Learning machine approach reveals microbial signatures of diet and sex in dog

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Reviewed Marked as Reviewed by Peace Sandy on 2024-2-27
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
Authors
Scarsella E, Stefanon B, Cintio M, Licastro D, Sgorlon S, Dal Monego S, Sandri M
Journal
PloS one
Year
2020
The characterization of the microbial population of many niches of the organism, as the gastrointestinal tract, is now possible thanks to the use of high-throughput DNA sequencing technique. Several studies in the companion animals field already investigated faecal microbiome in healthy or affected subjects, although the methodologies used in the different laboratories and the limited number of animals recruited in each experiment does not allow a straight comparison among published results. In the present study, we report data collected from several in house researches carried out in healthy dogs, with the aim to seek for a variability of microbial taxa in the faeces, caused by factors such as diet and sex. The database contains 340 samples from 132 dogs, collected serially during dietary intervention studies. The procedure of samples collection, storage, DNA extraction and sequencing, bioinformatic and statistical analysis followed a standardized pipeline. Microbial profiles of faecal samples have been analyzed applying dimensional reduction discriminant analysis followed by random forest analysis to the relative abundances of genera in the feces as variables. The results supported the responsiveness of microbiota at a genera taxonomic level to dietary factor and allowed to cluster dogs according this factor with high accuracy. Also sex factor clustered dogs, with castrated males and spayed females forming a separated group in comparison to intact dogs, strengthening the hypothesis of a bidirectional interaction between microbiota and endocrine status of the host. The findings of the present analysis are promising for a better comprehension of the mechanisms that regulate the connection of the microorganisms living the gastrointestinal tract with the diet and the host. This preliminary study deserves further investigation for the identification of the factors affecting faecal microbiome in dogs.

Experiment 1


Reviewed Marked as Reviewed by Peace Sandy on 2024-2-27

Curated date: 2023/11/07

Curator: Davvve

Revision editor(s): Davvve, Peace Sandy

Subjects

Location of subjects
Italy
Host species Species from which microbiome was sampled. Contact us to have more species added.
Canis lupus familiaris
Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
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

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-27

Curated date: 2024/02/26

Curator: Peace Sandy

Revision editor(s): Peace Sandy

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

NCBI Quality ControlLinks
Bacteroides
Fusobacterium
Ruminococcus
Allobaculum
Anaerobiospirillum
Blautia
Catenibacterium
Clostridium
Collinsella
Coprobacillus
Escherichia
Helicobacter
Lachnospira
Lactobacillus
Megamonas
Peptococcus
Roseburia
Slackia

Revision editor(s): Peace Sandy

Signature 2

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-27

Curated date: 2024/02/26

Curator: Peace Sandy

Revision editor(s): Peace Sandy

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

NCBI Quality ControlLinks
Bacillota
Bacteroidales
Eubacterium
Paraprevotella
Adlercreutzia
Blautia
Butyricicoccus
Coprobacillus
Coprococcus
Dorea
Enterococcus
Candidatus Epulonipiscium
Faecalibacterium
Oscillospira
Parabacteroides
Phascolarctobacterium
Prevotella
Streptococcus
Sutterella
Turicibacter

Revision editor(s): Peace Sandy

Experiment 2


Reviewed Marked as Reviewed by Peace Sandy on 2024-2-27

Curated date: 2024/02/26

Curator: Peace Sandy

Revision editor(s): Peace Sandy

Differences from previous experiment shown

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

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-27

Curated date: 2024/02/26

Curator: Peace Sandy

Revision editor(s): Peace Sandy

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 ControlLinks
Adlercreutzia
Butyricicoccus
Clostridium
Dorea
Enterococcus
Lactobacillus
Parabacteroides
Prevotella
Streptococcus

Revision editor(s): Peace Sandy

Signature 2

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-27

Curated date: 2024/02/26

Curator: Peace Sandy

Revision editor(s): Peace Sandy

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

NCBI Quality ControlLinks
Bacteroides
Fusobacteriia
Eubacterium
Paraprevotella
Ruminococcus
Allobaculum
Anaerobiospirillum
Blautia
Catenibacterium
Collinsella
Coprobacillus
Coprococcus
Candidatus Epulonipiscium
Escherichia
Faecalibacterium
Fusobacterium
Helicobacter
Lachnospira
Megamonas
Oscillospira
Peptococcus
Phascolarctobacterium
Roseburia
Slackia
Sutterella
Turicibacter

Revision editor(s): Peace Sandy

Experiment 3


Reviewed Marked as Reviewed by Peace Sandy on 2024-2-27

Curated date: 2024/02/26

Curator: Peace Sandy

Revision editor(s): Peace Sandy

Differences from previous experiment shown

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

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-27

Curated date: 2024/02/26

Curator: Peace Sandy

Revision editor(s): Peace Sandy

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 ControlLinks
Fusobacteriia
Bacteroidota

Revision editor(s): Peace Sandy

Signature 2

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-27

Curated date: 2024/02/26

Curator: Peace Sandy

Revision editor(s): Peace Sandy

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 ControlLinks
Bacillota

Revision editor(s): Peace Sandy

Experiment 4


Reviewed Marked as Reviewed by Peace Sandy on 2024-2-27

Curated date: 2024/02/26

Curator: Peace Sandy

Revision editor(s): Peace Sandy

Differences from previous experiment shown

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

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-27

Curated date: 2024/02/26

Curator: Peace Sandy

Revision editor(s): Peace Sandy

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 ControlLinks
Bacteroidota
Fusobacteriia

Revision editor(s): Peace Sandy

Signature 2

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-27

Curated date: 2024/02/26

Curator: Peace Sandy

Revision editor(s): Peace Sandy

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 ControlLinks
Bacillota

Revision editor(s): Peace Sandy