Metagenomic dissection of the canine gut microbiota: insights into taxonomic, metabolic and nutritional features.

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PubMed ID: 30680877

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Alessandri G, Milani C, Mancabelli L, Mangifesta M, Lugli GA, Viappiani A, Duranti S, Turroni F, Ossiprandi MC, van Sinderen D, Ventura M

Environ Microbiol. Jan 2019. doi: 10.1111/1462-2920.14540

COMMENT: The authors investigate the canine gut microbiota analyzing a large number of canine fecal samples from healthy dogs belonging to 51 different breeds. 


In the current study we investigated the taxonomical composition of the canine gut microbiota based on 16S rRNA gene and bifidobacterial ITS profiling, involving a total of six wolves and 169 canine fecal samples belonging to 51 different breeds. Moreover, shotgun metagenomics was employed to assess the metabolic repertoire of the dog gut microbiome fed with two distinct diets in order to shed light on microbial and associated functional changes due to the different protein and carbohydrate intakes.


Our detailed reconstruction of the core gut microbiota based on metagenomic data revealed that Bacteroidetes, Fusobacteria, Firmicutes, Proteobacteria and Actinobacteria were the dominant phyla of the canine core intestinal population, which encompasses 43 shared bacterial genera, with Fusobacterium as the most abundant genus.

Diet plays an important role in modulating the canine core gut microbiota, leading to higher bacterial diversity in the CF group when compared to that of the BARF group. In addition, when comparing the intestinal core microbial community of dogs fed on a BARF diet with that of CF-fed dogs, we observed an alteration in the average relative abundance of 14 of the 43 core microbial genera. Interestingly, bacterial genera, such as Faecalibacterium,Sutterella and Prevotella, which are known to be able to degrade a diverse range of carbohydrates, were more abundant in the CF group, whose diet is typically enriched in carbohydrates and fibers.

Comparison of the core gut microbiota of dogs vs. that of wolves and human beings highlighted that the domesticated canine core gut microbial community appears to have lost six bacterial genera typical of the wolf core microbiota, yet, at the same time, has acquired five taxa that are also present in the human core gut microbiota.

Canine gut microbiota was colonized by some of the most dominant bifidobacterial taxa of the mammalian gut, but also by certain Bifidobacterium species that are typical of the human microbiota.

In silico functional characterization of the canine gut microbiome of BARF and CF groups showed that CF diet, typically enriched in plant carbohydrates selects for an intestinal community characterized by a more extensive and diverse repertoire of genes encoding glycan- degrading enzymes. At the same time, prediction of bacterial metabolic pathways revealed that genes involved in amino acid, fatty acid and lipid degradation are more abundant in gut microbiomes of dogs fed on a BARF diet as compared to that of dogs from the CF group.


Altogether, the metagenomic investigations presented in this study revealed that, while maintaining common characteristics with its wild relative in terms of taxonomic composition and metabolic potential, the domesticated canine gut microbiota has been extensively shaped by artificial selection, altered diet and close contact with humans.


Raquel Ruiz-Arroyo