Similarity of the dog and human gut microbiomes in gene content and response to diet

Abstract

BackgroundGut microbes influence their hosts in many ways, in particular by modulating the impact of diet. These effects have been studied most extensively in humans and mice. In this work, we used whole genome metagenomics to investigate the relationship between the gut metagenomes of dogs, humans, mice, and pigs.ResultsWe present a dog gut microbiome gene catalog containing 1,247,405 genes (based on 129 metagenomes and a total of 1.9 terabasepairs of sequencing data). Based on this catalog and taxonomic abundance profiling, we show that the dog microbiome is closer to the human microbiome than the microbiome of either pigs or mice. To investigate this similarity in terms of response to dietary changes, we report on a randomized intervention with two diets (high-protein/low-carbohydrate vs. lower protein/higher carbohydrate). We show that diet has a large and reproducible effect on the dog microbiome, independent of breed or sex. Moreover, the responses were in agreement with those observed in previous human studies.ConclusionsWe conclude that findings in dogs may be predictive of human microbiome results. In particular, a novel finding is that overweight or obese dogs experience larger compositional shifts than lean dogs in response to a high-protein diet.Electronic supplementary materialThe online version of this article (10.1186/s40168-018-0450-3) contains supplementary material, which is available to authorized users.

Shallow metagenomics with Nanopore sequencing in canine fecal microbiota improved bacterial taxonomy and identified an uncultured CrAssphage

“…Previous studies on dog fecal shotgun metagenomics suggested that the canine gut microbiota resembles that from humans (11); more recently, Coelho and collaborators showed that canine gut microbiota resembles more to human gut microbiota than the most commonly used animal models, such as pig or mouse (12). Our results suggest another similarity: uncultured crAssphage was the most abundant virus in the fecal microbiota of one cohort of healthy dogs, similar to what has been previously reported in humans (13)(14)(15).…”

“…Until the date, two studies have characterized dog fecal microbiota using shotgun metagenomics, and both of them showed similarities to human gut microbiota (11,12). We aim to profile the canine fecal microbiota at lower taxonomical level -such as species-performing low deep metagenomics with Nanopore long-reads to complement the individual taxonomic profiles obtained with V4 16S rRNA sequencing.…”

TSG-6 in extracellular vesicles from canine mesenchymal stem/stromal is a major factor in relieving DSS-induced colitis

“…villous atrophy and fusion). In severe cases, intestinal protein loss, similar to in human disease, can be observed [1,31,32]. This study has been carried out with EVs derived from canine cells and is of great value in facilitating subsequent experiments in dogs.…”

Natural infection withGiardiais associated with altered community structure of the human and canine gut microbiome

“…As companion animals, dogs are 68 increasingly recognized as an ideal model system for translational gut microbiome research. In 69 addition to a harboring similar gut microbiota as humans, dogs often share their environment 70 with humans, consume a similar omnivorous diet, and can spontaneously develop GI disease 71 that shares many features in common with inflammatory bowel disease in humans (19)(20)(21)(22)(23)(24)(25)(26). In 72 addition, like humans, dogs frequently become infected with enteric parasites in early 73 life.…”