A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
Subjects
- Location of subjects
- Japan
- 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
- Skin of abdomen Abdomen skin,Abdomen zone of skin,Abdominal skin,Skin of abdomen proper,Zone of skin of abdomen,Skin of abdomen,skin of abdomen
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Atopic eczema allergic,allergic dermatitis,allergic form of dermatitis,Atopic Dermatitides,Atopic Dermatitis,Atopic dermatitis,atopic dermatitis and related conditions,Atopic dermatitis and related conditions (disorder),atopic eczema,Atopic Neurodermatitides,Atopic Neurodermatitis,Atopic neurodermatitis,Besnier's prurigo,Dermatitides, Atopic,Dermatitis, Atopic,Disseminated Neurodermatitides,Disseminated Neurodermatitis,eczema,Eczema, Atopic,Eczema, Infantile,eczematous dermatitis,Infantile Eczema,Neurodermatitides, Atopic,Neurodermatitides, Disseminated,Neurodermatitis, Atopic,Neurodermatitis, Disseminated,OTHER ATOPIC DERMATITIS,Other atopic dermatitis and related conditions,Atopic eczema
- 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
- cADtreat dogs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V2
- 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).
- centered log-ratio
- Statistical test
- Beta Binomial Regression
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.1
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Table S4, Table S3
Description: Differentially abundant bacterial taxa at the genus level between two groups; healthy dogs and cADtreat dogs
Abundance in Group 1: increased abundance in cADtreat dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| Bacteroidota |
Revision editor(s): Deacme, KateRasheed, WikiWorks
Signature 2
Source: Table S4, Table S3
Description: Differentially abundant bacterial taxa at the genus level between two groups; healthy dogs and cADtreat dogs
Abundance in Group 1: decreased abundance in cADtreat dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Arthrobacter | ||
| Corynebacterium | ||
| Pseudomonadota |
Revision editor(s): KateRasheed, WikiWorks
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- cADpre dogs
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cADpost dogs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Table S4, Table S3
Description: Differentially abundant bacterial taxa at the genus level between two groups; cADpre dogs and cADpost dogs
Abundance in Group 1: decreased abundance in cADpost dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Arthrobacter | ||
| Bacillus | ||
| Deinococcus | ||
| Pseudomonas | ||
| Skermanella | ||
| Pseudomonadota | ||
| Bacteroidota | ||
| Deinococcota |
Revision editor(s): Deacme, KateRasheed, WikiWorks
Signature 2
Source: Table S4, Table S3
Description: Differentially abundant bacterial taxa at the genus level between two groups; cADpre dogs and cADpost dogs
Abundance in Group 1: increased abundance in cADpost dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Corynebacterium | ||
| Cutibacterium | ||
| Methylobacterium | ||
| Nocardioides | ||
| Paracoccus | ||
| Roseomonas | ||
| Rubellimicrobium | ||
| Sphingomonas | ||
| Staphylococcus | ||
| Streptococcus | ||
| Actinomycetota | ||
| Acidobacteriota |
Revision editor(s): Deacme, KateRasheed, WikiWorks
Experiment 3
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Forelimb skin Anteriormost limb skin,Fore limb skin,Skin of fore limb,Skin of forelimb,Skin of upper limb,Upper limb skin,Wing skin,Forelimb skin,forelimb skin
- 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
- cADPre dogs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Table S4, Table S3
Description: Differentially abundant bacterial taxa at the genus level between two groups; healthy dogs and cADpre dogs
Abundance in Group 1: decreased abundance in cADPre dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Hymenobacter | ||
| Acidobacteriota | ||
| Deinococcota | ||
| Verrucomicrobiota |
Revision editor(s): Deacme, KateRasheed, WikiWorks
Signature 2
Source: Table S4, Table S3
Description: Differentially abundant bacterial taxa at the genus level between two groups; healthy dogs and cADpre dogs
Abundance in Group 1: increased abundance in cADPre dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Acetobacter | ||
| Pseudomonadota |
Revision editor(s): Deacme, KateRasheed, WikiWorks
Experiment 4
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cADtreat dogs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Source: Table S4
Description: Differentially abundant bacterial taxa at the genus level between two groups; healthy dogs and cADtreat dogs
Abundance in Group 1: decreased abundance in cADtreat dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Acinetobacter | ||
| Frederiksenia |
Revision editor(s): Deacme, KateRasheed, WikiWorks
Signature 2
Source: Table S4
Description: Differentially abundant bacterial taxa at the genus level between two groups; healthy dogs and cADtreat dogs
Abundance in Group 1: increased abundance in cADtreat dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Acetobacter | ||
| Capnocytophaga | ||
| Marmoricola | ||
| Megamonas |
Revision editor(s): Deacme, KateRasheed, WikiWorks
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- cADpre dogs
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cADpost dogs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Table S4
Description: Differentially abundant bacterial taxa at the genus level between two groups; cADpre dogs and cADpost dogs
Abundance in Group 1: decreased abundance in cADpost dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Corynebacterium | ||
| Cutibacterium | ||
| Deinococcus | ||
| Fusobacterium | ||
| Marmoricola | ||
| Nocardioides | ||
| Ottowia | ||
| Paracoccus | ||
| Pseudomonas | ||
| Rubellimicrobium | ||
| Truepera |
Revision editor(s): Deacme, KateRasheed, WikiWorks
Signature 2
Source: Table S4
Description: Differentially abundant bacterial taxa at the genus level between two groups; cADpre dogs and cADpost dogs
Abundance in Group 1: increased abundance in cADpost dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Flavisolibacter | ||
