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

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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


incomplete

Curated date: 2023/06/26

Curator: Andre

Revision editor(s): Andre

Subjects

Location of subjects
Gambia
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
Conjunctiva Conjunctivae,Conjunctivas,Tunica conjunctiva,Wall of conjunctival sac,Conjunctiva
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Chlamydia trachomatis Chlamydozoon trachomatis,Rickettsia trachomae,Rickettsia trachomatis,Chlamydia trachomatis
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Controls aged <= 10 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
21
Group 1 sample size Number of subjects in the case (exposed) group
84
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)
0.1
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

incomplete

Curated date: 2023/06/28

Curator: Andre

Revision editor(s): Andre

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
Corynebacterium
Paracoccus
Propionibacterium
Myceligenerans
Promicromonosporaceae
Actinomycetales

Revision editor(s): Andre

Signature 2

incomplete

Curated date: 2023/06/28

Curator: Andre

Revision editor(s): Andre

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
Streptococcus
Kocuria
Staphylococcus
Micrococcus
Brachybacterium

Revision editor(s): Andre

Experiment 2


incomplete

Curated date: 2023/06/28

Curator: Andre

Revision editor(s): Andre

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 wet season
Group 1 name Corresponds to the case (exposed) group for case-control studies
Controls aged > 10 years 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
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 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
ethnic group, geographic area, sex

Alpha Diversity

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

Signature 1

incomplete

Curated date: 2023/06/28

Curator: Andre

Revision editor(s): Andre

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 dry season

NCBI Quality ControlLinks
Bacillus
Tumebacillus

Revision editor(s): Andre

Experiment 3


incomplete

Curated date: 2023/07/19

Curator: Andre

Revision editor(s): Andre

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Controls aged <= 10 years
Group 1 name Corresponds to the case (exposed) group for case-control studies
Cases aged <= 10 years
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Children (age <= 10 years old) with follicles (F>0) or papillae (1 case of F0P3C0). Of note, all samples in children were collected in the wet season.
Group 1 sample size Number of subjects in the case (exposed) group
29
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

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
Not specified
Matched on Factors on which subjects have been matched on in a case-control study
geographic area, sex

Alpha Diversity

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

Experiment 4


incomplete

Curated date: 2023/07/20

Curator: Andre

Revision editor(s): Andre

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 during the dry season
Group 1 name Corresponds to the case (exposed) group for case-control studies
Cases aged > 10 years with samples collected 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 (Cicatricae > 0 with or without trachomatous trichiasis (TT))
Group 0 sample size Number of subjects in the control (unexposed) group
Not specified
Group 1 sample size Number of subjects in the case (exposed) group
Not specified

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

incomplete

Curated date: 2023/07/20

Curator: Andre

Revision editor(s): Andre

Source: Table 2

Description: Changes in taxa abundance between groups

Abundance in Group 1: increased abundance in Cases aged > 10 years with samples collected during the dry season

NCBI Quality ControlLinks
Corynebacterium
Streptococcus

Revision editor(s): Andre

Signature 2

incomplete

Curated date: 2023/07/20

Curator: Andre

Revision editor(s): Andre

Source: Table 2

Description: Changes in taxa abundance between groups

Abundance in Group 1: decreased abundance in Cases aged > 10 years with samples collected during the dry season

NCBI Quality ControlLinks
Globicatella

Revision editor(s): Andre

Experiment 5


incomplete

Curated date: 2023/07/20

Curator: Andre

Revision editor(s): Andre

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

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

Experiment 6


incomplete

Curated date: 2023/07/20

Curator: Andre

Revision editor(s): Andre

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))

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

incomplete

Curated date: 2023/07/20

Curator: Andre

Revision editor(s): Andre

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

Signature 2

incomplete

Curated date: 2023/07/20

Curator: Andre

Revision editor(s): Andre

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
Myceligenerans
Promicromonosporaceae
Actinomycetales
Paracoccus

Revision editor(s): Andre

Experiment 7


incomplete

Curated date: 2023/07/20

Curator: Andre

Revision editor(s): Andre

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 wet 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 wet season

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