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

Kim, Junhyung; An, Jae-Uk; Kim, Woohyun; Lee, Soomin; Cho, Seongbeom

doi:10.1186/s13099-017-0218-5

Gut Pathogens

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
	Fusobacteria^a	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
	Fusobacteriaceae^a	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
	Prevotellaceae^a	2.24	2.19	Enterococcaceae	2.32	1.40
	Coriobacteriaceae^a	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	Porphyromonadaceae^b	0.79	0.79
	Enterobacteriaceae	0.35	0.12	Bifidobacteriaceae^b	0.59	0.58
	Ruminococcaceae^a	0.30	0.13	Sutterella_f^b	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_s^a	5.76	2.19	Escherichia coli group	7.30	3.74
	ADLB_s^a	5.59	2.11	GQ493555_s^b	7.24	3.45
	Ruminococcus gnavus	4.60	1.25	GQ179695_s^b	3.34	1.89
	Clostridium hiranonis ^a	3.69	2.38	GL872355_s	2.52	1.39
	Bacteroides_uc	3.44	2.18	DQ795137_s^b	2.49	1.34
	EF403475_s^a	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_uc^a	1.66	0.64	Ruminococcus_g6_uc	1.36	0.54
	Megamonas_uc^a	1.57	1.41	Clostridium ramosum ^b	1.05	0.41
	Streptococcus equinus group^a	1.47	1.43	Lachnospiraceae_uc_s	0.96	0.30
	Clostridium sordellii ^a	1.44	0.95	Escherichia_uc^b	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_s^b	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_uc^b	0.41	0.13
	Eubacterium tenue ^a	0.70	0.59	Eubacterium_g1_uc^b	0.39	0.15
	Fusobacterium varium ^a	0.65	0.24	Dorea_uc	0.39	0.13
	Fusobacteriaceae_uc_s^a	0.57	0.21	Clostridium_uc	0.34	0.13
	Ruminococcus_g6_uc	0.53	0.13	Enterobacteriaceae_uc_s^b	0.24	0.12
	Clostridiaceae_uc_s	0.54	0.27	Anaerostipes caccae ^b	0.18	0.15
	EF401353_s^a	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_s^a	0.46	0.23	Clostridium_g4_uc	0.14	0.10
	Veillonellaceae_uc_s^a	0.43	0.36	Clostridiaceae_uc_s	0.13	0.03
	Eubacterium dolichum ^a	0.37	0.14	Coprobacillus_f_uc_s^b	0.13	0.05
	EU772949_s^a	0.29	0.13	Allobaculum_f_uc_s^b	0.12	0.04
	Escherichia coli group	0.29	0.11
	Peptostreptococcaceae_uc_s^a	0.25	0.08
	Clostridium glycyrrhizinilyticum ^a	0.24	0.16
	Hungatella_uc	0.18	0.06
	FJ681620_s^a	0.17	0.13
	EF400787_s^a	0.15	0.08
	Prevotella_uc^a	0.10	0.10

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

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ISSN: 1757-4749

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