| Hymenobacter | ||
| Methylobacterium | ||
| Neisseria | ||
| Porphyromonas | ||
| Skermanella | ||
| Sphingomonas | ||
| Staphylococcus |
Revision editor(s): Deacme, KateRasheed, WikiWorks
Experiment 6
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Mouth Adult mouth,Cavital oralis,Cavitas oris,Cavum oris,Mouth cavity,Oral region,Oral vestibule,Regio oralis,Rima oris,Stoma,Stomatodaeum,Trophic apparatus,Vestibule of mouth,Vestibulum oris,Mouth,mouth
- 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
- cADPre dogs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Table S4, Table S3
Description: Differentially abundant bacterial taxa at the genus level between two groups; healthy dogs and cADpre dogs
Abundance in Group 1: decreased abundance in cADPre dogs
Revision editor(s): Deacme, KateRasheed, WikiWorks
Signature 2
Source: Table S4, Table S3
Description: Differentially abundant bacterial taxa at the genus level between two groups; healthy dogs and cADpre dogs
Abundance in Group 1: increased abundance in cADPre dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Skermanella | ||
| Staphylococcus | ||
| Bacillota |
Revision editor(s): Deacme, KateRasheed, WikiWorks
Experiment 7
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cADtreat dogs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Table S4, Table S3
Description: Differentially abundant bacterial taxa at the genus level between two groups; healthy dogs and cADtreat dogs
Abundance in Group 1: decreased abundance in cADtreat dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Blautia | ||
| Lautropia | ||
| Porphyromonas | ||
| Pseudarthrobacter | ||
| Rubrobacter | ||
| Skermanella | ||
| Deinococcota |
Revision editor(s): Deacme, KateRasheed, WikiWorks
Signature 2
Source: Table S4, Table S3
Description: Differentially abundant bacterial taxa between two groups; healthy dogs and cADtreat dogs
Abundance in Group 1: increased abundance in cADtreat dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Acinetobacter | ||
| Conchiformibius | ||
| Methylobacterium | ||
| Microbacterium | ||
| Pasteurella | ||
| Variovorax | ||
| Acidobacteriota |
Revision editor(s): Deacme, KateRasheed, WikiWorks
Experiment 8
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- cADpre dogs
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cADpost dogs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Table S4, Table S3
Description: Differentially abundant bacterial taxa between two groups; cADpre dogs and cADpost dogs
Abundance in Group 1: decreased abundance in cADpost dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Capnocytophaga | ||
| Enterobacter | ||
| Filifactor | ||
| Fusobacterium | ||
| Microvirga | ||
| Pasteurella | ||
| Staphylococcus | ||
| Bacteroidota | ||
| Bacillota | ||
| Fusobacteriota |
Revision editor(s): Deacme, KateRasheed, WikiWorks
Signature 2
Source: Table S4, Table S3
Description: Differentially abundant bacterial taxa between two groups; cADpre dogs and cADpost dogs
Abundance in Group 1: increased abundance in cADpost dogs
Revision editor(s): Deacme, KateRasheed, WikiWorks
Experiment 9
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Ventral side of post-anal tail Ventral side of post-anal tail,ventral side of post-anal tail
- 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
- cADpre dogs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Table S4
Description: Differentially abundant bacterial taxa at the genus level between two groups; Healthy dogs and cADpre dogs
Abundance in Group 1: decreased abundance in cADpre dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Porphyromonas | ||
| Rothia |
Revision editor(s): Deacme, KateRasheed, WikiWorks
Signature 2
Source: Table S4
Description: Differentially abundant bacterial taxa at the genus level between two groups; Healthy dogs and cADpre dogs
Abundance in Group 1: increased abundance in cADpre dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Hymenobacter | ||
| Marmoricola |
Revision editor(s): Deacme, KateRasheed, WikiWorks
Experiment 10
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cADtreat dogs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Table S4
Description: Differentially abundant bacterial taxa at the genus level between two groups; Healthy dogs and cADtreat dogs
Abundance in Group 1: decreased abundance in cADtreat dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Cloacibacterium |
Revision editor(s): Deacme, KateRasheed, WikiWorks
Signature 2
Source: Table S4
Description: Differentially abundant bacterial taxa at the genus level between two groups; Healthy dogs and cADtreat dogs
Abundance in Group 1: increased abundance in cADtreat dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Massilia | ||
| Porphyromonas | ||
| Roseomonas | ||
| Staphylococcus | ||
| Turicibacter |
Revision editor(s): Deacme, KateRasheed, WikiWorks
Experiment 11
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- cADpre dogs
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cADpost dogs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Table S4, Table S3
Description: Differentially abundant bacterial taxa between two groups; cADpre dogs and cADpost dogs
Abundance in Group 1: decreased abundance in cADpost dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Blastococcus | ||
| Blautia | ||
| Deinococcus | ||
| Flavisolibacter | ||
| Proteus | ||
| Rubellimicrobium | ||
| Staphylococcus | ||
| Acidobacteriota | ||
| Actinomycetota | ||
| Deinococcota |
Revision editor(s): Deacme, KateRasheed, WikiWorks
Signature 2
Source: Table S4, Table S3
Description: Differentially abundant bacterial taxa between two groups; cADpre dogs and cADpost dogs
Abundance in Group 1: increased abundance in cADpost dogs
Revision editor(s): Deacme, KateRasheed, WikiWorks
Experiment 12
Subjects
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cADpre dogs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
Lab analysis
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Table 2, Table 1
Description: Differentially abundant faecal bacterial taxa between two groups cADpre and Healthy dogs
