Human pharyngeal microbiota in age-related macular degeneration

From BugSigDB
  • Quality control
    • Retracted paper
    • Contamination issues suspected
    • Batch effect issues suspected
    • Uncontrolled confounding suspected
    • Results are suspect (various reasons)
    • Apply tags
      Tags applied
Reviewed Marked as Reviewed by KateRasheed on 2025-7-31
study design
case-control
Citation
PMID PubMed identifier for scientific articles.
30089174
DOI Digital object identifier for electronic documents.
10.1371/journal.pone.0201768
URI Uniform resource identifier for web resources.
Authors
Ho EXP, Cheung CMG, Sim S, Chu CW, Wilm A, Lin CB, Mathur R, Wong D, Chan CM, Bhagarva M, Laude A, Lim TH, Wong TY, Cheng CY, Davila S, Hibberd M
Journal
PloS one
Year
2018
BACKGROUND: While the aetiology of age-related macular degeneration (AMD)-a major blinding disease-remains unknown, the disease is strongly associated with variants in the complement factor H (CFH) gene. CFH variants also confer susceptibility to invasive infection with several bacterial colonizers of the nasopharyngeal mucosa. This shared susceptibility locus implicates complement deregulation as a common disease mechanism, and suggests the possibility that microbial interactions with host complement may trigger AMD. In this study, we address this possibility by testing the hypothesis that AMD is associated with specific microbial colonization of the human nasopharynx. RESULTS: High-throughput Illumina sequencing of the V3-V6 region of the microbial 16S ribosomal RNA gene was used to comprehensively and accurately describe the human pharyngeal microbiome, at genus level, in 245 AMD patients and 386 controls. Based on mean and differential microbial abundance analyses, we determined an overview of the pharyngeal microbiota, as well as candidate genera (Prevotella and Gemella) suggesting an association towards AMD health and disease conditions. CONCLUSIONS: Utilizing an extensive study population from Singapore, our results provided an accurate description of the pharyngeal microbiota profiles in AMD health and disease conditions. Through identification of candidate genera that are different between conditions, we provide preliminary evidence for the existence of microbial triggers for AMD. Ethical approval for this study was obtained through the Singapore Health Clinical Institutional Review Board, reference numbers R799/63/2010 and 2010/585/A.

Experiment 1


EditHistoryDelete
Flag for review
Your review change was submittedDuplicate this ExperimentAdd a new Signature
Reviewed Marked as Reviewed by KateRasheed on 2025-7-31

Curated date: 2025/06/27

Curator: Anne-mariesharp

Revision editor(s): Anne-mariesharp

Subjects

Location of subjects
Singapore
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
Throat Gula,Throat,throat
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Age-related macular degeneration AAMD - Age related macular degeneration,AGE RELAT MACULOPATHIES,AGE RELAT MACULOPATHY,Age Related Macular Degeneration,age related macular degeneration,Age related macular degeneration (disorder) [Ambiguous],Age Related Maculopathies,age related Maculopathies,Age related maculopathy,age related maculopathy,age-related macular degeneration,Age-related macular degeneration (disorder),Age-Related Macular Degenerations,Age-Related Maculopathies,Age-Related Maculopathy,AMD,AMD - Age-related macular degeneration,Amended,ARMD,ARMD - Age-related macular degeneration,Degeneration, Age-Related Macular,Degeneration, Macular,Degenerations, Age-Related Macular,Degenerations, Macular,Dystrophies, Macular,Dystrophy, Macular,Macular Degeneration,Macular degeneration (disorder),Macular degeneration (senile) of retina, unspecified,MACULAR DEGENERATION NOS,Macular Degeneration, Age-Related,macular degeneration, age-related,Macular Degenerations,Macular Degenerations, Age-Related,Macular Dystrophies,Macular Dystrophy,MACULOPATHIES AGE RELAT,Maculopathies, Age Related,Maculopathies, Age-Related,MACULOPATHY AGE RELAT,Maculopathy, Age Related,Maculopathy, Age-Related,Senile macular degeneration,Senile macular degeneration of retina,Senile macular retinal degeneration,SMD - Senile macular degeneration,Unspecified senile macular degeneration,Age-related macular degeneration
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Control
Group 1 name Corresponds to the case (exposed) group for case-control studies
AMD(Age-related macular degeneration)-positive
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Patients with Age-related macular degeneration
Group 0 sample size Number of subjects in the control (unexposed) group
386
Group 1 sample size Number of subjects in the case (exposed) group
245

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V3-V6
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).
raw counts
Statistical test
DESeq2
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
Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
age, sex

Alpha Diversity

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

Signature 1

EditHistoryDelete
Flag for review
Your review change was submitted
Reviewed Marked as Reviewed by KateRasheed on 2025-7-31

Curated date: 2025/06/27

Curator: Anne-mariesharp

Revision editor(s): Anne-mariesharp

Source: Figure 2

Description: DESeq2 differential abundance analysis expressed as Log2FC comparison of AMD-positive samples and control samples.

