The small bowel microbiome changes significantly with age and aspects of the ageing process/Experiment 1
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
- Small intestine Anterior intestine,Intestinum tenue,Mid intestine,Small bowel,Small intestine,small intestine
- 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
- Group 1- youngest age group (18 to 35 years old)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Group 4- oldest age group (66 to 80 years old. elderly people)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This is the oldest age advanced group from the study
- Group 0 sample size Number of subjects in the control (unexposed) group
- 32
- Group 1 sample size Number of subjects in the case (exposed) group
- 82
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- None.
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
- PLS-DA (Partial least square discriminant analysis)
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.0001
- 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
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- decreased
Signature 1
Source: Figure S6 + Results (text): Page 6, under sub-heading "Microbiome differences are most pronounced between younger (group 1) and elderly (group 4) adults."
Description: Variable importance in projection (VIP) selected during PLS-DA analysis of families in the duodenal microbiome of subjects in Groups 4 compared to Group 1.
Abundance in Group 1: increased abundance in Group 4- oldest age group (66 to 80 years old. elderly people)
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridiaceae | ||
| Desulfovibrionaceae | ||
| Enterobacteriaceae | ||
| Enterococcaceae | ||
| Klebsiella | ||
| Lactobacillus | ||
| Lactobacillaceae | ||
| Escherichia |
Revision editor(s): Davvve, ChiomaBlessing
Signature 2
Source: Figure S6
Description: Variable importance in projection (VIP) selected during PLS-DA analysis of families in the duodenal microbiome of subjects in Groups 4 compared to Group 1.
Abundance in Group 1: decreased abundance in Group 4- oldest age group (66 to 80 years old. elderly people)
Revision editor(s): ChiomaBlessing
