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SARS-CoV-2 Infection Reduces Human Nasopharyngeal Commensal Microbiome With Inclusion of Pathobionts
29 Pages Posted: 8 May 2021
More...Abstract
Background: The SARS-CoV-2 primarily enters into the human body through nasopharyngeal tract (NT) and is the etiological agent of COVID-19. The microbiota of the nasopharyngeal tract may 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.
Methods: Twenty-two (n=22) nasopharyngeal swab samples (including COVID-19 = 8, Recovered = 7, and Healthy = 7) were collected, and underwent for total RNA-Seq approach for metagenomics investigation. The cDNA of all 22 samples was used to prepare paired-end libraries, and sequencing was performed to generate RNA-Seq data which was analyzed using both mapping-based and assembly-based annotation methods of PathoScope 2 and MG-RAST for taxonomic and genomic functional characterization.
Findings: Our RNA-Seq data mapped to 2281 bacterial species (including 1477, 919 and 676 in samples of healthy human, COVID-19 patients and COVID-19 recovered individuals, respectively) indicating a distinct microbiome dysbiosis in COVID-19 and COVID-19 recovered patients compared to healthy individuals. The samples from COVID-19 patients and Recovered individuals had inclusion of 67% (including Streptococcus salivarius, S. mitis, Neisseria subflava, Veillonella dispar, Acinetobacter junii, Prevotella melaninogenica, etc.) and 77% (including Pseudomonas stutzeri, Staphylococcus capitis, S. epidermidis, P. mendocina, Moraxella osloensis, A. indicus, Escherichia coli, etc.) opportunistic pathogenic bacteria, respectively compared to Healthy individuals. Notably, 79% commensal bacteria (e.g., Pseudomonas sp. LPH1, Brevundimonas sp. Bb-A, P. oleovorans, Pseudomonas sp. phDV1, Brevundimonas sp. DS20, Idiomarinaceae bacterium HL-53, Alishewanella sp. 205, Sphingobacterium psychroaquaticum etc.) were found in healthy individuals but not detected in COVID-19 patients and Recovered individuals. Similar dysbiosis was also found in viral and archaeal fraction of the microbiomes. Although 55 viral and 48 archaeal genera were detected, only 16.37% viral and 27.08% archaeal genera were shared across these three metagenomes. We also detected altered metabolic pathways and functional genes including resistance to antibiotics and toxic compounds associated with COVID-19 pathogenesis.
Interpretation: The nasopharyngeal microbiome dysbiosis and their genomic features in COVID-19, Recovered and Healthy individuals determined by our RNA-Seq 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.
Funding Statement: This project is financed by the Ministry of Science and Technology, Government of the People’s Republic of Bangladesh (Grant No. GOB 224125200).
Declaration of Interests: The authors declare no competing interests.
Ethics Approval Statement: The protocol for sample collection from COVID-19, Recovered and Healthy humans, sample processing, transport, and RNA extraction was approved by the Director General of Health Services of Bangladesh.
Keywords: Nasopharyngeal tract, Microbiomes, Bacteria, Viruses, Archaea, Dysbiosis, SARS-CoV-2 infections
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