Enriched Opportunistic Pathogens Revealed by Metagenomic Sequencing Hint Potential Linkages between Pharyngeal Microbiota and COVID-19
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
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
Reviewed Marked as Reviewed by Fatima on 2022/05/17
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
Reviewed Marked as Reviewed by Fatima on 2022/05/17
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 | ||
| Prevotella ruminicola | ||
| Prevotella sp. |
Revision editor(s): Claregrieve1
Experiment 2
Reviewed Marked as Reviewed by Fatima on 2022/05/17
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
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
Revision editor(s): Aiyshaaaa
Experiment 3
Reviewed Marked as Reviewed by Fatima on 2022/05/17
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
Needs review
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
Reviewed Marked as Reviewed by Fatima on 2022/05/17
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
Revision editor(s): Claregrieve1
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