The conjunctival microbiome in health and trachomatous disease: a case control study
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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
- Gambia
- 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
- Conjunctiva Conjunctivae,Conjunctivas,Tunica conjunctiva,Wall of conjunctival sac,Conjunctiva
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Chlamydia trachomatis Chlamydozoon trachomatis,Rickettsia trachomae,Rickettsia trachomatis,Chlamydia trachomatis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Controls aged <= 10 years
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Controls aged > 10 years
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Control individuals with normal conjunctiva (F0P0C0 - 1981 WHO trachoma grading system) and age > 10 years old.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 21
- Group 1 sample size Number of subjects in the case (exposed) group
- 84
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- not mentioned
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V3
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
Statistical Analysis
- Statistical test
- Metastats
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.1
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- Matched on Factors on which subjects have been matched on in a case-control study
- age, ethnic group, geographic area, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Source: Table 2
Description: Changes in taxa abundance between control individuals aged <= 10 years and > 10 years
Abundance in Group 1: increased abundance in Controls aged > 10 years
NCBI | Quality Control | Links |
---|---|---|
Corynebacterium | ||
Paracoccus | ||
Propionibacterium | ||
Myceligenerans | ||
Promicromonosporaceae | ||
Actinomycetales |
Revision editor(s): Andre
Signature 2
Source: Table 2
Description: Changes in taxa abundance between control individuals aged <= 10 years and > 10 years
Abundance in Group 1: decreased abundance in Controls aged > 10 years
NCBI | Quality Control | Links |
---|---|---|
Streptococcus | ||
Kocuria | ||
Staphylococcus | ||
Micrococcus | ||
Brachybacterium |
Revision editor(s): Andre
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Controls aged > 10 years with samples collected in the wet season
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Controls aged > 10 years with samples collected in the dry season
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Control individuals with normal conjunctiva (F0P0C0 - 1981 WHO trachoma grading system) and age > 10 years old with samples collected during the dry season. Of note, all samples from participants <= 10 years old were collected during the wet season, therefore, were not included in the analysis of the seasonal effect on the conjunctival microbiome.
- Group 1 sample size Number of subjects in the case (exposed) group
- 63
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- ethnic group, geographic area, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Richness Number of species
- increased
Signature 1
Source: Table 2
Description: Difference in taxa abundance between normal conjunctiva in wet season and normal conjunctiva in dry season
Abundance in Group 1: increased abundance in Controls aged > 10 years with samples collected in the dry season
NCBI | Quality Control | Links |
---|---|---|
Bacillus | ||
Tumebacillus |
Revision editor(s): Andre
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Controls aged <= 10 years
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Cases aged <= 10 years
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Children (age <= 10 years old) with follicles (F>0) or papillae (1 case of F0P3C0). Of note, all samples in children were collected in the wet season.
- Group 1 sample size Number of subjects in the case (exposed) group
- 29
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Not mentioned
Lab analysis
Statistical Analysis
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Not specified
- Matched on Factors on which subjects have been matched on in a case-control study
- geographic area, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Controls aged > 10 years with samples collected during the dry season
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Cases aged > 10 years with samples collected during the dry season
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants aged > 10 years with clinical signs of conjunctival scarring (Cicatricae > 0 with or without trachomatous trichiasis (TT))
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Table 2
Description: Changes in taxa abundance between groups
Abundance in Group 1: increased abundance in Cases aged > 10 years with samples collected during the dry season
NCBI | Quality Control | Links |
---|---|---|
Corynebacterium | ||
Streptococcus |
Revision editor(s): Andre
Signature 2
Source: Table 2
Description: Changes in taxa abundance between groups
Abundance in Group 1: decreased abundance in Cases aged > 10 years with samples collected during the dry season
NCBI | Quality Control | Links |
---|---|---|
Globicatella |
Revision editor(s): Andre
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Controls aged > 10 years with samples collected during the wet season
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Cases aged > 10 years with samples collected during the wet season
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Cases with conjunctival scarring (C>0) alone, with samples collected in the dry season
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Cases with conjunctival scarring (C>0) and trachomatous trichiasis (TT),with samples collected in the dry season
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants aged >10 years with clinical signs of conjunctival scarring (Cicatricae > 0) and with trachomatous trichiasis (TT))
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- unchanged
Signature 1
Source: Table 2
Description: Changes in taxa abundance between groups
Abundance in Group 1: increased abundance in Cases with conjunctival scarring (C>0) and trachomatous trichiasis (TT),with samples collected in the dry season
NCBI | Quality Control | Links |
---|---|---|
Corynebacterium | ||
Kocuria |
Revision editor(s): Andre
Signature 2
Source: Table 2
Description: Changes in taxa abundance between groups
Abundance in Group 1: decreased abundance in Cases with conjunctival scarring (C>0) and trachomatous trichiasis (TT),with samples collected in the dry season
NCBI | Quality Control | Links |
---|---|---|
Myceligenerans | ||
Promicromonosporaceae | ||
Actinomycetales | ||
Paracoccus |
Revision editor(s): Andre
Experiment 7
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Cases with conjunctival scarring (C>0) alone, with samples collected in the wet season
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Cases with conjunctival scarring (C>0) and trachomatous trichiasis (TT),with samples collected in the wet season
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged