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
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
Authors
Zhou Y, Holland MJ, Makalo P, Joof H, Roberts CH, Mabey DC, Bailey RL, Burton MJ, Weinstock GM, Burr SE
Journal
Genome medicine
Year
2014
BACKGROUND: Trachoma, caused by Chlamydia trachomatis, remains the world's leading infectious cause of blindness. Repeated ocular infection during childhood leads to scarring of the conjunctiva, in-turning of the eyelashes (trichiasis) and corneal opacity in later life. There is a growing body of evidence to suggest non-chlamydial bacteria are associated with clinical signs of trachoma, independent of C. trachomatis infection. METHODS: We used deep sequencing of the V1-V3 region of the bacterial 16S rRNA gene to characterize the microbiome of the conjunctiva of 220 residents of The Gambia, 105 with healthy conjunctivae and 115 with clinical signs of trachoma in the absence of detectable C. trachomatis infection. Deep sequencing was carried out using the Roche-454 platform. Sequence data were processed and analyzed through a pipeline developed by the Human Microbiome Project. RESULTS: The microbiome of healthy participants was influenced by age and season of sample collection with increased richness and diversity seen in younger participants and in samples collected during the dry season. Decreased diversity and an increased abundance of Corynebacterium and Streptococcus were seen in participants with conjunctival scarring compared to normal controls. Abundance of Corynebacterium was higher still in adults with scarring and trichiasis compared to adults with scarring only. CONCLUSIONS: Our results indicate that changes in the conjunctival microbiome occur in trachomatous disease; whether these are a cause or a consequence is yet unknown.

Experiment 1


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

Curated date: 2023/06/26

Curator: Andre

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

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

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

NCBI Quality ControlLinks
Actinomycetales
Corynebacterium
Myceligenerans
Paracoccus
Promicromonosporaceae
Propionibacterium

Revision editor(s): Andre, Folakunmi

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

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

NCBI Quality ControlLinks
Brachybacterium
Kocuria
Micrococcus
Staphylococcus
Streptococcus

Revision editor(s): Andre, Folakunmi

Experiment 2


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

Curated date: 2023/06/28

Curator: Andre

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

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

Lab analysis

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): Andre, Folakunmi, Peace Sandy

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

NCBI Quality ControlLinks
Bacillus
Tumebacillus

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

Experiment 3


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

Curated date: 2024/02/16

Curator: Peace Sandy

Revision editor(s): Peace Sandy

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

Lab analysis

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

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

NCBI Quality ControlLinks
Globicatella

Revision editor(s): Peace Sandy

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

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 ControlLinks
Corynebacterium
Streptococcus

Revision editor(s): Peace Sandy

Experiment 4


Needs review

Curated date: 2023/07/20

Curator: Andre

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

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

Lab analysis

Statistical Analysis

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): Andre, Folakunmi, Peace Sandy

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 ControlLinks
Globicatella

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

Signature 2

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

Curated date: 2023/07/20

Curator: Andre

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

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 ControlLinks
Corynebacterium
Streptococcus

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

Experiment 6


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

Curated date: 2023/07/20

Curator: Andre

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

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.

Lab analysis

Statistical Analysis

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

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 ControlLinks
Corynebacterium
Kocuria

Revision editor(s): Andre, Folakunmi

Signature 2

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

Curated date: 2023/07/20

Curator: Andre

Revision editor(s): Andre, Folakunmi

Source: Table 2

Description: Changes in taxa abundance between groups

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

NCBI Quality ControlLinks
Actinomycetales
Myceligenerans
Paracoccus
Promicromonosporaceae

Revision editor(s): Andre, Folakunmi