Abundance in Group 1: decreased abundance in cADpre dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacterium | ||
| Fusobacteriota |
Revision editor(s): Barrakat, KateRasheed, WikiWorks
Signature 2
Source: Table 2
Description: Differentially abundant faecal bacterial taxa at the genus level between two groups cADpre and Healthy dogs
Abundance in Group 1: increased abundance in cADpre dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Amedibacterium | ||
| Anaerostipes | ||
| Blautia | ||
| Clostridium | ||
| Escherichia/Shigella sp. | ||
| Flavonifractor | ||
| Porphyromonas | ||
| Staphylococcus |
Revision editor(s): Barrakat, KateRasheed, WikiWorks
Experiment 13
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- cADpre
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cADpost dogs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Curated date: 2024/03/30
Curator: Barrakat
Revision editor(s): WikiWorks, MyleeeA, Barrakat, KateRasheed
Source: Table 2, Table 1
Description: Differentially abundant bacterial taxa between two groups; cADpre dogs and cADpost dogs
Abundance in Group 1: decreased abundance in cADpost dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Amedibacterium | ||
| Bacteroides | ||
| Blautia | ||
| Clostridium | ||
| Escherichia/Shigella sp. | ||
| Faecalimonas | ||
| Flavonifractor | ||
| Terrisporobacter | ||
| Thomasclavelia | ||
| Actinomycetota | ||
| Bacteroidota | ||
| Bacillota |
Revision editor(s): WikiWorks, MyleeeA, Barrakat, KateRasheed
Signature 2
Source: Table 2, Table 1
Description: Differentially abundant bacterial taxa between two groups; cADpre dogs and cADpost dogs
Abundance in Group 1: increased abundance in cADpost dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerotignum | ||
| Enterocloster | ||
| Fusobacterium | ||
| Lachnospiraceae incertae sedis | ||
| Porphyromonas | ||
| Proteus | ||
| Romboutsia | ||
| Roseburia | ||
| Staphylococcus | ||
| Fusobacteriota | ||
| Pseudomonadota |
Revision editor(s): Barrakat, KateRasheed, WikiWorks
Experiment 14
Subjects
- 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
- cADtreat dogs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Table 2, Table 1
Description: Differentially abundant bacterial taxa between two groups; healthy dogs and cADtreat dogs
Abundance in Group 1: decreased abundance in cADtreat dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerotignum | ||
| Corynebacterium | ||
| Faecalimonas | ||
| Campylobacterota |
Revision editor(s): Barrakat, KateRasheed, WikiWorks
Signature 2
Curated date: 2024/03/30
Curator: Barrakat
Revision editor(s): WikiWorks, MyleeeA, Barrakat, KateRasheed
Source: Table 2
Description: Differentially abundant bacterial taxa at the genus level between two groups; healthy dogs and cADtreat dogs
Abundance in Group 1: increased abundance in cADtreat dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridium | ||
| Turicibacter | ||
| Blautia |
Revision editor(s): WikiWorks, MyleeeA, Barrakat, KateRasheed
Experiment 15
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Skin of abdomen Abdomen skin,Abdomen zone of skin,Abdominal skin,Skin of abdomen proper,Zone of skin of abdomen,Skin of abdomen,skin of abdomen
- 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
- cAD Pre
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments
Lab analysis
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V2
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- Not specified
- Statistical test
- ANCOM
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Table S7 and Fig 3
Description: Statistical summary of differentially abundant Staphylococcus spp. between dog groups.
Abundance in Group 1: increased abundance in cAD Pre
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus pseudintermedius |
Experiment 16
Curated date: 2024/04/01
Curator: MyleeeA
Revision editor(s): WikiWorks, MyleeeA, Victoria, KateRasheed
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- cAD Pre
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cAD post
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Table S4, Fig 3, Supplementary Table S7
Description: Statistical summary of differentially abundant taxa between dog groups.
Abundance in Group 1: decreased abundance in cAD post
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus coagulans | ||
| Staphylococcus pseudintermedius | ||
| Staphylococcus schleiferi | ||
| Bacillus |
Revision editor(s): MyleeeA, KateRasheed, WikiWorks
Experiment 17
Curated date: 2024/04/01
Curator: MyleeeA
Revision editor(s): WikiWorks, MyleeeA, Victoria, KateRasheed
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cAD Treat
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Table S7, Supplementary Table S4 and Fig 3
Description: Statistical summary of differentially abundant of taxa between dog groups.
Abundance in Group 1: decreased abundance in cAD Treat
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus equorum | ||
| Curvibacter |
Revision editor(s): MyleeeA, KateRasheed, WikiWorks
Signature 2
Source: Supplementary Table S7 and Fig 3
Description: Statistical summary of differentially abundant Staphylococcus spp. between dog groups.
Abundance in Group 1: increased abundance in cAD Treat
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus epidermidis |
Experiment 18
Curated date: 2024/04/01
Curator: MyleeeA
Revision editor(s): WikiWorks, MyleeeA, Victoria, KateRasheed
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Axilla skin Axillary skin,Skin of axilla,Axilla skin,axilla skin
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cAD Pre
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Table S7 and Fig 3
Description: Statistical summary of differentially abundant Staphylococcus spp. between dog groups.
Abundance in Group 1: increased abundance in cAD Pre
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus pseudintermedius |
Experiment 19
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- cAD Pre
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cAD post
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Table S7 and Fig 3
Description: Statistical summary of differentially abundant Staphylococcus spp. between dog groups.
