The Influence of Age and Sex on Ocular Surface Microbiota in Healthy Adults

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Reviewed Marked as Reviewed by Peace Sandy on 2024-1-26

Curated date: 2023/09/10

Curator: Mary Bearkland

Revision editor(s): WikiWorks, Mary Bearkland, Peace Sandy, MyleeeA

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): 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

Reviewed Marked as Reviewed by Peace Sandy on 2024-1-26

Curated date: 2023/09/10

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland, Peace Sandy, WikiWorks

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

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Anaerococcus prevotii
Corynebacterium aurimucosum
Corynebacterium jeikeium
Corynebacterium resistens
Corynebacterium urealyticum
Cutibacterium avidum
Deinococcus radiodurans
Escherichia coli
Finegoldia magna
Leptotrichia buccalis
Micrococcus luteus
Neisseria gonorrhoeae
Neisseria lactamica
Prevotella melaninogenica
Rothia dentocariosa
Rothia mucilaginosa
Rubrivivax gelatinosus
Staphylococcus haemolyticus
Staphylococcus lugdunensis
Staphylococcus warneri
Streptococcus gordonii
Streptococcus oralis
Streptococcus parasanguinis
Streptococcus pneumoniae
Streptococcus pseudopneumoniae
Streptococcus sanguinis
Streptococcus sp.
Wolbachia pipientis wVitA
Wolbachia sp.

Revision editor(s): Mary Bearkland, Peace Sandy, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Peace Sandy on 2024-1-26

Curated date: 2023/09/10

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland, WikiWorks

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

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Mycoplasmopsis pulmonis
Lactobacillus crispatus
Chlorobium phaeobacteroides
Listeria monocytogenes
Enterococcus faecalis
Brachyspira murdochii
Candidatus Karelsulcia
Mycoplasmopsis bovis
Pseudomonas aeruginosa
Brucella anthropi
Mesomycoplasma hyorhinis
Cutibacterium acnes

Revision editor(s): Mary Bearkland, WikiWorks

Experiment 2

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Peace Sandy on 2024-1-26

Curated date: 2023/09/24

Curator: Mary Bearkland

Revision editor(s): WikiWorks, Mary Bearkland, Peace Sandy, MyleeeA

Differences from previous experiment shown

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

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Peace Sandy on 2024-1-26

Curated date: 2023/09/24

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland, Peace Sandy, WikiWorks

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

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Escherichia coli
Micrococcus luteus
[Acidovorax] ebreus
Staphylococcus haemolyticus
Acinetobacter baumannii

Revision editor(s): Mary Bearkland, Peace Sandy, WikiWorks

Signature 2