Nasopharyngeal Microbiome Community Composition and Structure Is Associated with Severity of COVID-19 Disease and Breathing Treatment

Study information

Reviewed Marked as Reviewed by Atrayees on 2023-7-27

study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

N/A

DOI Digital object identifier for electronic documents.

https://doi.org/10.3390/applmicrobiol1020014

URI

https://www.mdpi.com/2673-8007/1/2/14

Authors

Feehan, A.K., Rose, R., Nolan, D.J., Spitz, A.M., Graubics, K., Colwell, R.R., Garcia-Diaz, J. and Lamers, S.L.

Journal

Applied Microbiology

Year

2021

Pages:

177-188

First page:

177

Keywords:

SARS-CoV-2, Serratia, hospital, metagenomic sequencing

Viral infections are known to modulate the upper respiratory tract microbiome, but few studies have addressed differences in the nasopharyngeal microbiome following SARS-CoV-2 infection. Using nasopharyngeal swab medical waste samples from 79 confirmed SARS-CoV-2 positive and 20 SARS-CoV-2 negative patients, we assessed microbiome composition with metagenomic sequencing. COVID-19 status and breathing assistive device use was associated with differences in beta diversity, principal component analyses, community composition and abundance of several species. Serratia more frequently appeared in COVID-19 patient samples compared to negative patient samples, and Serratia, Streptococcus, Enterobacter, Veillonella, Prevotella, and Rothia appeared more frequently in samples of those who used breathing assistive devices. Smoking and age were associated with differences in alpha diversity. Cross-sectional differences in the microbiome were apparent with SARS-CoV-2 infection, but longitudinal studies are needed to understand the dynamics of viral and breathing treatment modulation of microbes.

Experiment 1

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Reviewed Marked as Reviewed by Atrayees on 2023-7-27

Curated date: 2021/08/06

Curator: Claregrieve1

Revision editor(s): Atrayees, WikiWorks, Claregrieve1

Subjects

Location of subjects: United States of America

Host species Species from which microbiome was sampled. Contact us to have more species added.: Homo sapiens

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Nasopharynx Epipharynx,Nasal part of pharynx,Nasenrachenraum,Pars nasalis pharyngis,Rhinopharynx,Nasopharynx,nasopharynx

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: COVID-19 2019 novel coronavirus,2019 novel coronavirus infection,2019-nCoV,2019-nCoV infection,beta-CoV,beta-CoVs,betacoronavirus,coronavirus disease 2019,SARS-coronavirus 2,SARS-CoV-2,severe acute respiratory syndrome coronavirus 2,severe acute respiratory syndrome coronavirus 2 infectious disease,β-coronavirus,β-CoV,β-CoVs,COVID-19,cOVID-19

Group 0 name Corresponds to the control (unexposed) group for case-control studies: COVID-19 negative controls

Group 1 name Corresponds to the case (exposed) group for case-control studies: COVID-19 positive patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Patients who were confirmed PCR positive for SARS-CoV-2

Group 0 sample size Number of subjects in the control (unexposed) group: 20

Group 1 sample size Number of subjects in the case (exposed) group: 79

Lab analysis

Sequencing type: WMS

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: Not specified

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: relative abundances

Statistical test: Fisher's Exact Test

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.05

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: No

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa: unchanged

Richness Number of species: unchanged

Signature 1

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Curated date: 2021/08/06

Curator: Claregrieve1

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Source: Table S5

Description: Differential microbial abundance between COVID-19 patients and non-COVID-19 patients

Abundance in Group 1: increased abundance in COVID-19 positive patients

NCBI	Quality Control	Links
Serratia
Veillonella

Revision editor(s): Claregrieve1

Experiment 2

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Curated date: 2021/08/06

Curator: Claregrieve1

Revision editor(s): Atrayees, WikiWorks, Claregrieve1

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: COVID-19 positive patients without breathing assistance

Group 1 name Corresponds to the case (exposed) group for case-control studies: COVID-19 positive patients with breathing assistance

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Patients who were confirmed PCR positive for SARS-CoV-2 and had treatment with oxygen mask, non-rebreather mask, nasal cannula, BiPAP, CPAP, or ventilator

Group 0 sample size Number of subjects in the control (unexposed) group: 67

Group 1 sample size Number of subjects in the case (exposed) group: 12

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa: unchanged

Richness Number of species: unchanged

Signature 1

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Reviewed Marked as Reviewed by Atrayees on 2023-7-27

Curated date: 2021/08/06

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Source: Table S5

Description: Differential microbial abundance between COVID-19 patients who had breathing assistance and those who did not

Abundance in Group 1: increased abundance in COVID-19 positive patients with breathing assistance

NCBI	Quality Control	Links
Enterobacter
Prevotella
Veillonella
Streptococcus
Rothia
Serratia

Revision editor(s): Claregrieve1

Experiment 3

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Reviewed Marked as Reviewed by Atrayees on 2023-7-27

Curated date: 2023/07/27

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: COVID-19 positive patients without antibiotic use

Group 1 name Corresponds to the case (exposed) group for case-control studies: COVID-19 positive patients with antibiotic use

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: COVID-19 positive patients with antibiotic use

Group 0 sample size Number of subjects in the control (unexposed) group: 81

Group 1 sample size Number of subjects in the case (exposed) group: 27

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa: unchanged

Richness Number of species: unchanged

Signature 1

Edit History Delete

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Reviewed Marked as Reviewed by Atrayees on 2023-7-27

Curated date: 2023/07/27

Curator: Atrayees

Revision editor(s): Atrayees

Source: Table S5

Description: Differential microbial abundance between COVID-19 patients who used antibiotics and who didn't

Abundance in Group 1: increased abundance in COVID-19 positive patients with antibiotic use

NCBI	Quality Control	Links
Finegoldia
Serratia

Revision editor(s): Atrayees