Author:
Hoque M. Nazmul,Sarkar Md. Murshed Hasan,Rahman M. Shaminur,Akter Shahina,Banu Tanjina Akhtar,Goswami Barna,Jahan Iffat,Hossain M. Saddam,Shamsuzzaman A. K. Mohammad,Nafisa Tasnim,Molla M. Maruf Ahmed,Yeasmin Mahmuda,Ghosh Asish Kumar,Osman Eshrar,Alam S. K. Saiful,Uzzaman Mohammad Samir,Habib Md Ahashan,Mahmud Abu Sayeed Mohammad,Crandall Keith A.,Islam Tofazzal,Khan Md. Salim
Abstract
AbstractThe 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.
Publisher
Springer Science and Business Media LLC
Reference56 articles.
1. He, X. et al. Temporal dynamics in viral shedding and transmissibility of COVID-19. Nat. Med. 26, 672–675 (2020).
2. Hoque, M. N., Chaudhury, A., Akanda, M. A. M., Hossain, M. A. & Islam, M. T. Genomic diversity and evolution, diagnosis, prevention, and therapeutics of the pandemic COVID-19 disease. PeerJ 8, e9689 (2020).
3. Reid, A. H., Fanning, T. G., Hultin, J. V. & Taubenberger, J. K. Origin and evolution of the 1918 “Spanish” influenza virus hemagglutinin gene. Proc. Natl. Acad. Sci. 96, 1651–1656 (1999).
4. Gallo, O., Locatello, L. G., Mazzoni, A., Novelli, L. & Annunziato, F. The central role of the nasal microenvironment in the transmission, modulation, and clinical progression of SARS-CoV-2 infection. Mucosal Immunol. 20, 1–12 (2020).
5. Hoque, M. N. et al. Microbial co-infections in COVID-19: Associated microbiota and underlying mechanisms of pathogenesis. Microbial Pathog. 20, 104941 (2021).
Cited by
30 articles.
订阅此论文施引文献
订阅此论文施引文献，注册后可以免费订阅5篇论文的施引文献，订阅后可以查看论文全部施引文献