The closed eye harbours a unique microbiome in dry eye disease/Experiment 1
Subjects
- Location of subjects
- United States of America
- 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
- Tear film Precorneal film,Tear film,tear film
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Dry eye syndrome dry eye,Dry Eye Syndrome,dry eye syndrome,Dry Eye Syndromes,dry eye(s),eye(s), dry,KCS,Keraconjunctivitis sicca,Keratoconjunctivitis Sicca,Keratoconjunctivitis sicca,keratoconjunctivitis sicca,Keratoconjunctivitis sicca (disorder),sicca, keratoconjunctivitis,Tear film insufficiency,tear film insufficiency,Dry eye syndrome
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normal Control (NC)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Dry Eye
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants with moderate or severe dry eye disease
- Group 0 sample size Number of subjects in the control (unexposed) group
- 36
- Group 1 sample size Number of subjects in the case (exposed) group
- 36
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Within 1 month was exclusionary
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
- 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)?
- Yes
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Fig. S5 and Fig. S6.
Description: The acquisition of unique taxa separates the dry from the normal eye at baseline. (b) Linear discriminant analysis of effect size (LEfSe).
Additional unique taxa separate the dry from the normal eye after a month. (b) Linear discriminant analysis of effect size (LEfSe).
Abundance in Group 1: increased abundance in Dry Eye
| NCBI | Quality Control | Links |
|---|---|---|
| unclassified Lactobacillaceae | ||
| Streptococcus | ||
| Calothrix | ||
| Varibaculum | ||
| Rothia | ||
| Haemophilus | ||
| Meiothermus | ||
| Dialister | ||
| Dermacoccus | ||
| Prevotella | ||
| Faecalibacterium | ||
| Agrobacterium |
Revision editor(s): Peace Sandy
Signature 2
Source:
Description: The acquisition of unique taxa separates the dry from the normal eye at baseline. (b) Linear discriminant analysis of effect size (LEfSe).
Additional unique taxa separate the dry from the normal eye after a month. (b) Linear discriminant analysis of effect size (LEfSe).
Abundance in Group 1: decreased abundance in Dry Eye
Revision editor(s): Peace Sandy
