Gut Microbiome of Healthy and Arthritic Dogs/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2022/12/31
Curated date: 2022/12/31
Curator: Claregrieve1
Revision editor(s): WikiWorks, Lwaldron, Claregrieve1, Peace Sandy
Subjects
- Location of subjects
- Italy
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Canis lupus familiaris
- 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
- Arthritis arthritic joint disease,arthritides,arthritis,inflammation of skeletal joint,inflammatory disorder of joint,skeletal joint inflammation,Arthritis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- healthy dogs
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- dogs with hip or elbow arthritis
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- dogs with evidence of hip/elbow arthritis as follows: clinical anamnesis for limping forelimbs and/or associated with posterior limping; rapid fatigue after effort; decrease in motor activity; radiographic evidence of osteoarthritis (AD) in one or two joints (elbow, hips)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 13
- Group 1 sample size Number of subjects in the case (exposed) group
- 14
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 1 month
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- 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)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/12/31
Source: Figure 3b
Description: Differential microbial abundance between healthy dogs and arthritic dogs
Abundance in Group 1: decreased abundance in dogs with hip or elbow arthritis
| NCBI | Quality Control | Links |
|---|---|---|
| Aeromonadales | ||
| Anaerobiospirillum | ||
| Bacteria | ||
| Parabacteroides | ||
| Peptococcaceae | ||
| Peptococcus | ||
| Phascolarctobacterium | ||
| Porphyromonadaceae | ||
| Succinivibrionaceae | ||
| unclassified Mogibacterium |
Revision editor(s): Claregrieve1
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/12/31
Source: Figure 3b
Description: Differential microbial abundance between healthy dogs and arthritic dogs
Abundance in Group 1: increased abundance in dogs with hip or elbow arthritis
| NCBI | Quality Control | Links |
|---|---|---|
| Megamonas |
Revision editor(s): Claregrieve1
