Oral microbiome in HIV-associated periodontitis/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2022/08/31
Curated date: 2022/01/10
Curator: Joyessa
Revision editor(s): WikiWorks, LGeistlinger, Claregrieve1, Joyessa
Subjects
- Location of subjects
- United States of America
- 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
- Dental plaque , Internal cheek pouch , Saliva Bacterial plaque,Plaque,Dental plaque,dental plaque,Internal buccal pouch,Internal cheek pouch,internal cheek pouch,Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Periodontitis chronic pericementitis,inflammation of periodontium,Pericementitides,Pericementitis,Periodontitides,periodontitis,Periodontitis (disorder),Periodontitis, NOS,periodontium inflammation,periodontosis,Periodontitis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HIV–
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HIV+
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants who were positive for HIV-1 infection, as verified by ELISA and confirmed by Western blot.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
- Group 1 sample size Number of subjects in the case (exposed) group
- 40
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
- Statistical test
- Wald Test
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/08/31
Source: Table 1, Figure 3
Description: Differential microbial abundance between HIV+ and HIV- participants
Abundance in Group 1: increased abundance in HIV+
| NCBI | Quality Control | Links |
|---|---|---|
| Aggregatibacter | ||
| Kingella | ||
| Neisseria | ||
| Rothia | ||
| unclassified Neisseriaceae | ||
| unclassified Pasteurellaceae | ||
| Abiotrophia |
Revision editor(s): Joyessa, Claregrieve1
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/08/31
Source: Table 1, Figure 3
Description: Differential microbial abundance between HIV+ and HIV- participants
Abundance in Group 1: decreased abundance in HIV+
| NCBI | Quality Control | Links |
|---|---|---|
| Centipeda | ||
| Tannerella | ||
| Leptotrichia | ||
| Selenomonas | ||
| Treponema | ||
| unclassified Veillonellaceae | ||
| Prevotella |
Revision editor(s): Joyessa, Claregrieve1
