Title

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

Authors

M. Nazmul Hoque, Bangabandhu Sheikh Mujibur Rahman Agricultural University
Md Murshed Hasan Sarkar, Bangladesh Council of Scientific and industrial Research (BCSIR)
M. Shaminur Rahman, Jashore University of Science Technology
Shahina Akter, Bangladesh Council of Scientific and industrial Research (BCSIR)
Tanjina Akhtar Banu, Bangladesh Council of Scientific and industrial Research (BCSIR)
Barna Goswami, Bangladesh Council of Scientific and industrial Research (BCSIR)
Iffat Jahan, Bangladesh Council of Scientific and industrial Research (BCSIR)
M. Saddam Hossain, Bangladesh Council of Scientific and industrial Research (BCSIR)
A. K.Mohammad Shamsuzzaman, National Institute of Laboratory Medicine and Referral Center
Tasnim Nafisa, National Institute of Laboratory Medicine and Referral Center
M. Maruf Ahmed Molla, National Institute of Laboratory Medicine and Referral Center
Mahmuda Yeasmin, National Institute of Laboratory Medicine and Referral Center
Asish Kumar Ghosh, National Institute of Laboratory Medicine and Referral Center
Eshrar Osman, SciTech Consulting and Solutions
S. K.Saiful Alam, Shaheed Tajuddin Ahmed Medical College and Hospital
Mohammad Samir Uzzaman, SciTech Consulting and Solutions
Md Ahashan Habib, Bangladesh Council of Scientific and industrial Research (BCSIR)
Abu Sayeed Mohammad Mahmud, Bangladesh Council of Scientific and industrial Research (BCSIR)
Keith A. Crandall, Milken Institute School of Public Health
Tofazzal Islam, Bangabandhu Sheikh Mujibur Rahman Agricultural University
Md Salim Khan, Bangladesh Council of Scientific and industrial Research (BCSIR)

Document Type

Journal Article

Publication Date

12-1-2021

Journal

Scientific Reports

Volume

11

Issue

1

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.

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