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

Abstract

Background: Recent advances in next-generation sequencing technologies have enabled comprehensive analysis of the gut microbiota, which is closely linked to the health of the host. Consequently, several studies have explored the factors affecting gut microbiota composition. In recent years, increasing number of dog owners are feeding their pets a natural diet i.e., one consisting of bones, raw meat (such as chicken and beef), and vegetables, instead of commercial feed. However, the effect of these diets on the microbiota of dogs (Canis lupus familiaris) is unclear.

Methods and results: Six dogs fed a natural diet and five dogs fed a commercial feed were selected; dog fecal metagenomic DNA samples were analyzed using the Illumina MiSeq platform. Pronounced differences in alpha and beta diversities, and taxonomic composition of the core gut microbiota were observed between the two groups. According to alpha diversity, the number of operational taxonomic units, the richness estimates, and diversity indices of microbiota were significantly higher (p < 0.05) in the natural diet group than in the commercial feed group. Based on beta diversity, most samples clustered together according to the diet type (p = 0.004). Additionally, the core microbiota between the two groups was different at the phylum, family, and species levels. Marked differences in the taxonomic composition of the core microbiota of the two groups were observed at the species level; Clostridium perfringens (p = 0.017) and Fusobacterium varium (p = 0.030) were more abundant in the natural diet group.

Conclusions: The gut microbiota of dogs is significantly influenced by diet type (i.e., natural diet and commercial feed). Specifically, dogs fed a natural diet have more diverse and abundant microbial composition in the gut microbiota than dogs fed a commercial feed. In addition, this study suggests that in dogs fed a natural diet, the potential risk of opportunistic infection could be higher, than in dogs fed a commercial feed. The type of diet might therefore play a key role in animal health by affecting the gut microbiota. This study could be the basis for future gut microbiota research in dogs.

Keywords: Canis lupus familiaris; Gut microbiota; Natural diet; Next-generation sequencing.

Fig. 1

Rarefaction curves for gut microbial communities in 11 dogs. The number of operational taxonomic units (OTUs) in the natural diet (ND) group was higher, while the number of valid reads was lower, than in the commercial feed (CF) group (p = 0.004 for both comparisons)

Fig. 2

Box plots of the alpha diversity indices in the two diet groups. ND, natural diet group; CF, commercial feed group. Asterisks refer to extreme values, and circles refer to potential outliers. a The number of OTUs, b Ace richness estimates, c Chao1 richness values, d Shannon diversity indices, and e Simpson diversity indices

Fig. 3

Principal component analysis (PCA) plot of the two diet groups. Beta diversity based on the Fast UniFrac distance matrix. The microbiota of the two diet groups showed pronounced differences in the PCA plot

Fig. 4

Differences in the taxonomic composition of core gut microbiota in the two diet groups. ND, natural diet group; CF, commercial feed group. *p < 0.05; **p < 0.01. The relative abundance of taxa differing between the two groups at the (a) phylum and (b) family levels is shown. c A heat map of the differences in the taxonomic composition of the core microbiota of the two groups. Red color, low abundance; green color, high abundance. Sequence data of taxon that did not match the existing standard strains were deposited in public database (http://www.ezbiocloud.net)