Gut Microbiome of Healthy and Arthritic Dogs/Experiment 1

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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

Curated date: 2022/12/31

Curator: Claregrieve1

Revision editor(s): Claregrieve1

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 ControlLinks
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

Curated date: 2022/12/31

Curator: Claregrieve1

Revision editor(s): Claregrieve1

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 ControlLinks
Megamonas

Revision editor(s): Claregrieve1