Learning machine approach reveals microbial signatures of diet and sex in dog
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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
- 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
- Diet Dietary,Diets,Diet,diet
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Home Made Diet - H
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Base Diet - B
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- A raw meat diet with the addition of a complementary food, from here on called Base
- Group 0 sample size Number of subjects in the control (unexposed) group
- 30
- Group 1 sample size Number of subjects in the case (exposed) group
- 56
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- NIL
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- Kruskall-Wallis
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- diet, sex
Signature 1
Source: Fig 2 , S5 Table.
Description: Relative Abundances (RA) for the factor diets of the three represented phyla in the fecal microbiota. RA were compared with the Kruskal-Wallis non-parametric test: (A) Firmicutes; (B) Bacteroidetes; (C) Fusobacteria. Data are reported as mean and standard error. W = Commercial moist complete diet; K = Commercial extruded complete diet; H = Home-made diet; B = Base diet.
Comparison of the mean relative abundances (RA) through a non-parametric Kruskal-Wallis test of the three groups of diets.
Abundance in Group 1: increased abundance in Base Diet - B
Revision editor(s): Peace Sandy
Signature 2
Source: Fig 2 , S5 Table.
Description: Relative Abundances (RA) for the factor diets of the three represented phyla in the fecal microbiota. RA were compared with the Kruskal-Wallis non-parametric test: (A) Firmicutes; (B) Bacteroidetes; (C) Fusobacteria. Data are reported as mean and standard error. W = Commercial moist complete diet; K = Commercial extruded complete diet; H = Home-made diet; B = Base diet.
Comparison of the mean relative abundances (RA) through a non-parametric Kruskal-Wallis test of the three groups of diets.
Abundance in Group 1: decreased abundance in Base Diet - B
Revision editor(s): Peace Sandy
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Commercial moist complete diet - W
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Complete diet - K
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Commercial extruded complete diet (K)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 83
- Group 1 sample size Number of subjects in the case (exposed) group
- 171
Lab analysis
Statistical Analysis
Signature 1
Source: Fig 2 , S5 Table.
Description: Relative Abundances (RA) for the factor diets of the three represented phyla in the fecal microbiota. RA were compared with the Kruskal-Wallis non-parametric test: (A) Firmicutes; (B) Bacteroidetes; (C) Fusobacteria. Data are reported as mean and standard error. W = Commercial moist complete diet; K = Commercial extruded complete diet; H = Home-made diet; B = Base diet.
Abundance in Group 1: increased abundance in Complete diet - K
| NCBI | Quality Control | Links |
|---|---|---|
| Adlercreutzia | ||
| Butyricicoccus | ||
| Clostridium | ||
| Dorea | ||
| Enterococcus | ||
| Lactobacillus | ||
| Parabacteroides | ||
| Prevotella | ||
| Streptococcus |
Revision editor(s): Peace Sandy
Signature 2
Source: Fig 2 , S5 Table.
Description: Relative Abundances (RA) for the factor diets of the three represented phyla in the fecal microbiota. RA were compared with the Kruskal-Wallis non-parametric test: (A) Firmicutes; (B) Bacteroidetes; (C) Fusobacteria. Data are reported as mean and standard error. W = Commercial moist complete diet; K = Commercial extruded complete diet; H = Home-made diet; B = Base diet.
Comparison of the mean relative abundances (RA) through a non-parametric Kruskal-Wallis test of the three groups of diets.
Abundance in Group 1: decreased abundance in Complete diet - K
Revision editor(s): Peace Sandy
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Spayed Female - FC
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Whole Female - F
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Whole Female
- Group 0 sample size Number of subjects in the control (unexposed) group
- 28
- Group 1 sample size Number of subjects in the case (exposed) group
- 145
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
Signature 1
Source: Fig 5
Description: Relative Abundances (RA) for the category sex of the three represented phyla in the fecal microbiota. RA were compared with the Kruskal-Wallis non-parametric test: (A) Firmicutes; (B) Bacteroidetes; (C) Fusobacteria. Data are reported as mean and standard error. F = whole females subjects; M = whole males subjects; FC = spayed females subjects; MC = neutered males subjects.
Abundance in Group 1: increased abundance in Whole Female - F
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacteriia | ||
| Bacteroidota |
Revision editor(s): Peace Sandy
Signature 2
Source: Fig 5
Description: Relative Abundances (RA) for the category sex of the three represented phyla in the fecal microbiota. RA were compared with the Kruskal-Wallis non-parametric test: (A) Firmicutes; (B) Bacteroidetes; (C) Fusobacteria. Data are reported as mean and standard error. F = whole females subjects; M = whole males subjects; FC = spayed females subjects; MC = neutered males subjects.
Abundance in Group 1: decreased abundance in Whole Female - F
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota |
Revision editor(s): Peace Sandy
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Castrated Male - MC
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Whole Male - M
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Whole Male
- Group 0 sample size Number of subjects in the control (unexposed) group
- 89
- Group 1 sample size Number of subjects in the case (exposed) group
- 78
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- age, diet
Signature 1
Source: Fig 5
Description: Relative Abundances (RA) for the category sex of the three represented phyla in the fecal microbiota. RA were compared with the Kruskal-Wallis non-parametric test: (A) Firmicutes; (B) Bacteroidetes; (C) Fusobacteria. Data are reported as mean and standard error. F = whole females subjects; M = whole males subjects; FC = spayed females subjects; MC = neutered males subjects.
Abundance in Group 1: increased abundance in Whole Male - M
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidota | ||
| Fusobacteriia |
Revision editor(s): Peace Sandy
Signature 2
Source: Fig 5
Description: Relative Abundances (RA) for the category sex of the three represented phyla in the fecal microbiota. RA were compared with the Kruskal-Wallis non-parametric test: (A) Firmicutes; (B) Bacteroidetes; (C) Fusobacteria. Data are reported as mean and standard error. F = whole females subjects; M = whole males subjects; FC = spayed females subjects; MC = neutered males subjects.
Abundance in Group 1: decreased abundance in Whole Male - M
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota |
Revision editor(s): Peace Sandy
