Local oral and nasal microbiome diversity in age-related macular degeneration/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by KateRasheed on 2025-8-19
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
Reviewed Marked as Reviewed by KateRasheed on 2025-8-19
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
Reviewed Marked as Reviewed by KateRasheed on 2025-8-19
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
