we conducted a high throughput RNAseq analysis of the nasopharyngeal swabs of randomly selected healthy humans, COVID-19 and recovered patients. This report for the first time demonstrates the association of microbiome diversity and composition (Fig. 1), and their concomitant genomic features in the nasal cavity of COVID-19 and recovered patients compared to healthy humans, and discusses the role of the altered microbiome in the pathophysiology of the SARS-CoV-2 infections

Methods

Results

Discussion

Conclusion