Characterization of the Human Oropharyngeal Microbiomes in SARS-CoV-2 Infection and Recovery Patients

Study information

Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/5

study design

prospective cohort

Citation

PMID PubMed identifier for scientific articles.

34423593

DOI Digital object identifier for electronic documents.

10.1002/advs.202102785

URI

Authors

Gao M, Wang H, Luo H, Sun Y, Wang L, Ding S, Ren H, Gang J, Rao B, Liu S, Wang X, Gao X, Li M, Zou Y, Liu C, Yuan C, Sun J, Cui G, Ren Z

Journal

Advanced science (Weinheim, Baden-Wurttemberg, Germany)

Year

2021

Keywords:

COVID-19, SARS-CoV-2, noninvasive biomarkers, oropharyngeal microbiome

Respiratory tract microbiome is closely related to respiratory tract infections, while characterization of oropharyngeal microbiome in recovered coronavirus disease 2019 (COVID-19) patients is not studied. Herein, oropharyngeal swabs are collected from confirmed cases (CCs) with COVID-19 (73 subjects), suspected cases (SCs) (36), confirmed cases who recovered (21), suspected cases who recovered (36), and healthy controls (Hs) (140) and then completed MiSeq sequencing. Oropharyngeal microbial α-diversity is markedly reduced in CCs versus Hs. Opportunistic pathogens are increased, while butyrate-producing genera are decreased in CCs versus Hs. The classifier based on eight optimal microbial markers is constructed through a random forest model and reached great diagnostic efficacy in both discovery and validation cohorts. Notably, the classifier successfully diagnosed SCs with positive IgG antibody as CCs and is demonstrated from the perspective of the microbiome. Importantly, several genera with significant differences gradually increase and decrease along with recovery from COVID-19. Forty-four oropharyngeal operational taxonomy units (OTUs) are closely correlated with 11 clinical indicators of SARS-CoV-2 infection and Hs based on Spearman correlation analysis. Together, this research is the first to characterize oropharyngeal microbiota in recovered COVID-19 cases and suspected cases, to successfully construct and validate the diagnostic model for COVID-19 and to depict the correlations between microbial OTUs and clinical indicators.

Experiment 1

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Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/5

Curated date: 2021/09/28

Curator: Claregrieve1

Revision editor(s): Claregrieve1, WikiWorks, Victoria

Subjects

Location of subjects: China

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: Oropharynx Mesopharynx,Oral part of pharynx,Pars oralis pharyngis,Oropharynx,oropharynx

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: Healthy controls

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Confirmed COVID-19 cases by RT-PCR

Group 0 sample size Number of subjects in the control (unexposed) group: 48

Group 1 sample size Number of subjects in the case (exposed) group: 94

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V3-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).: relative abundances

Statistical test: LEfSe

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

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 2.5

Matched on Factors on which subjects have been matched on in a case-control study: age, body mass index, sex

Alpha Diversity

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

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

Signature 1

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Curated date: 2021/09/28

Curator: Claregrieve1

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Source: Figure 3b, 3d

Description: Differential microbial abundance between COVID-19 cases and healthy controls

Abundance in Group 1: increased abundance in COVID-19 cases

NCBI	Quality Control	Links
Halomonas
Granulicatella
Leptotrichia
Streptococcus
unclassified Bacteria
Bacillota

Revision editor(s): Claregrieve1

Signature 2

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Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/5

Curated date: 2021/09/28

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Figure 3b, 3d

Description: Differential microbial abundance between COVID-19 cases and healthy controls

Abundance in Group 1: decreased abundance in COVID-19 cases

NCBI	Quality Control	Links
Bacteroidota
Pseudomonadota
Patescibacteria group
Campylobacterota
Spirochaetota
Desulfobacterales
Synergistota
Deferribacteres
Verrucomicrobiota
Neisseria
Prevotella
Alloprevotella
Fusobacterium
Haemophilus

Revision editor(s): Claregrieve1