Background
Methods
Animals and diets
Group | Name | Breed | Age (months) | Gender | Weight (kg) | Diet and quantity (g) | Number of meals per day |
---|---|---|---|---|---|---|---|
Natural diet group | ND-1 | Poodle | 46 | SF | 4.3 | Kangaroo (75 g), vegetables (10 g) | 1/day |
ND-2 | Poodle | 28 | CM | 5.2 | Kangaroo (110 g), vegetables (15 g) | 1/day | |
ND-3 | BF | 24 | SF | 4.5 | Beef (90 g), vegetables (10 g) | 2/day | |
ND-4 | WH | 12 | CM | 7 | Chicken + duck (150 g), vegetables (10 g) | 2/day | |
ND-5 | BF | 36 | SF | 6.7 | Duck (150 g), vegetables (10 g) | 1/day | |
ND-6 | BF | 27 | CM | 8.3 | Duck (200 g), vegetables (15 g) | 1/day | |
Commercial feed group | CF-1 | Mal | 144 | F | 3 | Natural balance | 2/day |
CF-2 | Mal | 94 | CM | 2.8 | LAMER Dr. Heal skin care | 1/day | |
CF-3 | YT | 77 | CM | 4.2 | LAMER Dr. Heal skin care | 1/day | |
CF-4 | Pom | 36 | M | 4 | Natural balance | 2/day | |
CF-5 | YT | 57 | SF | 3.2 | Natural balance | 2/day |
Sample collection and DNA extraction
Polymerase chain reaction (PCR) amplification and Illumina sequencing
MiSeq pipeline
Data and statistical analyses
Results
Sequence analysis
Alpha diversity
Beta diversity
The core gut microbiota of dogs fed a natural diet or a commercial feed
Natural diet group | Mean | SEM | Commercial feed group | Mean | SEM | |
---|---|---|---|---|---|---|
Phylum | Firmicutes | 64.17 | 9.83 | Firmicutes | 73.33 | 14.19 |
Bacteroidetes | 19.89 | 9.79 | Bacteroidetes | 17.32 | 10.07 | |
Fusobacteriaa
| 13.58 | 4.58 | Proteobacteria | 8.67 | 4.42 | |
Actinobacteria | 1.50 | 0.67 | Actinobacteria | 0.65 | 0.59 | |
Proteobacteria | 0.86 | 0.25 | ||||
Family | Lachnospiraceae | 31.92 | 7.50 | Lachnospiraceae | 46.04 | 14.47 |
Bacteroidaceae | 17.59 | 9.81 | Bacteroidaceae | 16.49 | 9.58 | |
Clostridiaceae | 16.12 | 8.77 | Enterobacteriaceae | 8.40 | 4.31 | |
Fusobacteriaceaea
| 13.55 | 4.57 | Clostridiaceae | 4.56 | 1.94 | |
Peptostreptococcaceae | 7.62 | 3.11 | Streptococcaceae | 3.27 | 3.25 | |
Veillonellaceae | 4.51 | 3.64 | Allobaculum_f | 2.84 | 0.92 | |
Streptococcaceae | 2.43 | 1.72 | Peptostreptococcaceae | 2.56 | 1.55 | |
Prevotellaceaea
| 2.24 | 2.19 | Enterococcaceae | 2.32 | 1.40 | |
Coriobacteriaceaea
| 1.46 | 0.66 | Coprobacillus_f | 1.67 | 0.59 | |
Allobaculum_f | 0.51 | 0.14 | Veillonellaceae | 1.02 | 1.01 | |
Enterococcaceae | 0.37 | 0.23 | Porphyromonadaceaeb
| 0.79 | 0.79 | |
Enterobacteriaceae | 0.35 | 0.12 | Bifidobacteriaceaeb
| 0.59 | 0.58 | |