Abundance in Group 1: increased abundance in AMD(Age-related macular degeneration)-positive

NCBI Quality ControlLinks
Gemella   

Revision editor(s): Anne-mariesharp

Signature 2

EditHistoryDelete
Flag for review
Your review change was submitted
Reviewed Marked as Reviewed by KateRasheed on 2025-7-31

Curated date: 2025/06/27

Curator: Anne-mariesharp

Revision editor(s): Anne-mariesharp

Source: Figure 2

Description: DESeq2 differential abundance analysis expressed as Log2FC comparison of AMD-positive samples and control samples.

Abundance in Group 1: decreased abundance in AMD(Age-related macular degeneration)-positive

NCBI Quality ControlLinks
Prevotella   

Revision editor(s): Anne-mariesharp

Experiment 2


EditHistoryDelete
Flag for review
Your review change was submittedDuplicate this ExperimentAdd a new Signature
Reviewed Marked as Reviewed by KateRasheed on 2025-7-31

Curated date: 2025/06/27

Curator: Anne-mariesharp

Revision editor(s): Anne-mariesharp

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Control ( - )
Group 1 name Corresponds to the case (exposed) group for case-control studies
AMD(Age-related macular degeneration)-positive ( + )

Lab analysis

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
relative abundances
Statistical test
Linear Regression

Alpha Diversity

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

Signature 1

EditHistoryDelete
Flag for review
Your review change was submitted
Reviewed Marked as Reviewed by KateRasheed on 2025-7-31

Curated date: 2025/06/27

Curator: Anne-mariesharp

Revision editor(s): Anne-mariesharp

Source: Figure 3, Supplementary Table 4

Description: Relative abundances of significant genera between case (Age-related macular degeneration - positive) and control samples

Abundance in Group 1: increased abundance in AMD(Age-related macular degeneration)-positive ( + )

NCBI Quality ControlLinks
Gemella   
Streptococcus   

Revision editor(s): Anne-mariesharp

Signature 2

EditHistoryDelete
Flag for review
Your review change was submitted
Reviewed Marked as Reviewed by KateRasheed on 2025-7-31

Curated date: 2025/06/27

Curator: Anne-mariesharp

Revision editor(s): Anne-mariesharp

Source: Figure 3, Supplementary Table 4

Description: Relative abundances of significant genera between case (Age-related macular degeneration - positive) and control samples

Abundance in Group 1: decreased abundance in AMD(Age-related macular degeneration)-positive ( + )

NCBI Quality ControlLinks
Prevotella   
Leptotrichia   

Revision editor(s): Anne-mariesharp

Experiment 3


EditHistoryDelete
Flag for review
Your review change was submittedDuplicate this ExperimentAdd a new Signature
Reviewed Marked as Reviewed by KateRasheed on 2025-7-31

Curated date: 2025/06/27

Curator: Anne-mariesharp

Revision editor(s): Anne-mariesharp

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Microbiome Microbiome,microbiome
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Rest (The rest of the study population)
Group 1 name Corresponds to the case (exposed) group for case-control studies
High Prevotella
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Subjects with high relative abundance of Prevotella
Group 0 sample size Number of subjects in the control (unexposed) group
604
Group 1 sample size Number of subjects in the case (exposed) group
27

Lab analysis

Statistical Analysis

Signature 1

EditHistoryDelete
Flag for review
Your review change was submitted
Reviewed Marked as Reviewed by KateRasheed on 2025-7-31

Curated date: 2025/06/27

Curator: Anne-mariesharp

Revision editor(s): Anne-mariesharp

Source: Table 2

Description: Microbial genera significantly associated with high Prevotella relative abundance.