Abundance in Group 1: increased abundance in cAD post
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus equorum |
Signature 2
Source: Supplementary Table S7 and Fig 3
Description: Statistical summary of differentially abundant Staphylococcus spp. between dog groups.
Abundance in Group 1: decreased abundance in cAD post
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus hominis |
Experiment 20
Subjects
- 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
- cADtreat dogs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Table S7 and Figure 3
Description: Statistical summary of differentially abundant Staphylococcus spp. between dog groups.
Abundance in Group 1: increased abundance in cADtreat dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus epidermidis | ||
| Staphylococcus haemolyticus |
Revision editor(s): Deacme, KateRasheed, WikiWorks
Experiment 21
Curated date: 2024/04/02
Curator: Deacme
Revision editor(s): WikiWorks, Deacme, Victoria, KateRasheed
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Brachialis muscle Casserio's muscle,Brachialis,Brachialis anticus muscle,Musculus brachialis,Brachialis muscle,brachialis muscle
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cADPre dogs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Supplementary Table S7 and Figure 3
Description: Statistical summary of differentially abundant Staphylococcus spp. between dog groups.
Abundance in Group 1: increased abundance in cADPre dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus pseudintermedius |
Revision editor(s): Deacme, KateRasheed, WikiWorks
Experiment 22
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cADtreat dogs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Table S7 and Figure 3
Description: Statistical summary of differentially abundant Staphylococcus spp. between dog groups.
Abundance in Group 1: decreased abundance in cADtreat dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus equorum | ||
| Staphylococcus schleiferi |
Revision editor(s): Deacme, KateRasheed, WikiWorks
Experiment 23
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Lateral lumbar region of abdomen Flank,Lateral region,Lateral region of abdomen,Latus,Regio lateralis,Lateral lumbar region of abdomen,lateral lumbar region of abdomen
- 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
- cAD Pre
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 2
Curated date: 2024/04/02
Curator: Barrakat
Revision editor(s): WikiWorks, Deacme, Barrakat, KateRasheed
Source: Supplementary Table S7 and Fig 3
Description: Statistical summary of differentially abundant Staphylococcus spp. between dog groups.
Abundance in Group 1: increased abundance in cAD Pre
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus pseudintermedius |
Revision editor(s): WikiWorks, Deacme, Barrakat, KateRasheed
Experiment 24
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cAD Treat
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Curated date: 2024/04/02
Curator: Barrakat
Revision editor(s): WikiWorks, Deacme, Barrakat, KateRasheed
Source: Supplementary Table S7 and Figure 3
Description: Statistical summary of differentially abundant Staphylococcus spp. between dog groups.
Abundance in Group 1: decreased abundance in cAD Treat
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus coagulans | ||
| Staphylococcus equorum | ||
| Staphylococcus schleiferi |
Revision editor(s): WikiWorks, Deacme, Barrakat, KateRasheed
Signature 2
Source: Supplementary Table S7 and Figure 3
Description: Statistical summary of differentially abundant Staphylococcus spp. between dog groups.
Abundance in Group 1: increased abundance in cAD Treat
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus haemolyticus |
Revision editor(s): Deacme, KateRasheed, WikiWorks
Experiment 25
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- cADpre
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cAD Post
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Curated date: 2024/04/02
Curator: Barrakat
Revision editor(s): WikiWorks, Deacme, Barrakat, KateRasheed
Source: Supplementary Table S7 and Fig 3
Description: Statistical summary of differentially abundant Staphylococcus spp. between dog groups.
Abundance in Group 1: decreased abundance in cAD Post
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus hominis |
Revision editor(s): WikiWorks, Deacme, Barrakat, KateRasheed
Experiment 26
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Forelimb skin Anteriormost limb skin,Fore limb skin,Skin of fore limb,Skin of forelimb,Skin of upper limb,Upper limb skin,Wing skin,Forelimb skin,forelimb skin
- 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
- cAD Pre
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 2
Source: Supplementary Table S7, Supplementary Table S3-4 and Figure 3
Description: Statistical summary of differentially abundant taxa between dog groups.
Abundance in Group 1: increased abundance in cAD Pre
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus pseudintermedius | ||
| Fusobacterium | ||
| Bacillota |
Revision editor(s): Barrakat, KateRasheed, WikiWorks
Experiment 27
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cAD Treat
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Curated date: 2024/04/02
Curator: Barrakat
Revision editor(s): WikiWorks, Deacme, Barrakat, KateRasheed
Source: Supplementary Table S7, Supplementary Table S4 and Figure 3
Description: Statistical summary of differentially abundant taxa between dog groups.
Abundance in Group 1: decreased abundance in cAD Treat
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus equorum | ||
| Curvibacter |
Revision editor(s): WikiWorks, Deacme, Barrakat, KateRasheed
Signature 2
Source: Supplementary Table S3
Description: Statistical summary of differentially abundant taxa between dog groups.
Abundance in Group 1: increased abundance in cAD Treat
| NCBI | Quality Control | Links |
|---|---|---|
| Acidobacteriota |
Revision editor(s): KateRasheed, WikiWorks
Experiment 28
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- cADpre
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cAD Post
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Curated date: 2024/04/02
Curator: Barrakat
Revision editor(s): WikiWorks, Deacme, Barrakat, KateRasheed
Source: Supplementary Table S7, Supplementary Table S3 and Figure 3
Description: Statistical summary of differentially abundant taxa between dog groups.
