Distinct intestinal microbial signatures linked to accelerated systemic and intestinal biological aging/Experiment 3
From BugSigDB
Needs review
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
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Aging ageing,AGING BIOL,Aging, Biological,BIOL AGING,Biological Aging,Senescence,Aging,aging
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- PLWOH
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- PLWH on ART
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- People living with HIV(PLWH) on Anti-Retroviral Therapy (ART)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 23
- Group 1 sample size Number of subjects in the case (exposed) group
- 25
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Not stated
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V2
- 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
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, body mass index, ethnic group, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Needs review
Source: Fig 4D
Description: Log-scale differences in bacterial abundance across colon (triangle), ileum (square), and feces (circle) between PLWOH and PLWH on ART.
Abundance in Group 1: increased abundance in PLWH on ART
| NCBI | Quality Control | Links |
|---|---|---|
| Catenibacterium | ||
| Lachnospiraceae |
Revision editor(s): Imaspecial
Signature 2
Needs review
Source: Fig 4D
Description: Log-scale differences in bacterial abundance across colon (triangle), ileum (square), and feces (circle) between PLWOH and PLWH on ART.
Abundance in Group 1: decreased abundance in PLWH on ART
| NCBI | Quality Control | Links |
|---|---|---|
| uncultured Erysipelotrichaceae bacterium |
Revision editor(s): Imaspecial