Ruminococcaceaea
| 0.30 | 0.13 | Sutterella_fb
| 0.24 | 0.23 | |
Coprobacillus_f | 0.11 | 0.05 | ||||
Species |
Clostridium perfringens
a
| 8.90 | 5.07 |
Ruminococcus gnavus
| 18.49 | 6.39 |
Clostridium rectum
a
| 7.99 | 2.38 |
Bacteroides vulgatus
| 8.20 | 6.58 | |
EU465331_sa
| 5.76 | 2.19 |
Escherichia coli group | 7.30 | 3.74 | |
ADLB_sa
| 5.59 | 2.11 | GQ493555_sb
| 7.24 | 3.45 | |
Ruminococcus gnavus
| 4.60 | 1.25 | GQ179695_sb
| 3.34 | 1.89 | |
Clostridium hiranonis
a
| 3.69 | 2.38 | GL872355_s | 2.52 | 1.39 | |
Bacteroides_uc | 3.44 | 2.18 | DQ795137_sb
| 2.49 | 1.34 | |
EF403475_sa
| 2.99 | 1.45 |
Bacteroides_uc | 2.29 | 1.34 | |
GL872355_s | 2.65 | 0.52 |
Bacteroides dorei
b
| 2.26 | 2.17 | |
Bacteroides vulgatus
| 1.98 | 1.03 |
Clostridium difficile
b
| 1.81 | 1.32 | |
Clostridium_uc | 1.71 | 0.94 |
Blautia_uc | 1.44 | 0.79 | |
Fusobacterium_uca
| 1.66 | 0.64 |
Ruminococcus_g6_uc | 1.36 | 0.54 | |
Megamonas_uca
| 1.57 | 1.41 |
Clostridium ramosum
b
| 1.05 | 0.41 | |
Streptococcus equinus groupa
| 1.47 | 1.43 |
Lachnospiraceae_uc_s | 0.96 | 0.30 | |
Clostridium sordellii
a
| 1.44 | 0.95 |
Escherichia_ucb
| 0.76 | 0.41 | |
Bacteroidaceae_uc_s | 1.33 | 0.79 |
Bacteroidaceae_uc_s | 0.67 | 0.39 | |
Blautia_uc | 1.28 | 0.41 | JH590969_sb
| 0.56 | 0.38 | |
Lachnospiraceae_uc_s | 1.22 | 0.14 |
Clostridium paraputrificum
b
| 0.51 | 0.14 | |
Dorea_uc | 1.15 | 0.26 |
Clostridium_g6_ucb
| 0.41 | 0.13 | |
Eubacterium tenue
a
| 0.70 | 0.59 |
Eubacterium_g1_ucb
| 0.39 | 0.15 | |
Fusobacterium varium
a
| 0.65 | 0.24 |
Dorea_uc | 0.39 | 0.13 | |
Fusobacteriaceae_uc_sa
| 0.57 | 0.21 |
Clostridium_uc | 0.34 | 0.13 | |
Ruminococcus_g6_uc | 0.53 | 0.13 |
Enterobacteriaceae_uc_sb
| 0.24 | 0.12 | |
Clostridiaceae_uc_s | 0.54 | 0.27 |
Anaerostipes caccae
b
| 0.18 | 0.15 | |
EF401353_sa
| 0.51 | 0.05 |
Hungatella_uc | 0.17 | 0.09 | |
Clostridium_g4_uc | 0.50 | 0.21 |
Romboutsia sedimentorum
b
| 0.14 | 0.10 | |
FJ370676_sa
| 0.46 | 0.23 |
Clostridium_g4_uc | 0.14 | 0.10 | |
Veillonellaceae_uc_sa
| 0.43 | 0.36 |
Clostridiaceae_uc_s | 0.13 | 0.03 | |
Eubacterium dolichum
a
| 0.37 | 0.14 |
Coprobacillus_f_uc_sb
| 0.13 | 0.05 | |
EU772949_sa
| 0.29 | 0.13 |
Allobaculum_f_uc_sb
| 0.12 | 0.04 | |
Escherichia coli group | 0.29 | 0.11 | ||||
Peptostreptococcaceae_uc_sa
| 0.25 | 0.08 | ||||
Clostridium glycyrrhizinilyticum
a
| 0.24 | 0.16 | ||||
Hungatella_uc | 0.18 | 0.06 | ||||
FJ681620_sa
| 0.17 | 0.13 | ||||
EF400787_sa
| 0.15 | 0.08 | ||||
Prevotella_uca
| 0.10 | 0.10 |