Abundance in Group 1: decreased abundance in cAD Post
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus coagulans | ||
| Staphylococcus schleiferi | ||
| Staphylococcus warneri | ||
| Bacillota | ||
| Fusobacteriota |
Revision editor(s): WikiWorks, Deacme, Barrakat, KateRasheed
Experiment 29
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Hindlimb skin Hind limb skin,Lower limb skin,Skin of hind limb,Skin of hindlimb,Skin of lower extremity,Skin of lower limb,Hindlimb skin,hindlimb skin
- 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
- cAD Pre
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Curated date: 2024/04/02
Curator: Barrakat
Revision editor(s): WikiWorks, Deacme, Barrakat, KateRasheed
Source: Supplementary Table S7 and Figure 3
Description: Statistical summary of differentially abundant Staphylococcus spp. between dog groups.
Abundance in Group 1: increased abundance in cAD Pre
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus pseudintermedius |
Revision editor(s): WikiWorks, Deacme, Barrakat, KateRasheed
Experiment 30
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cADtreat dogs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Curated date: 2024/04/02
Curator: Barrakat
Revision editor(s): WikiWorks, Deacme, Barrakat, KateRasheed
Source: Supplementary Table S7 and Figure 3
Description: Statistical summary of differentially abundant Staphylococcus spp. between dog groups.
Abundance in Group 1: decreased abundance in cADtreat dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus coagulans | ||
| Staphylococcus haemolyticus | ||
| Staphylococcus schleiferi |
Revision editor(s): WikiWorks, Deacme, Barrakat, KateRasheed
Experiment 31
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- cADpre dogs
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cADpost dogs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Curated date: 2024/04/02
Curator: Barrakat
Revision editor(s): WikiWorks, Deacme, Barrakat, KateRasheed
Source: Supplementary Table S7 and Figure 3
Description: Statistical summary of differentially abundant Staphylococcus spp. between dog groups.
Abundance in Group 1: decreased abundance in cADpost dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus caprae | ||
| Staphylococcus epidermidis | ||
| Staphylococcus lugdunensis | ||
| Staphylococcus pseudintermedius | ||
| Staphylococcus warneri |
Revision editor(s): WikiWorks, Deacme, Barrakat, KateRasheed
Signature 2
Curated date: 2024/04/02
Curator: Barrakat
Revision editor(s): WikiWorks, Deacme, Barrakat, KateRasheed
Source: Supplementary Table S7 and Figure 3
Description: Statistical summary of differentially abundant Staphylococcus spp. between dog groups.
Abundance in Group 1: increased abundance in cADpost dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus aureus |
Revision editor(s): WikiWorks, Deacme, Barrakat, KateRasheed
Experiment 32
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Inguinal part of abdomen Groin,Groin area,Groin region,Iliac fossa viewed surgically,Iliac region,Inguen,Inguinal region,Inguinal part of abdomen,inguinal part of abdomen
- 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
- cADpre dogs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Curated date: 2024/04/02
Curator: Barrakat
Revision editor(s): WikiWorks, Deacme, Barrakat, KateRasheed
Source: Supplementary Table S7 and Figure 3
Description: Statistical summary of differentially abundant Staphylococcus spp. between dog groups.
Abundance in Group 1: increased abundance in cADpre dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus pseudintermedius |
Revision editor(s): WikiWorks, Deacme, Barrakat, KateRasheed
Experiment 33
Curated date: 2024/04/05
Curator: Deacme
Revision editor(s): WikiWorks, Deacme, Victoria, KateRasheed
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- cADpre dogs
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cADpost dogs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Table S7 and Figure 3
Description: Statistical summary of differentially abundant Staphylococcus spp. between dog groups.
Abundance in Group 1: decreased abundance in cADpost dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus equorum |
Revision editor(s): Deacme, KateRasheed, WikiWorks
Experiment 34
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Pinna Auricle,Auricle of ear,Auricle of external ear,Auricula,Auricula (auris externa),Pinna of ear,Pinnae,Pinna,pinna
- 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
- cADpre dogs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Supplementary Table S7 and Figure 3
Description: Statistical summary of differentially abundant Staphylococcus spp. between dog groups.
Abundance in Group 1: decreased abundance in cADpre dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus equorum | ||
| Staphylococcus warneri |
Revision editor(s): Deacme, KateRasheed, WikiWorks
Experiment 35
Curated date: 2024/04/05
Curator: Deacme
Revision editor(s): WikiWorks, Deacme, Victoria, KateRasheed
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cADtreat dogs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Table S7 and Figure 3
Description: Statistical summary of differentially abundant Staphylococcus spp. between dog groups.
Abundance in Group 1: decreased abundance in cADtreat dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus equorum | ||
| Staphylococcus schleiferi | ||
| Staphylococcus warneri |
Revision editor(s): Deacme, KateRasheed, WikiWorks
Experiment 36
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- cADpre dogs
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cADpost dogs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Source: Supplementary Table S7 and Figure 3
Description: Statistical summary of differentially abundant Staphylococcus spp. between dog groups.
Abundance in Group 1: increased abundance in cADpost dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus warneri |
Revision editor(s): Deacme, KateRasheed, WikiWorks
Experiment 37
Curated date: 2024/04/06
Curator: Deacme
Revision editor(s): WikiWorks, Deacme, Victoria, KateRasheed
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Skin of palmar/plantar part of autopod Skin of palmar/plantar part of autopod,skin of palmar/plantar part of autopod
- 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
- cADPre dogs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Table S7 and Figure 3
Description: Statistical summary of differentially abundant Staphylococcus spp. between dog groups.
