Gastro-intestinal and oral microbiome signatures associated with healthy aging/Experiment 2
From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2023-4-16
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
- Age Age,age
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- healthy aging (HA)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- non-healthy aging (NHA)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- participants aged 70–82 who had a medical history linked to one or more of the following major disease categories: cancer, acute or chronic cardiovascular disease, acute or chronic pulmonary disease, chronic liver disease, diabetes and diabetic complications, and stroke or neurodegenerative disorder.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 33
- Group 1 sample size Number of subjects in the case (exposed) group
- 32
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 6 weeks
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V3
- 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)?
- 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
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2023-4-16
Source: Figure 4a, Figure 5, Supplemental File S2
Description: Gut microbiomes diversity and taxonomic differences between healthy aging (HA) and non-healthy aging (NHA) cohorts
Abundance in Group 1: increased abundance in non-healthy aging (NHA)
| NCBI | Quality Control | Links |
|---|---|---|
| Escherichia | ||
| Lactobacillus | ||
| Shigella | ||
| Streptococcus | ||
| unclassified Mollicutes | ||
| Clostridiales bacterium | ||
| Anaerotruncus | ||
| Pseudobutyrivibrio | ||
| Ruminiclostridium |
Revision editor(s): WikiWorks, Claregrieve1
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2023-4-16
Source: Figure 4a, Figure 5, Supplemental File S2
Description: Gut microbiomes diversity and taxonomic differences between healthy aging (HA) and non-healthy aging (NHA) cohorts
Abundance in Group 1: decreased abundance in non-healthy aging (NHA)
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia | ||
| Bacteroides | ||
| Erysipelotrichaceae | ||
| Lachnospiraceae | ||
| Slackia | ||
| Clostridiales Family XIII bacterium |
Revision editor(s): WikiWorks, Claregrieve1
