The Fecal Microbiota of Dogs Switching to a Raw Diet Only Partially Converges to That of Wolves.

Jia Xu,Limin Ding,Geert P J Janssens,Wenfu Zhang,Bingqian Ge,Jianmei Wang,Chunqing Leng,Xiaoyu Fu,Yu Luo,Guyue Wang,Anne A M J Becker

doi:10.3389/fmicb.2021.701439

Abstract

The genomic signature of dog domestication reveals adaptation to a starch-rich diet compared with their ancestor wolves. Diet is a key element to shape gut microbial populations in a direct way as well as through coevolution with the host. We investigated the dynamics in the gut microbiota of dogs when shifting from a starch-rich, processed kibble diet to a nature-like raw meat diet, using wolves as a wild reference. Six healthy wolves from a local zoo and six healthy American Staffordshire Terriers were included. Dogs were fed the same commercial kibble diet for at least 3 months before sampling at day 0 (DC), and then switched to a raw meat diet (the same diet as the wolves) for 28 days. Samples from the dogs were collected at day 1 (DR1), week 1 (DR7), 2 (DR14), 3 (DR21), and 4 (DR28). The data showed that the microbial population of dogs switched from kibble diet to raw diet shifts the gut microbiota closer to that of wolves, yet still showing distinct differences. At phylum level, raw meat consumption increased the relative abundance of Fusobacteria and Bacteroidetes at DR1, DR7, DR14, and DR21 (q < 0.05) compared with DC, whereas no differences in these two phyla were observed between DC and DR28. At genus level, Faecalibacterium, Catenibacterium, Allisonella, and Megamonas were significantly lower in dogs consuming the raw diet from the first week onward and in wolves compared with dogs on the kibble diet. Linear discriminant analysis effect size (LEfSe) showed a higher abundance of Stenotrophomonas, Faecalibacterium, Megamonas, and Lactobacillus in dogs fed kibble diet compared with dogs fed raw diet for 28 days and wolves. In addition, wolves had greater unidentified Lachnospiraceae compared with dogs irrespective of the diets. These results suggested that carbohydrate-fermenting bacteria give way to protein fermenters when the diet is shifted from kibble to raw diet. In conclusion, some microbial phyla, families, and genera in dogs showed only temporary change upon dietary shift, whereas some microbial groups moved toward the microbial profile of wolves. These findings open the discussion on the extent of coevolution of the core microbiota of dogs throughout domestication.

Highlights

The concept of “hologenome” has been proposed to imply the genetic role of both the host and its associated microorganisms throughout evolution (Zilber-Rosenberg and Rosenberg, 2008)
Our study has shown that when dogs shift from a starch-rich, processed kibble to a more nature-like raw-meat diet, the gut microbial populations have three patterns of changes within 4 weeks after diet alteration: (1) Some microbial populations changed when switching the diet but tended to stabilize and return to the starting point after 4 weeks
(3) Differences remain between dogs and wolves regardless of the diet

Summary

Introduction

The concept of “hologenome” has been proposed to imply the genetic role of both the host and its associated microorganisms throughout evolution (Zilber-Rosenberg and Rosenberg, 2008). Wolves can be considered true carnivores in their nature with vegetal matter being a minor to negligible component of their overall diet, whereas dogs have adapted to a more flexible anthropogenic diet including starchy food (Bosch et al, 2015). Compared with their wild ancestors, dogs have become more adapted to a starch-rich diet as demonstrated by the pancreatic α-amylase 2B (AMY2B) copy number expansion in the genome of the dog (Axelsson et al, 2013; Arendt et al, 2016; Ollivier et al, 2016; Reiter et al, 2016). The gut microbiota of another strict carnivore, the cheetah, was distinctly different in composition from the gut microbiota of domestic cats fed starch-rich, processed diets (Becker et al, 2014)

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Conclusion