Identifying microbial signatures for patients with postmenopausal osteoporosis using gut microbiota analyses and feature selection approaches/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Folakunmi on 2023-12-21
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
- Postmenopausal osteoporosis Bone Loss, Perimenopausal,Bone Loss, Postmenopausal,Bone Losses, Perimenopausal,Bone Losses, Postmenopausal,bone mineral density quantitative trait locus,Osteoporoses, Post-Menopausal,Osteoporoses, Postmenopausal,Osteoporosis, Post Menopausal,Osteoporosis, Post-Menopausal,Osteoporosis, Postmenopausal,osteoporosis, postmenopausal,Perimenopausal Bone Loss,Perimenopausal Bone Losses,Post-Menopausal Osteoporoses,Post-Menopausal Osteoporosis,Postmenopausal Bone Loss,Postmenopausal Bone Losses,Postmenopausal Osteoporoses,postmenopausal osteoporosis,Postmenopausal osteoporosis
- 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
- Postmenopausal osteoporosis (PMOP) patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Postmenopausal osteoporosis (PMOP)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 37
- Group 1 sample size Number of subjects in the case (exposed) group
- 21
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Subjects who were on antibiotics one (1) month preceding the sample collection were excluded from the study
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
- Mann-Whitney (Wilcoxon)
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.1
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2023-12-21
Source: Table S2, Figure 1
Description: Gut microbiota compositions between healthy controls and patients with postmenopausal osteoporosis (PMOP)
Abundance in Group 1: increased abundance in Postmenopausal osteoporosis (PMOP) patients
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2023-12-21
Source: Table S2
Description: Gut microbiota compositions and statistical results between healthy controls and patients with postmenopausal osteoporosis (PMOP)
Abundance in Group 1: decreased abundance in Postmenopausal osteoporosis (PMOP) patients
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides eggerthii | ||
| Oscillospiraceae |
