Nasopharyngeal Microbiota in SARS-CoV-2 Positive and Negative Patients

Study information

Reviewed Marked as Reviewed by Chloe on 2021/08/10

study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

34058978

DOI Digital object identifier for electronic documents.

10.1186/s12575-021-00148-6

URI

Authors

Engen PA, Naqib A, Jennings C, Green SJ, Landay A, Keshavarzian A, Voigt RM

Journal

Biological procedures online

Year

2021

Keywords:

COVID-19, Dysbiosis, Microbiota, Nasopharyngeal, SARS-CoV-2

We investigated nasopharyngeal microbial community structure in COVID-19-positive and -negative patients. High-throughput 16S ribosomal RNA gene amplicon sequencing revealed significant microbial community structure differences between COVID-19-positive and -negative patients. This proof-of-concept study demonstrates that: (1) nasopharyngeal microbiome communities can be assessed using collection samples already collected for SARS-CoV-2 testing (viral transport media) and (2) SARS-CoV-2 infection is associated with altered dysbiotic microbial profiles which could be a biomarker for disease progression and prognosis in SARS-CoV-2.

Experiment 1

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Reviewed Marked as Reviewed by Chloe on 2021/08/10

Curated date: 2021/06/17

Curator: Claregrieve1

Revision editor(s): WikiWorks, Chloe, Claregrieve1, Peace Sandy

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 Nasenrachenraum,Epipharynx,Nasal part of pharynx,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 are COVID-19 positive by RT-PCR

Group 0 sample size Number of subjects in the control (unexposed) group: 10

Group 1 sample size Number of subjects in the case (exposed) group: 9

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V4

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).: raw counts

Statistical test: DESeq2

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

Pielou Quantifies how equal the community is numerically: unchanged

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

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

Richness Number of species: unchanged

Signature 1

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Reviewed Marked as Reviewed by Chloe on 2021/08/11

Curated date: 2021/06/17

Curator: Claregrieve1

Revision editor(s): WikiWorks, Chloe, Claregrieve1, Merit

Source: Supplementary Tables 5 & 6

Description: Differential abundance of nasopharyngeal bacteria between COVID-19-positive and COVID-19-negative samples

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

NCBI	Quality Control	Links
Alloprevotella
Anaerococcus
Bacteroidota
Blastococcus
Butyricicoccus
Campylobacter
Capnocytophaga
Chryseobacterium
Finegoldia
Flavobacterium
Gemella
Kocuria
Micrococcus
Moraxella
Peptoniphilus
Porphyromonas
Prevotella
Rothia
Selenomonas
Veillonella
Vibrio
unclassified Bacilli