Characterization of the Oral Microbiome of Medicated Type-2 Diabetes Patients/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Chloe on 2022/03/14
Curated date: 2021/06/13
Curator: Madhubani Dey
Revision editor(s): WikiWorks, Chloe, Madhubani Dey, Peace Sandy
Subjects
- Location of subjects
- Portugal
- 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
- Saliva
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Medicated Type II Diabetes individuals
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Medicated Type II Diabetes individuals
- Group 0 sample size Number of subjects in the control (unexposed) group
- 24
- Group 1 sample size Number of subjects in the case (exposed) group
- 22
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 2 months
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-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).
- relative abundances
- Statistical test
- ANCOM
- Mann-Whitney (Wilcoxon)
- 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
Signature 1
Needs review
Curated date: 2021/06/17
Curator: Madhubani Dey
Revision editor(s): WikiWorks, Chloe, Madhubani Dey, Merit
Source: Supplementary Table 6
Description: Decreased abundance of microbes in individuals with medicated Type 2 Diabetes (Mann-Whitney's U results)
Abundance in Group 1: decreased abundance in Medicated Type II Diabetes individuals
| NCBI | Quality Control | Links |
|---|---|---|
| Synergistia | ||
| Synergistaceae | ||
| Synergistales | ||
| unclassified Synergistaceae |
Revision editor(s): WikiWorks, Chloe, Madhubani Dey, Merit
Signature 2
Source: Table S6
Description: Decreased abundance of microbes in individuals with medicated Type 2 Diabetes (ANCOM results)
Abundance in Group 1: decreased abundance in Medicated Type II Diabetes individuals
| NCBI | Quality Control | Links |
|---|---|---|
| Synergistaceae | ||
| Synergistales | ||
| Synergistia | ||
| unclassified Synergistaceae |
