Enriched Opportunistic Pathogens Revealed by Metagenomic Sequencing Hint Potential Linkages between Pharyngeal Microbiota and COVID-19

Study information

Reviewed Marked as Reviewed by Fatima on 2022/05/17

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

33978940

DOI Digital object identifier for electronic documents.

10.1007/s12250-021-00391-x

URI Uniform resource identifier for web resources.

Authors

Xiong D, Muema C, Zhang X, Pan X, Xiong J, Yang H, Yu J, Wei H

Journal

Virologica Sinica

Year

2021

As a respiratory tract virus, SARS-CoV-2 infected people through contacting with the upper respiratory tract first. Previous studies indicated that microbiota could modulate immune response against pathogen infection. In the present study, we performed metagenomic sequencing of pharyngeal swabs from eleven patients with COVID-19 and eleven Non-COVID-19 patients who had similar symptoms such as fever and cough. Through metagenomic analysis of the above two groups and a healthy group from the public data, there are 6502 species identified in the samples. Specifically, the Pielou index indicated a lower evenness of the microbiota in the COVID-19 group than that in the Non-COVID-19 group. Combined with the linear discriminant analysis (LDA) and the generalized linear model, eighty-one bacterial species were found with increased abundance in the COVID-19 group, where 51 species were enriched more than 8 folds. The top three enriched genera were Streptococcus, Prevotella and Campylobacter containing some opportunistic pathogens. More interestingly, through experiments, we found that two Streptococcus strains, S. suis and S. agalactiae, could stimulate the expression of ACE2 of Vero cells in vitro, which may promote SARS-CoV-2 infection. Therefore, these enriched pathogens in the pharynxes of COVID-19 patients may involve in the virus-host interactions to affect SARS-CoV-2 infection and cause potential secondary bacterial infections through changing the expression of the viral receptor ACE2 and/or modulate the host's immune system.

Experiment 1

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Reviewed Marked as Reviewed by Fatima on 2022/05/17

Curated date: 2021/07/03

Curator: Claregrieve1

Revision editor(s): Claregrieve1, WikiWorks

Subjects

Location of subjects: China

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 patients with fever and cough
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: COVID-19 positive patients with fever and cough symptoms
Group 0 sample size Number of subjects in the control (unexposed) group: 11
Group 1 sample size Number of subjects in the case (exposed) group: 11

Lab analysis

Sequencing type: WMS

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: MGISEQ-2000

Statistical Analysis

Statistical test: ANOVA

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

Signature 1

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Source: Figure S2

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	Links
Streptococcus sp. A12
Streptococcus agalactiae
Streptococcus suis
Campylobacter jejuni
Prevotella ruminicola
Prevotella sp.

Revision editor(s): Claregrieve1

Experiment 2

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Curated date: 2021/07/03

Curator: Claregrieve1

Revision editor(s): WikiWorks753, Claregrieve1

Subjects

Location of subjects: China

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: Healthy 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: COVID-19 positive patients with fever and cough symptoms
Group 0 sample size Number of subjects in the control (unexposed) group: 7
Group 1 sample size Number of subjects in the case (exposed) group: 11

Lab analysis

Sequencing type: WMS

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: MGISEQ-2000

Statistical Analysis

Statistical test: ANOVA

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

Experiment 3

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Curated date: 2021/07/03

Curator: Claregrieve1

Revision editor(s): WikiWorks753, Claregrieve1

Subjects

Location of subjects: China

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: Healthy controls
Group 1 name Corresponds to the case (exposed) group for case-control studies: COVID-19 negative patients with fever and cough
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: COVID-19 negative patients with fever and cough
Group 0 sample size Number of subjects in the control (unexposed) group: 7
Group 1 sample size Number of subjects in the case (exposed) group: 11

Lab analysis

Sequencing type: WMS

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: MGISEQ-2000

Statistical Analysis

Statistical test: ANOVA

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

Experiment 4

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Needs review

Curated date: 2021/07/03

Curator: Claregrieve1

Revision editor(s): Claregrieve1, WikiWorks

Subjects

Location of subjects: China

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 patients with fever and cough
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: COVID-19 positive patients with fever and cough symptoms
Group 0 sample size Number of subjects in the control (unexposed) group: 11
Group 1 sample size Number of subjects in the case (exposed) group: 11

Lab analysis

Sequencing type: WMS

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: MGISEQ-2000

Statistical Analysis

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

Alpha Diversity

Pielou Quantifies how equal the community is numerically: decreased
Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged
Richness Number of species: unchanged

Signature 1

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Curated date: 2021/07/03

Curator: Claregrieve1

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Source: Supplemental Table S5

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

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

NCBI	Links
Streptococcus sp. A12
[Eubacterium] eligens ATCC 27750
Aerococcus sanguinicola
Campylobacter jejuni
Lachnoanaerobaculum umeaense
Porphyromonas gingivalis
Campylobacter concisus
Streptococcus ilei
Prevotella ruminicola 23
Streptococcus australis
Gemella haemolysans
Prevotella sp. oral taxon 299 str. F0039
Veillonella atypica
Fusobacterium pseudoperiodonticum
Campylobacter showae
Erysipelothrix sp. HDW6B
Treponema phagedenis
Capnocytophaga sputigena
Streptococcus troglodytae
Erysipelothrix larvae
Streptococcus sp. HSISM1
Streptococcus suis
Streptococcus ilei
Streptococcus parasanguinis
Veillonella parvula
Vagococcus teuberi
Streptococcus koreensis
Streptococcus ruminicola
Treponema brennaborense DSM 12168
Bergeyella cardium
Prevotella denticola F0289
Streptococcus sanguinis
Chryseobacterium camelliae ⚠
Brochothrix thermosphacta ⚠
Porphyromonas cangingivalis
Streptococcus marmotae
Streptococcus salivarius JIM8777
Streptococcus thermophilus
Carnobacterium divergens
Fermentimonas caenicola
Prevotella oris
Carnobacterium maltaromaticum
Streptococcus cristatus
Lachnoclostridium phytofermentans ISDg
Leptotrichia sp. oral taxon 212
Porphyromonas asaccharolytica DSM 20707
Bacteroides heparinolyticus
Campylobacter ureolyticus RIGS 9880
Streptococcus uberis
Streptococcus agalactiae

Revision editor(s): Claregrieve1