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

Authors

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

Journal

Virologica Sinica

Year

2021

Keywords:

ACE2, COVID-19, Campylobacter, Metagenome sequencing, Prevotella, Streptococcus

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

Edit History Delete

Flag for review

Your review change was submittedDuplicate this Experiment Add a new Signature

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

Curated date: 2021/07/03

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: 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 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

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: MGISEQ-2000

Statistical Analysis

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

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

Edit History Delete

Flag for review

Your review change was submitted

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

Curated date: 2021/07/03

Curator: Claregrieve1

Revision editor(s): Claregrieve1

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	Quality Control	Links
Streptococcus sp. A12
Streptococcus agalactiae
Streptococcus suis
Campylobacter jejuni
Xylanibacter ruminicola
Prevotella sp.

Revision editor(s): Claregrieve1

Experiment 2

Edit History Delete

Flag for review

Your review change was submittedDuplicate this Experiment Add a new Signature

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

Curated date: 2021/07/03

Curator: Claregrieve1

Revision editor(s): Claregrieve1, WikiWorks, Victoria

Differences from previous experiment shown

Subjects

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

Group 0 sample size Number of subjects in the control (unexposed) group: 7

Lab analysis

Statistical Analysis

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

Signature 1

Edit History Delete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2023/04/09

Curator: Aiyshaaaa

Revision editor(s): Aiyshaaaa

Source: Figure 3

Description: Analysis of species with differential abundance among the COVID-19 and healthy cohorts.

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

NCBI	Quality Control	Links
Aerococcus sanguinicola
Campylobacter concisus
Campylobacter showae
Clostridium botulinum
Fusobacterium pseudoperiodonticum
Haemophilus parainfluenzae
Lachnoanaerobaculum umeaense
Leptotrichia wadei
Porphyromonas gingivalis
Prevotella denticola
Prevotella intermedia
Prevotella jejuni
Prevotella melaninogenica
Segatella oris
Rothia mucilaginosa
Streptococcus australis
Streptococcus gordonii
Streptococcus koreensis
Streptococcus mitis
Streptococcus parasanguinis
Streptococcus pneumoniae
Streptococcus salivarius
Streptococcus sanguinis
Streptococcus suis
Streptococcus thermophilus
Streptococcus uberis
Veillonella atypica
Veillonella dispar
Veillonella parvula
Veillonella rodentium

Revision editor(s): Aiyshaaaa

Experiment 3

Edit History Delete

Flag for review

Your review change was submittedDuplicate this Experiment Add a new Signature

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

Curated date: 2021/07/03

Curator: Claregrieve1

Revision editor(s): Claregrieve1, WikiWorks, Victoria

Differences from previous experiment shown

Subjects

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

Lab analysis

Statistical Analysis

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

Edit History Delete

Mark reviewed

Your review change was submittedDuplicate this Experiment Add a new Signature

Needs review

Curated date: 2021/07/03

Curator: Claregrieve1

Revision editor(s): Claregrieve1, WikiWorks, Victoria

Differences from previous experiment shown

Subjects

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

Lab analysis

Statistical Analysis

Statistical test: LEfSe

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

Edit History Delete

Flag for review

Your review change was submitted

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

Curated date: 2021/07/03

Curator: Claregrieve1

Revision editor(s): Claregrieve1

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	Quality Control	Links
Streptococcus sp. A12
Lachnospira eligens ATCC 27750
Aerococcus sanguinicola
Campylobacter jejuni
Lachnoanaerobaculum umeaense
Porphyromonas gingivalis
Campylobacter concisus
Streptococcus ilei
Xylanibacter 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
Segatella 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