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

Autor: Hoque MN; Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, 1706, Bangladesh.; Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhanmondi, Dhaka, 1205, Bangladesh., Sarkar MMH; Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhanmondi, Dhaka, 1205, Bangladesh., Rahman MS; Department of Microbiology, Jashore University of Science Technology, Jashore, 7408, Bangladesh., Akter S; Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhanmondi, Dhaka, 1205, Bangladesh., Banu TA; Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhanmondi, Dhaka, 1205, Bangladesh., Goswami B; Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhanmondi, Dhaka, 1205, Bangladesh., Jahan I; Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhanmondi, Dhaka, 1205, Bangladesh., Hossain MS; Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhanmondi, Dhaka, 1205, Bangladesh., Shamsuzzaman AKM; National Institute of Laboratory Medicine and Referral Center, Dhaka, 1207, Bangladesh., Nafisa T; National Institute of Laboratory Medicine and Referral Center, Dhaka, 1207, Bangladesh., Molla MMA; National Institute of Laboratory Medicine and Referral Center, Dhaka, 1207, Bangladesh., Yeasmin M; National Institute of Laboratory Medicine and Referral Center, Dhaka, 1207, Bangladesh., Ghosh AK; National Institute of Laboratory Medicine and Referral Center, Dhaka, 1207, Bangladesh., Osman E; SciTech Consulting and Solutions, Dhaka, 1213, Bangladesh., Alam SKS; Shaheed Tajuddin Ahmad Medical College, Gazipur, 1700, Bangladesh., Uzzaman MS; SciTech Consulting and Solutions, Dhaka, 1213, Bangladesh., Habib MA; Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhanmondi, Dhaka, 1205, Bangladesh., Mahmud ASM; Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhanmondi, Dhaka, 1205, Bangladesh., Crandall KA; Computational Biology Institute and Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC, USA., Islam T; Institute of Biotechnology and Genetic Engineering (IBGE), BSMRAU, Gazipur, 1706, Bangladesh. tofazzalislam@yahoo.com., Khan MS; Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhanmondi, Dhaka, 1205, Bangladesh. k2salim@yahoo.com.
Jazyk: angličtina
Zdroj: Scientific reports [Sci Rep] 2021 Dec 15; Vol. 11 (1), pp. 24042. Date of Electronic Publication: 2021 Dec 15.
DOI: 10.1038/s41598-021-03245-4
Abstrakt: 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.
(© 2021. The Author(s).)
Databáze: MEDLINE
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