The conjunctival microbiome in health and trachomatous disease: a case control study

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Reviewed Marked as Reviewed by Peace Sandy on 2024-2-16

Curated date: 2023/06/26

Curator: Andre

Revision editor(s): WikiWorks, Andre, Peace Sandy, Folakunmi

Subjects

Location of subjects: Gambia

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: Conjunctiva Conjunctiva,conjunctiva,Conjunctivae,Conjunctivas,Tunica conjunctiva,Wall of conjunctival sac

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Chlamydia trachomatis Chlamydozoon trachomatis,Rickettsia trachomae,Rickettsia trachomatis,Chlamydia trachomatis,chlamydia trachomatis

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Controls aged < = 0 years

Group 1 name Corresponds to the case (exposed) group for case-control studies: Controls aged > 10 years

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Control individuals with normal conjunctiva (F0P0C0 - 1981 WHO trachoma grading system) and age > 10 years old.

Group 0 sample size Number of subjects in the control (unexposed) group: 50

Group 1 sample size Number of subjects in the case (exposed) group: 170

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): not mentioned

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V1-V3

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Roche454

Statistical Analysis

Statistical test: Metastats

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

Matched on Factors on which subjects have been matched on in a case-control study: age, ethnic group, geographic area, sex

Alpha Diversity

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

Richness Number of species: decreased

Signature 1

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-16

Curated date: 2023/06/28

Curator: Andre

Revision editor(s): Andre, Folakunmi, WikiWorks

Source: Table 2

Description: Changes in taxa abundance between control individuals aged <= 10 years and > 10 years

Abundance in Group 1: increased abundance in Controls aged > 10 years

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Actinomycetales
Corynebacterium
Myceligenerans
Paracoccus
Promicromonosporaceae
Propionibacterium

Revision editor(s): Andre, Folakunmi, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-16

Curated date: 2023/06/28

Curator: Andre

Revision editor(s): Andre, Folakunmi, WikiWorks

Source: Table 2

Description: Changes in taxa abundance between control individuals aged <= 10 years and > 10 years

Abundance in Group 1: decreased abundance in Controls aged > 10 years

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Brachybacterium
Kocuria
Micrococcus
Staphylococcus
Streptococcus

Revision editor(s): Andre, Folakunmi, WikiWorks

Experiment 2

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-16

Curated date: 2023/06/28

Curator: Andre

Revision editor(s): WikiWorks, Andre, Peace Sandy, Folakunmi

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Controls aged > 10 years with samples collected in the dry season

Group 1 name Corresponds to the case (exposed) group for case-control studies: Controls aged > 10 years with samples collected in the wet season

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Control individuals with normal conjunctiva (F0P0C0 - 1981 WHO trachoma grading system) and age > 10 years old with samples collected during the dry season. Of note, all samples from participants <= 10 years old were collected during the wet season, therefore, were not included in the analysis of the seasonal effect on the conjunctival microbiome.

Group 0 sample size Number of subjects in the control (unexposed) group: 126

Group 1 sample size Number of subjects in the case (exposed) group: 94

Statistical Analysis

Matched on Factors on which subjects have been matched on in a case-control study: ethnic group, geographic area, sex, age

Alpha Diversity

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

Richness Number of species: increased

Signature 1

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-16

Curated date: 2023/06/28

Curator: Andre

Revision editor(s): WikiWorks, Andre, Peace Sandy, Folakunmi

Source: Table 2

Description: Difference in taxa abundance between normal conjunctiva in wet season and normal conjunctiva in dry season

Abundance in Group 1: increased abundance in Controls aged > 10 years with samples collected in the wet season

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Bacillus
Tumebacillus

Revision editor(s): WikiWorks, Andre, Peace Sandy, Folakunmi

Experiment 3

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-16

Curated date: 2024/02/16

Curator: Peace Sandy

Revision editor(s): Peace Sandy, WikiWorks

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Cases with conjunctival scarring (C > 0) alone, with samples collected in the dry season

Group 1 name Corresponds to the case (exposed) group for case-control studies: Cases with conjunctival scarring (C = 0) alone, with samples collected in the dry season

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Participants aged = 10 years with clinical signs of conjunctival scarring (Cicatricae = 0) sampled in the dry season. Bacterial community structure was different between the two groups during the dry season but not during the wet season.

