The difference of oropharyngeal microbiome during acute respiratory viral infections in infants and children
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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.
Authors
Wu Z, Jiang M, Jia M, Sang J, Wang Q, Xu Y, Qi L, Yang W, Feng L
Journal
Communications biology
Year
2025
Acute respiratory infections (ARI) with multiple types of viruses are common in infants and children. This study was conducted to assess the difference of oropharyngeal microbiome during acute respiratory viral infection using whole-genome shotgun metagenomic sequencing. The overall taxonomic alpha diversity did not differ by the types of infected virus. The beta diversity differed by disease severity, disease-related symptoms, and types of infected virus. Nine species had significantly higher abundance in outpatients than in inpatients, with five of them in the genus Achromobacter. Three microbial community types were identified. The prevalence of community type (CT) 1 was higher among patients with influenza virus, enterovirus, and human adenvirus; CT2 was higher among patients with human metapneumovirus; and CT3 was higher among patients with respiratory syncytial virus and human adenvirus infections. Our results suggest that the oropharyngeal microbiome is associated with ARI disease severity, disease-related symptoms, and the types of infected virus.
Experiment 1
Reviewed Marked as Reviewed by KateRasheed on 2025-6-13
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
- Respiratory tract infectious disease infection, respiratory tract,infections, respiratory,infections, respiratory tract,infections, upper respiratory,infections, upper respiratory tract,respiratory infection, upper,respiratory infections,respiratory tract infection,upper respiratory infections,upper respiratory tract infections,Respiratory tract infectious disease,respiratory tract infectious disease
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Inpatients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Outpatients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Children with Acute respiratory infections (ARI) who visited the hospital but did not require hospitalization.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 49
- Group 1 sample size Number of subjects in the case (exposed) group
- 60
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
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
Alpha Diversity
- 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 KateRasheed on 2025-6-13
Source: Fig. 2F and G
Description: LDA score and relative abundance of 15 significantly different taxa calculated by LEfSe analysis.
Abundance in Group 1: increased abundance in Outpatients
Revision editor(s): Shulamite
Experiment 2
Reviewed Marked as Reviewed by KateRasheed on 2025-6-13
Differences from previous experiment shown
Subjects
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Children with ARI who visited the hospital but did not require hospitalization.
Lab analysis
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
Alpha Diversity
- 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 KateRasheed on 2025-6-13
Source: Table S3
Description: Two-fold changes of microbial abundances between inpatients and outpatients.
Abundance in Group 1: increased abundance in Outpatients
Revision editor(s): Shulamite
Experiment 3
Reviewed Marked as Reviewed by KateRasheed on 2025-6-13
Curated date: 2025/05/04
Curator: Shulamite
Revision editor(s): Shulamite, Anne-mariesharp, KateRasheed
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Fatigue Fatigue,Tired,Tiredness,fatigue
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-fatigue
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Fatigue
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Children who exhibited fatigue as part of their clinical presentation of ARI.
- Group 0 sample size Number of subjects in the control (unexposed) group
- Not specified
- Group 1 sample size Number of subjects in the case (exposed) group
- Not specified
Lab analysis
Statistical Analysis
- Statistical test
- LEfSe
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by KateRasheed on 2025-6-13
Source: Table S4
Description: Differences of taxonomic relative abundance between disease-related symptom groups by LEfSe analysis.
Abundance in Group 1: increased abundance in Fatigue
| NCBI | Quality Control | Links |
|---|---|---|
| Moraxella catarrhalis | ||
| Porphyromonas catoniae | ||
| GGB12794GGB12794 | ||
| GGB12794_SGB19881GGB12794_SGB19881 | ||
| Lactococcus | ||
| Lactococcus lactis |
Revision editor(s): Shulamite, Anne-mariesharp
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