Abundance in Group 1: decreased abundance in cADPre dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus aureus | ||
| Staphylococcus equorum |
Revision editor(s): Deacme, KateRasheed, WikiWorks
Signature 2
Source: Supplementary Table S7 and Figure 3
Description: Statistical summary of differentially abundant Staphylococcus spp. between dog groups.
Abundance in Group 1: increased abundance in cADPre dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus pseudintermedius |
Revision editor(s): Deacme, KateRasheed, WikiWorks
Experiment 38
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cADtreat dogs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Table S7 and Figure 3
Description: Statistical summary of differentially abundant Staphylococcus spp. between dog groups.
Abundance in Group 1: decreased abundance in cADtreat dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus equorum | ||
| Staphylococcus warneri |
Revision editor(s): Deacme, KateRasheed, WikiWorks
Experiment 39
Curated date: 2024/04/06
Curator: Deacme
Revision editor(s): WikiWorks, Deacme, Victoria, KateRasheed
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- cADpre dogs
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cADpost dogs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Table S7 and Figure 3
Description: Statistical summary of differentially abundant Staphylococcus spp. between dog groups.
Abundance in Group 1: decreased abundance in cADpost dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus hominis |
Revision editor(s): Deacme, KateRasheed, WikiWorks
Experiment 40
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Mouth Adult mouth,Cavital oralis,Cavitas oris,Cavum oris,Mouth cavity,Oral region,Oral vestibule,Regio oralis,Rima oris,Stoma,Stomatodaeum,Trophic apparatus,Vestibule of mouth,Vestibulum oris,Mouth,mouth
- 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
- cADpre dogs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Supplementary Table S7 and Figure 3
Description: Statistical summary of differentially abundant Staphylococcus spp. between dog groups.
Abundance in Group 1: decreased abundance in cADpre dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Mammaliicoccus sciuri |
Revision editor(s): Deacme, KateRasheed, WikiWorks
Signature 2
Source: Supplementary Table S7 and Figure 3
Description: Statistical summary of differentially abundant Staphylococcus spp. between dog groups.
Abundance in Group 1: increased abundance in cADpre dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus pseudintermedius |
Revision editor(s): Deacme, KateRasheed, WikiWorks
Experiment 41
Curated date: 2024/04/06
Curator: Deacme
Revision editor(s): WikiWorks, Deacme, Victoria, KateRasheed
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- cADpre dogs
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cADpost dogs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Table S7, Supplementary Table S3 and Figure 3
Description: Statistical summary of differentially abundant taxa between dog groups.
Abundance in Group 1: decreased abundance in cADpost dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus coagulans | ||
| Staphylococcus pseudintermedius | ||
| Staphylococcus schleiferi | ||
| Actinomycetota |
Revision editor(s): Deacme, KateRasheed, WikiWorks
Signature 2
Source: Supplementary Table S4
Description: Statistical summary of differentially abundant taxa between dog groups.
Abundance in Group 1: increased abundance in cADpost dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonadota | ||
| Acetobacter | ||
| Cutibacterium |
Revision editor(s): KateRasheed, WikiWorks
Experiment 42
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Perineum Perineal region,Regio perinealis,Perineum,perineum
- 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
- cADpre dogs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Table S7 and Figure 3
Description: Statistical summary of differentially abundant Staphylococcus spp. between dog groups.
Abundance in Group 1: decreased abundance in cADpre dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus warneri |
Revision editor(s): Deacme, KateRasheed, WikiWorks
Experiment 43
Curated date: 2024/04/06
Curator: Deacme
Revision editor(s): WikiWorks, Deacme, Victoria, KateRasheed
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Ventral side of post-anal tail Ventral side of post-anal tail,ventral side of post-anal tail
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Table S7, Supplementary Table S4 and Figure 3
Description: Statistical summary of differentially abundant taxa between dog groups.
Abundance in Group 1: increased abundance in cADpre dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus pseudintermedius | ||
| Staphylococcus |
Revision editor(s): Deacme, KateRasheed, WikiWorks
Experiment 44
Curated date: 2024/04/06
Curator: Deacme
Revision editor(s): WikiWorks, Deacme, Victoria, KateRasheed
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cADtreat dogs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Table S7, Supplementary Table S4 and Figure 3
Description: Statistical summary of differentially abundant taxa between dog groups.
Abundance in Group 1: decreased abundance in cADtreat dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus equorum | ||
| Moraxella |
Revision editor(s): Deacme, KateRasheed, WikiWorks
Signature 2
Source: Supplementary Table S7, Supplementary Table S4 and Figure 3
Description: Statistical summary of differentially abundant taxa between dog groups.
Abundance in Group 1: increased abundance in cADtreat dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus epidermidis | ||
| Staphylococcus hominis | ||
| Lautropia |
Revision editor(s): Deacme, KateRasheed, WikiWorks
Experiment 45
Curated date: 2024/04/06
Curator: Deacme
Revision editor(s): WikiWorks, Deacme, Victoria, KateRasheed
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- cADpre dogs
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cADpost dogs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Table S7 and Figure 3
Description: Statistical summary of differentially abundant Staphylococcus spp. between dog groups.
Abundance in Group 1: increased abundance in cADpost dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus hominis |
Revision editor(s): Deacme, KateRasheed, WikiWorks
Experiment 46
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Mouth Adult mouth,Cavital oralis,Cavitas oris,Cavum oris,Mouth cavity,Oral region,Oral vestibule,Regio oralis,Rima oris,Stoma,Stomatodaeum,Trophic apparatus,Vestibule of mouth,Vestibulum oris,Mouth,mouth
- 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
- cADtreat dogs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Table S3
Description: Statistical summary of differentially abundant taxa between dog groups.
