The Influence of Age and Sex on Ocular Surface Microbiota in Healthy Adults
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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
- 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
- Bulbar conjunctiva Ocular conjunctiva,Bulbar conjunctiva,bulbar conjunctiva
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Age at assessment Age at assessment,age at assessment
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Young
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Old
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Aged 47-84 years old
- Group 0 sample size Number of subjects in the control (unexposed) group
- 48
- Group 1 sample size Number of subjects in the case (exposed) group
- 42
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- No history of antibiotics in the past 6 months
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
- 3
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Figure 6
Description: FIGURE 6. The bacterial species with significant differences in relative abundance between old and young groups. The LefSe program is used to find the bacterial species that specifically distinguish the old (green) from young (red) conjunctival microbiomes (LDA score > 3).
Abundance in Group 1: increased abundance in Old
Revision editor(s): Mary Bearkland, Peace Sandy
Signature 2
Source: Figure 6
Description: FIGURE 6. The bacterial species with significant differences in relative abundance between old and young groups. The LefSe program is used to find the bacterial species that specifically distinguish the old (green) from young (red) conjunctival microbiomes (LDA score > 3).
Abundance in Group 1: decreased abundance in Old
Revision editor(s): Mary Bearkland
Experiment 2
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Biological sex Biological sex,biological sex
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Male
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Female
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Biological sex=female
- Group 0 sample size Number of subjects in the control (unexposed) group
- 42
- Group 1 sample size Number of subjects in the case (exposed) group
- 48
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Figure 4a
Description: FIGURE 4. Sex-differences in conjunctival microbiome of healthy adults. Male and female groups,... while no significant difference is observed in Shannon diversity index (A). (Note- no taxon were found to be decreased in females compared to males)
Abundance in Group 1: increased abundance in Female
| NCBI | Quality Control | Links |
|---|---|---|
| Escherichia coli | ||
| Micrococcus luteus | ||
| [Acidovorax] ebreus | ||
| Staphylococcus haemolyticus | ||
| Acinetobacter baumannii |
Revision editor(s): Mary Bearkland, Peace Sandy
Signature 2
Source: Figure 4a
Description: FIGURE 4. Sex-differences in conjunctival microbiome of healthy adults. Male and female groups,... while no significant difference is observed in Shannon diversity index (A). (Note- no taxon were found to be increased in females compared to males)
Abundance in Group 1: decreased abundance in Female
| NCBI | Quality Control | Links |
|---|---|---|
| Cutibacterium acnes | ||
| Staphylococcus epidermidis |
Revision editor(s): Mary Bearkland, Peace Sandy
