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

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Needs review

Curated date: 2023/09/10

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland

Subjects

Location of subjects: China

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: Bulbar conjunctiva Ocular conjunctiva,Bulbar conjunctiva

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

Not specified

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

Statistical test: LEfSe

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.05
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: increased

Signature 1

Needs review

Curated date: 2023/09/10

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland

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

Revision editor(s): Mary Bearkland

Signature 2

Needs review

Curated date: 2023/09/10

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland

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

Experiment 2

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Curated date: 2023/09/24

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland

Differences from previous experiment shown

Subjects

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

Needs review

Curated date: 2023/09/24

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland

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: decreased abundance in Female

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Revision editor(s): Mary Bearkland

Signature 2