Abundance in Group 1: increased abundance in cADtreat dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonadota |
Revision editor(s): KateRasheed, WikiWorks
Experiment 47
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Abdomen Abdominopelvic region,Abdominopelvis,Adult abdomen,Belly,Celiac region,Abdomen,abdomen
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cADpre dogs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- ANOVA
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Fig. 1C
Description: Differentially abundant taxa between dogs using ANOVA
Abundance in Group 1: increased abundance in cADpre dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus |
Revision editor(s): KateRasheed, WikiWorks
Experiment 48
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- cADpre dogs
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cADpost dogs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Fig. 1C
Description: Differentially abundant taxa between dogs using ANOVA
Abundance in Group 1: decreased abundance in cADpost dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus |
Revision editor(s): KateRasheed, WikiWorks
Experiment 49
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Axilla Arm pit,Armpit,Armpits,Axilla,Axillae,Axillary region,Oxter,Regio axillaris,Underarm,axilla
- 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
- cADpre dogs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Fig. 1C
Description: Differentially abundant taxa between dogs using ANOVA
Abundance in Group 1: increased abundance in cADpre dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus |
Revision editor(s): KateRasheed, WikiWorks
Experiment 50
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Brachialis muscle Casserio's muscle,Brachialis,Brachialis anticus muscle,Musculus brachialis,Brachialis muscle,brachialis muscle
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Fig. 1C
Description: Differentially abundant taxa between dogs using ANOVA
Abundance in Group 1: increased abundance in cADpre dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus |
Revision editor(s): KateRasheed, WikiWorks
Experiment 51
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- cADpre dogs
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cADpost dogs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Fig. 1C
Description: Differentially abundant taxa between dogs using ANOVA
Abundance in Group 1: decreased abundance in cADpost dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus |
Revision editor(s): KateRasheed, WikiWorks
Experiment 52
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cADtreat dogs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Fig. 1C
Description: Differentially abundant taxa between dogs using ANOVA
Abundance in Group 1: decreased abundance in cADtreat dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus |
Revision editor(s): KateRasheed, WikiWorks
Experiment 53
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Inguinal part of abdomen Groin,Groin area,Groin region,Iliac fossa viewed surgically,Iliac region,Inguen,Inguinal region,Inguinal part of abdomen,inguinal part of abdomen
- 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
- cADpre dogs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Fig. 1C
Description: Differentially abundant taxa between dogs using ANOVA
Abundance in Group 1: increased abundance in cADpre dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus |
Revision editor(s): KateRasheed, WikiWorks
Experiment 54
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Carpal bone Bone of carpus,Carpal,Carpal skeleton bone,Carpus bone,Carpal bone,carpal bone
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Fig. 1C
Description: Differentially abundant taxa between dogs using ANOVA
Abundance in Group 1: increased abundance in cADpre dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus |
Revision editor(s): KateRasheed, WikiWorks
Experiment 55
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- cADpre dogs
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cADpost dogs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Fig. 1C
Description: Differentially abundant taxa between dogs using ANOVA
Abundance in Group 1: decreased abundance in cADpost dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus |
Revision editor(s): KateRasheed, WikiWorks
Experiment 56
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cADtreat dogs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Dogs that were already diagnosed with cAD (canine atopic dermatitis) before the study cohort recruitment and had been on oclacitinib treatment
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Fig. 1C
Description: Differentially abundant taxa between dogs using ANOVA
Abundance in Group 1: decreased abundance in cADtreat dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus |
Revision editor(s): KateRasheed, WikiWorks
Experiment 57
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Mouth Adult mouth,Cavital oralis,Cavitas oris,Cavum oris,Mouth cavity,Oral region,Oral vestibule,Regio oralis,Rima oris,Stoma,Stomatodaeum,Trophic apparatus,Vestibule of mouth,Vestibulum oris,Mouth,mouth
- 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
- cADpre dogs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Dogs that were newly diagnosed with cAD (canine atopic dermatitis) without any previous medical treatments
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Fig. 1C
Description: Differentially abundant taxa between dogs using ANOVA
Abundance in Group 1: increased abundance in cADpre dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus |
Revision editor(s): KateRasheed, WikiWorks
Experiment 58
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- cADpre dogs
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cADpost dogs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- cADpre dogs that were consequently placed under oclacitinib treatment for two weeks after the diagnosis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Fig. 1C
Description: Differentially abundant taxa between dogs using ANOVA
Abundance in Group 1: decreased abundance in cADpost dogs
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus |
Revision editor(s): KateRasheed, WikiWorks
Experiment 59
Subjects
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Mitochondrial haplogroups A
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mitochondrial haplogroups C