Abundance in Group 1: decreased abundance in High Prevotella

NCBI Quality ControlLinks
Streptococcus   
Porphyromonas   
Granulicatella   
Gemella   

Revision editor(s): Anne-mariesharp

Experiment 4


EditHistoryDelete
Flag for review
Your review change was submittedDuplicate this ExperimentAdd a new Signature
Reviewed Marked as Reviewed by KateRasheed on 2025-7-31

Curated date: 2025/06/27

Curator: Anne-mariesharp

Revision editor(s): Anne-mariesharp

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
High Gemella
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Subjects with high relative abundance of Gemella
Group 0 sample size Number of subjects in the control (unexposed) group
610
Group 1 sample size Number of subjects in the case (exposed) group
21

Lab analysis

Statistical Analysis

Signature 1

EditHistoryDelete
Flag for review
Your review change was submitted
Reviewed Marked as Reviewed by KateRasheed on 2025-7-31

Curated date: 2025/06/27

Curator: Anne-mariesharp

Revision editor(s): Anne-mariesharp

Source: Table 3

Description: Microbial genera significantly associated with high Gemella relative abundance.

Abundance in Group 1: increased abundance in High Gemella

NCBI Quality ControlLinks
Aggregatibacter   
Filifactor   
Haemophilus   

Revision editor(s): Anne-mariesharp

Signature 2

EditHistoryDelete
Flag for review
Your review change was submitted
Reviewed Marked as Reviewed by KateRasheed on 2025-7-31

Curated date: 2025/06/27

Curator: Anne-mariesharp

Revision editor(s): Anne-mariesharp

Source: Table 3

Description: Microbial genera significantly associated with high Gemella relative abundance.

Abundance in Group 1: decreased abundance in High Gemella

NCBI Quality ControlLinks
Prevotella   
Veillonella   

Revision editor(s): Anne-mariesharp

Experiment 5


EditHistoryDelete
Flag for review
Your review change was submittedDuplicate this ExperimentAdd a new Signature
Reviewed Marked as Reviewed by KateRasheed on 2025-7-31

Curated date: 2025/06/27

Curator: Anne-mariesharp

Revision editor(s): Anne-mariesharp

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Age-related macular degeneration AAMD - Age related macular degeneration,AGE RELAT MACULOPATHIES,AGE RELAT MACULOPATHY,Age Related Macular Degeneration,age related macular degeneration,Age related macular degeneration (disorder) [Ambiguous],Age Related Maculopathies,age related Maculopathies,Age related maculopathy,age related maculopathy,age-related macular degeneration,Age-related macular degeneration (disorder),Age-Related Macular Degenerations,Age-Related Maculopathies,Age-Related Maculopathy,AMD,AMD - Age-related macular degeneration,Amended,ARMD,ARMD - Age-related macular degeneration,Degeneration, Age-Related Macular,Degeneration, Macular,Degenerations, Age-Related Macular,Degenerations, Macular,Dystrophies, Macular,Dystrophy, Macular,Macular Degeneration,Macular degeneration (disorder),Macular degeneration (senile) of retina, unspecified,MACULAR DEGENERATION NOS,Macular Degeneration, Age-Related,macular degeneration, age-related,Macular Degenerations,Macular Degenerations, Age-Related,Macular Dystrophies,Macular Dystrophy,MACULOPATHIES AGE RELAT,Maculopathies, Age Related,Maculopathies, Age-Related,MACULOPATHY AGE RELAT,Maculopathy, Age Related,Maculopathy, Age-Related,Senile macular degeneration,Senile macular degeneration of retina,Senile macular retinal degeneration,SMD - Senile macular degeneration,Unspecified senile macular degeneration,Age-related macular degeneration
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Control ( - )
Group 1 name Corresponds to the case (exposed) group for case-control studies
L-AMD(Late Age-related macular degeneration)-positive
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Patients with late-stage Age-related macular degeneration
Group 0 sample size Number of subjects in the control (unexposed) group
386
Group 1 sample size Number of subjects in the case (exposed) group
165

Lab analysis

Statistical Analysis

Signature 1

EditHistoryDelete
Flag for review
Your review change was submitted
Reviewed Marked as Reviewed by KateRasheed on 2025-7-31

Curated date: 2025/06/27

Curator: Anne-mariesharp

Revision editor(s): Anne-mariesharp

Source: Figure 4, Supplementary Table 6

Description: Relative abundances of significant genera between controls and individuals with late AMD(Age-related macular degeneration)

Abundance in Group 1: increased abundance in L-AMD(Late Age-related macular degeneration)-positive

NCBI Quality ControlLinks
Streptococcus   
Gemella   

Revision editor(s): Anne-mariesharp

Signature 2

EditHistoryDelete
Flag for review
Your review change was submitted
Reviewed Marked as Reviewed by KateRasheed on 2025-7-31

