Skip to main content

Table 2 The core gut microbiota of dogs fed a natural diet or a commercial feed, at phylum, family, and species level

From: Differences in the gut microbiota of dogs (Canis lupus familiaris) fed a natural diet or a commercial feed revealed by the Illumina MiSeq platform

  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    
  1. Sequence data of taxon that did not match the existing standard strains were deposited in public database (http://www.ezbiocloud.net)
  2. aThe core microbiota of the natural diet group, but not the commercial feed group
  3. bThe core microbiota of the commercial feed group, but not the natural diet group