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mitochondrial haplogroups C refers to dogs belonging to this haplogroup, determined using the Canis mtDNA HV1 database
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
- Group 1 sample size Number of subjects in the case (exposed) group
- 14
Lab analysis
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- centered log-ratio
- Statistical test
- Beta Binomial Regression
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.1
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Table 10
Description: Statistical summary of differentially abundant faecal bacterial taxa between mtDNA haplogroups A and C
Abundance in Group 1: decreased abundance in Mitochondrial haplogroups C
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| Campylobacterota | ||
| Anaerostipes | ||
| Bacillota | ||
| Streptococcus | ||
| Anaerotignum | ||
| Blautia | ||
| Amedibacterium | ||
| Clostridium XVIIIClostridium XVIII |
Revision editor(s): KateRasheed, WikiWorks
Experiment 60
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Axilla Arm pit,Armpit,Armpits,Axilla,Axillae,Axillary region,Oxter,Regio axillaris,Underarm,axilla
Lab analysis
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V2
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Table 10
Description: Statistical summary of differentially abundant skin bacterial taxa between mtDNA haplogroups A and C
Abundance in Group 1: decreased abundance in Mitochondrial haplogroups C
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| Arthrobacter | ||
| Bacteroides |
Revision editor(s): KateRasheed, WikiWorks
Experiment 61
Subjects
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- Not specified
- Statistical test
- ANCOM
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Table 10
Description: Statistical summary of differentially abundant skin bacterial taxa between mtDNA haplogroups A and C
Abundance in Group 1: increased abundance in Mitochondrial haplogroups C
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidota |
Revision editor(s): KateRasheed, WikiWorks
Signature 2
Source: Supplementary Table 10
Description: Statistical summary of differentially abundant skin bacterial taxa between mtDNA haplogroups A and C
Abundance in Group 1: decreased abundance in Mitochondrial haplogroups C
| NCBI | Quality Control | Links |
|---|---|---|
| Rubellimicrobium | ||
| Haemophilus |
Revision editor(s): KateRasheed, WikiWorks
Experiment 62
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Pinna Auricle,Auricle of ear,Auricle of external ear,Auricula,Auricula (auris externa),Pinna of ear,Pinnae,Pinna,pinna
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- centered log-ratio
- Statistical test
- Beta Binomial Regression
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Table 10
Description: Statistical summary of differentially abundant skin bacterial taxa between mtDNA haplogroups A and C
Abundance in Group 1: increased abundance in Mitochondrial haplogroups C
| NCBI | Quality Control | Links |
|---|---|---|
| Rothia | ||
| Tannerella | ||
| Stenotrophomonas |
Revision editor(s): KateRasheed, WikiWorks
Signature 2
Source: Supplementary Table 10
Description: Statistical summary of differentially abundant skin bacterial taxa between mtDNA haplogroups A and C
Abundance in Group 1: decreased abundance in Mitochondrial haplogroups C
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| Flavobacterium | ||
| Pasteurella |
Revision editor(s): KateRasheed, WikiWorks
Experiment 63
Subjects
- 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
Lab analysis
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- Not specified
- Statistical test
- ANCOM
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Table 10
Description: Statistical summary of differentially abundant faecal bacterial taxa between mtDNA haplogroups A and C
Abundance in Group 1: decreased abundance in Mitochondrial haplogroups C
| NCBI | Quality Control | Links |
|---|---|---|
| Roseburia |
Revision editor(s): KateRasheed, WikiWorks
Experiment 64
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Forelimb Anteriormost limb,Fore limb,Foreleg,Forelimb,Free part of upper limb,Free upper limb,Membrum superius,Pectoral flipper,Pectoral limb,Superior member,Upper extremity,Upper limb,forelimb
Lab analysis
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V2
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- centered log-ratio
- Statistical test
- Beta Binomial Regression
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Table 10
Description: Statistical summary of differentially abundant skin bacterial taxa between mtDNA haplogroups A and C
Abundance in Group 1: increased abundance in Mitochondrial haplogroups C
| NCBI | Quality Control | Links |
|---|---|---|
| Haemophilus |
Revision editor(s): KateRasheed, WikiWorks
Signature 2
Source: Supplementary Table 10
Description: Statistical summary of differentially abundant skin bacterial taxa between mtDNA haplogroups A and C
Abundance in Group 1: decreased abundance in Mitochondrial haplogroups C
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Capnocytophaga | ||
| Neisseria |
Revision editor(s): KateRasheed, WikiWorks
Contents
- 1 Experiment 1
- 2 Experiment 2
- 3 Experiment 3
- 4 Experiment 4
- 5 Experiment 5
- 6 Experiment 6
- 7 Experiment 7
- 8 Experiment 8
- 9 Experiment 9
- 10 Experiment 10
- 11 Experiment 11
- 12 Experiment 12
- 13 Experiment 13
- 14 Experiment 14
- 15 Experiment 15
- 16 Experiment 16
- 17 Experiment 17
- 18 Experiment 18
- 19 Experiment 19
- 20 Experiment 20
- 21 Experiment 21
- 22 Experiment 22
- 23 Experiment 23
- 24 Experiment 24
- 25 Experiment 25
- 26 Experiment 26
- 27 Experiment 27
- 28 Experiment 28
- 29 Experiment 29
- 30 Experiment 30
- 31 Experiment 31
- 32 Experiment 32
- 33 Experiment 33
- 34 Experiment 34
- 35 Experiment 35
- 36 Experiment 36
- 37 Experiment 37
- 38 Experiment 38
- 39 Experiment 39
- 40 Experiment 40
- 41 Experiment 41
- 42 Experiment 42
- 43 Experiment 43
- 44 Experiment 44
- 45 Experiment 45
- 46 Experiment 46
- 47 Experiment 47
- 48 Experiment 48
- 49 Experiment 49
- 50 Experiment 50
- 51 Experiment 51
- 52 Experiment 52
- 53 Experiment 53
- 54 Experiment 54
- 55 Experiment 55
- 56 Experiment 56
- 57 Experiment 57
- 58 Experiment 58
- 59 Experiment 59
- 60 Experiment 60
- 61 Experiment 61
- 62 Experiment 62
- 63 Experiment 63
- 64 Experiment 64