Curated date: 2025/06/27

Curator: Anne-mariesharp

Revision editor(s): Anne-mariesharp

Source: Figure 4, Supplementary Table 6

Description: Relative abundances of significant genera between controls and individuals with late AMD(Age-related macular degeneration)

Abundance in Group 1: decreased abundance in L-AMD(Late Age-related macular degeneration)-positive

NCBI Quality ControlLinks
Prevotella   
Leptotrichia   

Revision editor(s): Anne-mariesharp

Experiment 6


EditHistoryDelete
Flag for review
Your review change was submittedDuplicate this ExperimentAdd a new Signature
Reviewed Marked as Reviewed by KateRasheed on 2025-7-31

Curated date: 2025/06/27

Curator: Anne-mariesharp

Revision editor(s): Anne-mariesharp

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Control (Healthy participants)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Case (Age-related macular degeneration patients)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Patients with Age-related macular degeneration greater than 60years
Group 0 sample size Number of subjects in the control (unexposed) group
180
Group 1 sample size Number of subjects in the case (exposed) group
192

Lab analysis

Statistical Analysis

Signature 1

EditHistoryDelete
Flag for review
Your review change was submitted
Reviewed Marked as Reviewed by KateRasheed on 2025-7-31

Curated date: 2025/06/27

Curator: Anne-mariesharp

Revision editor(s): Anne-mariesharp

Source: Supplementary Table 5

Description: Association between microbial genera and AMD status in individuals >60 years. Genera with significantly different relative abundances in case/control conditions are shown.

Abundance in Group 1: increased abundance in Case (Age-related macular degeneration patients)

NCBI Quality ControlLinks
Streptococcus   

Revision editor(s): Anne-mariesharp

Signature 2

EditHistoryDelete
Flag for review
Your review change was submitted
Reviewed Marked as Reviewed by KateRasheed on 2025-7-31

Curated date: 2025/06/27

Curator: Anne-mariesharp

Revision editor(s): Anne-mariesharp

Source: Supplementary Table 5

Description: Association between microbial genera and AMD status in individuals >60 years. Genera with significantly different relative abundances in case/control conditions are shown.

Abundance in Group 1: decreased abundance in Case (Age-related macular degeneration patients)

NCBI Quality ControlLinks
Prevotella   
Leptotrichia   

Revision editor(s): Anne-mariesharp

Experiment 7


EditHistoryDelete
Flag for review
Your review change was submittedDuplicate this ExperimentAdd a new Signature
Reviewed Marked as Reviewed by KateRasheed on 2025-7-31

Curated date: 2025/06/27

Curator: Anne-mariesharp

Revision editor(s): Anne-mariesharp

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Control ( - ) (Healthy participants)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Case ( + ) (Age-related macular degeneration patients)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Patients with Age-related macular degeneration
Group 0 sample size Number of subjects in the control (unexposed) group
20
Group 1 sample size Number of subjects in the case (exposed) group
20

Lab analysis

Sequencing type
PCR
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
Not specified

Statistical Analysis

Statistical test
Mann-Whitney (Wilcoxon)
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.01
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
No

Alpha Diversity

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

Signature 1

EditHistoryDelete
Flag for review
Your review change was submitted
Reviewed Marked as Reviewed by KateRasheed on 2025-7-31

Curated date: 2025/06/27

Curator: Anne-mariesharp

Revision editor(s): Anne-mariesharp

Source: Figure 5

Description: Differential abundance of selected microbial genera between disease groups based on qPCR-derived copy numbers

Abundance in Group 1: increased abundance in Case ( + ) (Age-related macular degeneration patients)

NCBI Quality ControlLinks
Streptococcus   

Revision editor(s): Anne-mariesharp

Signature 2

EditHistoryDelete
Flag for review
Your review change was submitted
Reviewed Marked as Reviewed by KateRasheed on 2025-7-31

Curated date: 2025/06/27

Curator: Anne-mariesharp

Revision editor(s): Anne-mariesharp

Source: Figure 5

Description: Differential abundance of selected microbial genera between disease groups based on qPCR-derived copy numbers

Abundance in Group 1: decreased abundance in Case ( + ) (Age-related macular degeneration patients)

NCBI Quality ControlLinks
Prevotella   

Revision editor(s): Anne-mariesharp

Retrieved from "https://bugsigdb.org/w/index.php?title=30089174&oldid=206622"
The City University of New York
Bioconductor - Open Source Software for Bioinformatics
WikiWorks
Powered by MediaWiki
Powered by Semantic MediaWiki