Association of suboptimal health status with intestinal microbiota in Chinese youths/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/29
Subjects
- Location of subjects
- China
- 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
- Health trait Health trait,health trait
- 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
- suboptimal health status
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- subjects with SHSQ-25 (SHS score >= 35)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 50
- Group 1 sample size Number of subjects in the case (exposed) group
- 50
- 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
- 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
- LEfSe
- 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)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
- Matched on Factors on which subjects have been matched on in a case-control study
- age, body mass index, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/29
Source: Figure 5
Description: LDA score of LEfSe analysis between suboptimal health status (SHS) and control group
Abundance in Group 1: increased abundance in suboptimal health status
| NCBI | Quality Control | Links |
|---|---|---|
| Chryseobacterium | ||
| Cyanobacteriota | ||
| Oscillospira | ||
| Oscillospiraceae | ||
| Peptococcaceae | ||
| Rikenellaceae | ||
| Roseburia | ||
| Ruminococcus | ||
| Verrucomicrobiota | ||
| Clostridiales bacterium | ||
| Fusobacteriaceae |
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/29
Source: Figure 5
Description: LDA score of LEfSe analysis between suboptimal health status (SHS) and control group
Abundance in Group 1: decreased abundance in suboptimal health status
| NCBI | Quality Control | Links |
|---|---|---|
| Morganella | ||
| Ralstonia | ||
| Betaproteobacteria | ||
| Alcaligenaceae | ||
| Sutterella |
Revision editor(s): WikiWorks
