The salivary and nasopharyngeal microbiomes are associated with SARS‐CoV‐2 infection and disease severity
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Abstract
Emerging evidence suggests the oral and upper respiratory microbiota may play important roles in modulating host immune responses to viral infection. As the host microbiome may be involved in the pathophysiology of coronavirus disease 2019 (COVID‐19), we investigated associations between the oral and nasopharyngeal microbiome and COVID‐19 severity. We collected saliva ( n = 78) and nasopharyngeal swab ( n = 66) samples from a COVID‐19 cohort and characterized the microbiomes using 16S ribosomal RNA gene sequencing. We also examined associations between the salivary and nasopharyngeal microbiome and age, COVID‐19 symptoms, and blood cytokines. Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection status, but not COVID‐19 severity, was associated with community‐level differences in the oral and nasopharyngeal microbiomes. Salivary and nasopharyngeal microbiome alpha diversity negatively correlated with age and were associated with fever and diarrhea. Oral Bifidobacterium , Lactobacillus , and Solobacterium were depleted in patients with severe COVID‐19. Nasopharyngeal Paracoccus was depleted while nasopharyngeal Proteus , Cupravidus , and Lactobacillus were increased in patients with severe COVID‐19. Further analysis revealed that the abundance of oral Bifidobacterium was negatively associated with plasma concentrations of known COVID‐19 biomarkers interleukin 17F and monocyte chemoattractant protein‐1. Our results suggest COVID‐19 disease severity is associated with the relative abundance of certain bacterial taxa.
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SciScore for 10.1101/2022.05.31.494162: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: This study was approved by the Institutional Review Board at Washington University in St. Louis (IRB number 202003085).
Consent: All patients who were enrolled in the study provided informed consent prior to participation. 2.
Field Sample Permit: Sample collection, processing, and microbial DNA sequencing: Saliva and nasopharyngeal swab samples were collected at the time of enrollment, which was during or shortly following evaluation at a medical facility.Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources Sequencing data processing: Amplicon sequence variants (ASVs) … SciScore for 10.1101/2022.05.31.494162: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: This study was approved by the Institutional Review Board at Washington University in St. Louis (IRB number 202003085).
Consent: All patients who were enrolled in the study provided informed consent prior to participation. 2.
Field Sample Permit: Sample collection, processing, and microbial DNA sequencing: Saliva and nasopharyngeal swab samples were collected at the time of enrollment, which was during or shortly following evaluation at a medical facility.Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources Sequencing data processing: Amplicon sequence variants (ASVs) were inferred from de-muliplexed fastq files using the DADA2 R package (https://benjjneb.github.io/dada2/tutorial.html) (51) and taxonomy was assigned from de-muliplexed fastq files using the Ribosomal Database Project’s Training Set 16. DADA2suggested: (dadasnake, RRID:SCR_019149)To perform differential abundance testing, we used the R Package DESeq2 (https://bioconductor.org/packages/release/bioc/html/DESeq2.html) (53) which uses a generalized regression model with a logarithmic link, following a negative binomial distribution. DESeq2suggested: (DESeq, RRID:SCR_000154)https://bioconductor.org/packages/release/bioc/html/DESeq2.htmlsuggested: (DESeq2, RRID:SCR_015687)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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