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

From BugSigDB
Reviewed Marked as Reviewed by Atrayees on 2023-7-27
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
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


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

Curated date: 2021/08/06

Curator: Claregrieve1

Revision editor(s): Claregrieve1, WikiWorks, Atrayees

Subjects

Location of subjects
United States of America
Host species Species from which microbiome was sampled (if applicable)
Homo sapiens
Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Nasopharynx Nasenrachenraum,Epipharynx,Nasal part of pharynx,Pars nasalis pharyngis,Rhinopharynx,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
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
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

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

Curated date: 2021/08/06

Curator: Claregrieve1

Revision editor(s): Claregrieve1

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 ControlLinks
Serratia
Veillonella

Revision editor(s): Claregrieve1

Experiment 2


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

Curated date: 2021/08/06

Curator: Claregrieve1

Revision editor(s): Claregrieve1, WikiWorks, Atrayees

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

Lab analysis

Statistical Analysis

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

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

Curated date: 2021/08/06

Curator: Claregrieve1

Revision editor(s): Claregrieve1

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 ControlLinks
Enterobacter
Prevotella
Veillonella
Streptococcus
Rothia
Serratia

Revision editor(s): Claregrieve1

Experiment 3


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

Curated date: 2023/07/27

Curator: Atrayees

Revision editor(s): Atrayees

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

Lab analysis

Statistical Analysis

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

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 ControlLinks
Finegoldia
Serratia

Revision editor(s): Atrayees