The respiratory microbiome is linked to the severity of RSV infections and the persistence of symptoms in children
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
Subjects
- Location of subjects
- Belgium
- Finland
- Netherlands
- Spain
- United Kingdom
- 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 Epipharynx,Nasal part of pharynx,Nasenrachenraum,Pars nasalis pharyngis,Rhinopharynx,Nasopharynx,nasopharynx
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Respiratory Syncytial Virus Infection Human respiratory syncytial virus infection,infections, Human respiratory syncytial virus,respiratory syncytial virus infection,respiratory syncytial virus infectious disease,Respiratory Syncytial Virus Infection,respiratory Syncytial Virus Infection
- 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
- RSV (Respiratory Syncytial Virus) Infection
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Infants with RSV (Respiratory Syncytial Virus) infection during the first year of life.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 52
- Group 1 sample size Number of subjects in the case (exposed) group
- 257
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- 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
- MaAsLin2
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, Confounders controlled for: "gender" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.gender, Confounders controlled for: "study site" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.study site
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- decreased
Signature 1
Source: Fig 2E-F
Description: Taxonomic differences of nasopharyngeal microbiota in infants with RSV infection versus healthy controls.
Abundance in Group 1: increased abundance in RSV (Respiratory Syncytial Virus) Infection
| NCBI | Quality Control | Links |
|---|---|---|
| Haemophilus | ||
| Moraxella |
Revision editor(s): AmyUchay, PreciousChijioke
Signature 2
Source: Fig 2E-F
Description: Taxonomic differences of nasopharyngeal microbiota in infants with RSV infection versus healthy controls.
Abundance in Group 1: decreased abundance in RSV (Respiratory Syncytial Virus) Infection
| NCBI | Quality Control | Links |
|---|---|---|
| Corynebacterium | ||
| Dolosigranulum |
Revision editor(s): AmyUchay, PreciousChijioke
Experiment 2
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- RSV (Respiratory Syncytial Virus) Convalescence
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Infants with RSV (Respiratory Syncytial Virus) Convalescence during the first year of life.
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- Not specified
Signature 1
Source: Fig 2E - 2F
Description: Taxonomic differences of nasopharyngeal microbiota in infants with RSV infection versus healthy controls.
Abundance in Group 1: increased abundance in RSV (Respiratory Syncytial Virus) Convalescence
| NCBI | Quality Control | Links |
|---|---|---|
| Moraxella |
Revision editor(s): PreciousChijioke
Signature 2
Source: Fig 2E - 2F
Description: Taxonomic differences of nasopharyngeal microbiota in infants with RSV infection versus healthy controls.
Abundance in Group 1: decreased abundance in RSV (Respiratory Syncytial Virus) Convalescence
| NCBI | Quality Control | Links |
|---|---|---|
| Corynebacterium |
Revision editor(s): PreciousChijioke
Experiment 3
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mild RSV (Respiratory Syncytial Virus) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Infants with Mild RSV (Respiratory Syncytial Virus) during the first year of life.
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Not specified
Signature 1
Source: Fig 3E - 3F
Description: Associations between microbiota diversity, stability and composition, and RSV infection severity
Abundance in Group 1: increased abundance in Mild RSV (Respiratory Syncytial Virus) group
| NCBI | Quality Control | Links |
|---|---|---|
| Moraxella |
Revision editor(s): AmyUchay, PreciousChijioke
Signature 2
Source: Fig 3E - 3F
Description: Associations between microbiota diversity, stability and composition, and RSV infection severity.
Abundance in Group 1: decreased abundance in Mild RSV (Respiratory Syncytial Virus) group
| NCBI | Quality Control | Links |
|---|---|---|
| Corynebacterium |
Revision editor(s): AmyUchay, PreciousChijioke
Experiment 4
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Moderate RSV (Respiratory Syncytial Virus) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Infants with Moderate RSV (Respiratory Syncytial Virus) during the first year of life.
Lab analysis
Statistical Analysis
Signature 1
Source: Fig 3E - 3F
Description: Associations between microbiota diversity, stability and composition, and RSV infection severity
Abundance in Group 1: increased abundance in Moderate RSV (Respiratory Syncytial Virus) group
| NCBI | Quality Control | Links |
|---|---|---|
| Haemophilus | ||
| Moraxella |
Revision editor(s): PreciousChijioke
Signature 2
Source: Fig 3E - 3F
Description: Associations between microbiota diversity, stability and composition, and RSV infection severity
Abundance in Group 1: decreased abundance in Moderate RSV (Respiratory Syncytial Virus) group
| NCBI | Quality Control | Links |
|---|---|---|
| Corynebacterium | ||
| Dolosigranulum | ||
| Dolosigranulum pigrum |
Revision editor(s): PreciousChijioke
Experiment 5
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Severe RSV (Respiratory Syncytial Virus) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Infants with Severe RSV (Respiratory Syncytial Virus) during the first year of life.
Lab analysis
Statistical Analysis
Signature 1
Source: Fig 3E - 3F
Description: Associations between microbiota diversity, stability and composition, and RSV infection severity.
Abundance in Group 1: increased abundance in Severe RSV (Respiratory Syncytial Virus) group
| NCBI | Quality Control | Links |
|---|---|---|
| Haemophilus | ||
| Streptococcus | ||
| Porphyromonas |
Revision editor(s): PreciousChijioke
Signature 2
Source: Fig 3E - 3F
Description: Associations between microbiota diversity, stability and composition, and RSV infection severity.
Abundance in Group 1: decreased abundance in Severe RSV (Respiratory Syncytial Virus) group
| NCBI | Quality Control | Links |
|---|---|---|
| Corynebacterium | ||
| Dolosigranulum | ||
| Dolosigranulum pigrum |
Revision editor(s): PreciousChijioke
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- No (symptoms)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Blocked/runny nose
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Infants with Blocked/runny nose during the first year of life.
Lab analysis
Statistical Analysis
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Signature 1
Source: Fig 4A - 4B
Description: Associations between microbiota profiles at RSV convalescence and remaining symptoms.
Abundance in Group 1: increased abundance in Blocked/runny nose
| NCBI | Quality Control | Links |
|---|---|---|
| Haemophilus |
Revision editor(s): PreciousChijioke
Signature 2
Source: Fig 4A - 4B
Description: Associations between microbiota profiles at RSV convalescence and remaining symptoms.
Abundance in Group 1: decreased abundance in Blocked/runny nose
| NCBI | Quality Control | Links |
|---|---|---|
| Dolosigranulum | ||
| Dolosigranulum pigrum |
Revision editor(s): PreciousChijioke
Experiment 7
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Any (symptoms)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Infants with Any (symptoms) during the first year of life.
Lab analysis
Statistical Analysis
Signature 1
Source: Fig 4A - 4B
Description: Associations between microbiota profiles at RSV convalescence and remaining symptoms.
Abundance in Group 1: increased abundance in Any (symptoms)
| NCBI | Quality Control | Links |
|---|---|---|
| Haemophilus |
Revision editor(s): PreciousChijioke
