Local oral and nasal microbiome diversity in age-related macular degeneration

Study information

Reviewed Marked as Reviewed by KateRasheed on 2025-8-19

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

32123200

DOI Digital object identifier for electronic documents.

10.1038/s41598-020-60674-3

URI Uniform resource identifier for web resources.

Authors

Rullo J, Far PM, Quinn M, Sharma N, Bae S, Irrcher I, Sharma S

Journal

Scientific reports

Year

2020

Age-related macular degeneration (AMD) is a chronic degenerative disease of the retina. Recent reports have highlighted the potential role of mucosal surface microbes in the pathogenesis of AMD. In this case-control study, the composition of the nasal and oral microbiota in newly diagnosed neovascular age-related macular degeneration cases (6 male, 7 female) was compared to controls without retinal diseases (2 male, 3 female). PCR amplification of 16S rRNA genes was performed with universal primers amplifying the V4 variable region (515F-806R). Distinct microbial community characterization was achieved using Principal Coordinates Analysis (PCoA) of the Bray-Curtis index with comparative analysis between cases and controls performed within QIIME 2. Sequencing of all cases and controls revealed clear separation with strong beta diversity between oral and nasal microbial communities (p < 0.001). Microbial composition differed between cases and controls in both oral and nasal samples. The top three oral microbes identified as different compared to controls included Burkholderiales (7.41 log2fold change, p = 3.29E-05), Actinomyceataceae (6.22 log2fold change, p = 3.73E-06) and Gemella (5.28 log2fold change, p = 0.0002). The top three nasal microbes identified as different compared to controls included Rothia (13.6 log2fold change, p = 3.63E-18), Actinobacteria (10.29 log2fold change, p = 9.81E-10) and Propionibacteriales (8.73 log2fold change, p = 6.74E-09). These relative shifts in communities of bacteria detected in newly diagnosed neovascular AMD patients may suggest additional mechanistic links in disease pathogenesis.

Experiment 1

Edit History Delete

Flag for review

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by KateRasheed on 2025-8-19

Curated date: 2025/08/11

Curator: Anne-mariesharp

Revision editor(s): Anne-mariesharp

Subjects

Location of subjects: Canada

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: Nasal cavity mucosa Mucosa of nose,Mucous membrane of nose,Nasal mucosa,Tunica mucosa nasalis,Tunica mucosa nasi,Nasal cavity mucosa,nasal cavity mucosa

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: Controls

Group 1 name Corresponds to the case (exposed) group for case-control studies: Nasal Cases

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Nasal samples collected from treatment-naïve patients with newly diagnosed neovascular AMD (Age-related Macular Degeneration)

Group 0 sample size Number of subjects in the control (unexposed) group: 5

Group 1 sample size Number of subjects in the case (exposed) group: 13

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): Currently on antibiotics

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V4

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)?: No

Signature 1

Edit History Delete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by KateRasheed on 2025-8-19

Curated date: 2025/08/11

Curator: Anne-mariesharp

Revision editor(s): Anne-mariesharp

Source: Table 2

Description: Log2fold change in the relative abundance of operational taxonomic units of cases over controls.

Abundance in Group 1: increased abundance in Nasal Cases

NCBI	Quality Control	Links
Actinomyces sp.
Actinomycetaceae
Burkholderiales
Gemella
Streptococcus sp.
Veillonella sp.
Pseudomonadaceae

Revision editor(s): Anne-mariesharp

Signature 2

Edit History Delete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by KateRasheed on 2025-8-19

Curated date: 2025/08/11

Curator: Anne-mariesharp

Revision editor(s): Anne-mariesharp

Source: Table 2

Description: Log2fold change in the relative abundance of operational taxonomic units of cases over controls.

Abundance in Group 1: decreased abundance in Nasal Cases

NCBI	Quality Control	Links
Clostridia

Revision editor(s): Anne-mariesharp

Experiment 2

Edit History Delete

Flag for review

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by KateRasheed on 2025-8-19

Curated date: 2025/08/11

Curator: Anne-mariesharp

Revision editor(s): Anne-mariesharp

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Buccal mucosa Buccal mucosa,buccal mucosa

Group 1 name Corresponds to the case (exposed) group for case-control studies: Oral Cases

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Oral samples collected from treatment-naïve patients with newly diagnosed neovascular AMD (Age-related Macular Degeneration)

Lab analysis

Statistical Analysis

Signature 1

Edit History Delete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by KateRasheed on 2025-8-19

Curated date: 2025/08/11

Curator: Anne-mariesharp

Revision editor(s): Anne-mariesharp

Source: Table 2

Description: Log2fold change in the relative abundance of operational taxonomic units of cases over controls.

Abundance in Group 1: increased abundance in Oral Cases

NCBI	Quality Control	Links
Actinomyces sp.
Actinomycetota
Anaerococcus sp.
Campylobacter sp.
Finegoldia sp.
Peptoniphilus
Prevotella
Propionibacterium sp.
Rothia
Staphylococcus sp.
Bacillota
Corynebacterium
Propionibacteriaceae