Analysis of the Conjunctival Microbiome in Patients with Atopic Keratoconjunctivitis and Healthy Individuals/Experiment 1

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Reviewed Marked as Reviewed by Chloe on 2023-6-22

Curated date: 2023/06/21

Curator: Andre

Revision editor(s): Andre, Chloe

Subjects

Location of subjects

South Korea

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

Ocular surface region Eye surface,Eye surface region,Ocular surface,Ocular surface region,ocular surface region

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology

Keratoconjunctivitis Keratoconjunctivitis,keratoconjunctivitis

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

Atopic keratoconjunctivitis (AKC)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Patients diagnosed with Atopic keratoconjunctivitis (AKC) by an ophthalmologist, and with no systemic immune-associated diseases.

Group 0 sample size Number of subjects in the control (unexposed) group

10

Group 1 sample size Number of subjects in the case (exposed) group

20

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)

4 weeks for systemic treatment; 2 weeks for topical treatment

Lab analysis

Sequencing type

16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene

V3-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

Mann-Whitney (Wilcoxon)

Significance threshold p-value or FDR threshold used for differential abundance testing (if any)

0.05

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness

unchanged

Richness Number of species

unchanged

Signature 1

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Reviewed Marked as Reviewed by Chloe on 2023-6-22

Curated date: 2023/06/22

Curator: Andre

Revision editor(s): Andre

Source: Table 2

Description: Relative abundance of genus composition

Abundance in Group 1: increased abundance in Atopic keratoconjunctivitis (AKC)

NCBI	Quality Control	Links
Pseudomonas
Staphylococcus
Haemophilus

Revision editor(s): Andre

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Reviewed Marked as Reviewed by Chloe on 2023-6-22

Curated date: 2023/06/22

Curator: Andre

Revision editor(s): Andre, Chloe

Source: Table 1+ 2

Description: Relative abundance of phylum and genus composition

Abundance in Group 1: decreased abundance in Atopic keratoconjunctivitis (AKC)

NCBI	Quality Control	Links
Ralstonia
Bifidobacterium
Proteus
Parcubacteria group

Revision editor(s): Andre, Chloe

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Needs review

Curated date: 2023/06/23

Curator: Andre

Revision editor(s): Andre

Source: Table 1

Description: Relative abundance of phylum composition

Abundance in Group 1: decreased abundance in Atopic keratoconjunctivitis (AKC)

NCBI	Quality Control	Links
Parcubacteria group

Revision editor(s): Andre