Association of Gut Microbiome and Vitamin D Deficiency in Knee Osteoarthritis Patients: A Pilot Study/Experiment 2
From BugSigDB
Reviewed Marked as Reviewed by Fatima on 2022/03/9
Curated date: 2022/03/09
Curator: Fatima
Revision editor(s): WikiWorks, LGeistlinger, Fatima, Victoria
Subjects
- Location of subjects
- India
- 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
- Osteoarthritis, knee Knee Osteoarthritides\n,Knee Osteoarthritis\n,Knee, Osteoarthritis Of\n,Knees, Osteoarthritis Of\n,Osteoarthritides, Knee\n,Osteoarthritis Of Knee\n,Osteoarthritis Of Knees,osteoarthritis of the knee,osteoarthritis, knee,Osteoarthritis, knee
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Vitamin D deficiency
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Knee osteroarthritis with vit D deficiency
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Knee osteoarthritis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 7
- Group 1 sample size Number of subjects in the case (exposed) group
- 7
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- excluded if antibiotics for last 12 weeks
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
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Fatima on 2022/03/9
Source: Figure 3
Description: differential abundance between KOA_VDD and VDD patients.
Abundance in Group 1: decreased abundance in Knee osteroarthritis with vit D deficiency
| NCBI | Quality Control | Links |
|---|---|---|
| Alloprevotella | ||
| Odoribacter | ||
| Oribacterium | ||
| Prevotella |
Revision editor(s): Fatima
Signature 2
Reviewed Marked as Reviewed by Fatima on 2022/03/9
Source: Figure 3
Description: differential abundance between KOA_VDD and VDD patients.
Abundance in Group 1: increased abundance in Knee osteroarthritis with vit D deficiency
| NCBI | Quality Control | Links |
|---|---|---|
| Butyricimonas | ||
| Candidatus Saccharimonas | ||
| Delftia | ||
| Gordonibacter | ||
| Parabacteroides | ||
| Phascolarctobacterium | ||
| Porphyromonadaceae | ||
| unclassified Coriobacteriaceae | ||
| Clostridiales bacterium |
Revision editor(s): Fatima