Group 0 sample size Number of subjects in the control (unexposed) group: 63

Group 1 sample size Number of subjects in the case (exposed) group: 63

Statistical Analysis

Matched on Factors on which subjects have been matched on in a case-control study: age, ethnic group, geographic area, sex

Alpha Diversity

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

Richness Number of species: unchanged

Signature 1

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-16

Curated date: 2024/02/16

Curator: Peace Sandy

Revision editor(s): Peace Sandy, WikiWorks

Source: Table 2

Description: Changes in taxa abundance between groups

Abundance in Group 1: increased abundance in Cases with conjunctival scarring (C = 0) alone, with samples collected in the dry season

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Globicatella

Revision editor(s): Peace Sandy, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-16

Curated date: 2024/02/16

Curator: Peace Sandy

Revision editor(s): Peace Sandy, WikiWorks

Source: Table 2

Description: Changes in taxa abundance between groups

Abundance in Group 1: decreased abundance in Cases with conjunctival scarring (C = 0) alone, with samples collected in the dry season

NCBI	Quality Control	Links
Corynebacterium
Streptococcus

Revision editor(s): Peace Sandy, WikiWorks

Experiment 4

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Mark reviewed

Needs review

Curated date: 2023/07/20

Curator: Andre

Revision editor(s): WikiWorks, Andre, Peace Sandy, Folakunmi

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Cases aged > 10 years with clinical signs of conjunctival scarring sampled during the dry season

Group 1 name Corresponds to the case (exposed) group for case-control studies: Cases aged = 10 years with clinical signs of conjunctival scarring sampled during the dry season

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Participants aged 10 years with clinical signs of conjunctival scarring in dry season

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): Not mentioned

Alpha Diversity

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

Richness Number of species: unchanged

Signature 1

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-16

Curated date: 2023/07/20

Curator: Andre

Revision editor(s): WikiWorks, Andre, Peace Sandy, Folakunmi

Source: Table 2

Description: Changes in taxa abundance between groups

Abundance in Group 1: increased abundance in Cases aged = 10 years with clinical signs of conjunctival scarring sampled during the dry season

NCBI	Quality Control	Links
Globicatella

Revision editor(s): WikiWorks, Andre, Peace Sandy, Folakunmi

Signature 2

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-16

Curated date: 2023/07/20

Curator: Andre

Revision editor(s): WikiWorks, Andre, Peace Sandy, Folakunmi

Source: Table 2

Description: Changes in taxa abundance between groups

Abundance in Group 1: decreased abundance in Cases aged = 10 years with clinical signs of conjunctival scarring sampled during the dry season

NCBI	Quality Control	Links
Corynebacterium
Streptococcus

Revision editor(s): WikiWorks, Andre, Peace Sandy, Folakunmi

Experiment 6

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-16

Curated date: 2023/07/20

Curator: Andre

Revision editor(s): WikiWorks, Andre, Peace Sandy, Folakunmi

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Cases with conjunctival scarring (C>0) alone, with samples collected in the dry season

Group 1 name Corresponds to the case (exposed) group for case-control studies: Cases with conjunctival scarring (C>0) and trachomatous trichiasis (TT),with samples collected in the dry season

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Participants aged >10 years with clinical signs of conjunctival scarring (Cicatricae > 0) and with trachomatous trichiasis (TT)) sampled in the dry season. Bacterial community structure was different between the two groups during the dry season but not during the wet season.

Alpha Diversity

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

Richness Number of species: unchanged

Signature 1

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-16

Curated date: 2023/07/20

Curator: Andre

Revision editor(s): Andre, Folakunmi, WikiWorks

Source: Table 2

Description: Changes in taxa abundance between groups

Abundance in Group 1: increased abundance in Cases with conjunctival scarring (C>0) and trachomatous trichiasis (TT),with samples collected in the dry season

NCBI	Quality Control	Links
Corynebacterium
Kocuria

Revision editor(s): Andre, Folakunmi, WikiWorks

Signature 2