Microbes, as the smallest forms of life that exist in every corner of the world, including the animal body, have enormous impacts on their host. The gastrointestinal tract (GIT) is the primary microbial habitat in humans and other animal species. The recent availability of high-throughput DNA sequencing techniques coupled with new bioinformatic developments that allow for the identification and characterisation of microbes and their genes (microbiome) in and on the body has dramatically changed the research landscape.
Gastrointestinal microbes play a fundamental role in human health and disease, participating in energy harvest and storage, development of the immune system and many other processes. Dietary changes have been shown to have significant effects on the human gut microbiota, indicating that diet is important for the development of the gut microbiome and that nutritional interventions may be useful for re-establishing a healthy microbiome.
In addition to animal health implications, companion animal microbiota research may have relevance to human health, given the exchange of microbes between humans and their pets. It has been shown that dog owners share more microbiota with their own dogs than with other dogs, with stronger effects of cohabitation on the skin microbiota than on the oral or faecal microbiota. Moreover, enterococci from the intestinal microbiota of cats and dogs may act as a reservoir of resistance genes for human pathogens.
Canine and feline microbiomes
Compared with humans and other livestock species, dogs and cats have evolved as carnivores and have a relatively simple GIT and do not rely on the microbiota for maintaining energy balance. Domestic cats, which are obligate carnivores, rely on high protein (HP)-containing animal tissues to meet their unique nutritional requirements in the wild and are metabolically adapted to a lower glucose utilisation and a higher protein metabolism. Although it shares many anatomical and metabolic characteristics with the cat, the domestic dog is metabolically more omnivorous and can digest, absorb and metabolise a considerable amount of dietary carbohydrates. Although energy acquisition in dogs and cats does not rely heavily on microbial fermentation, a balanced and stable gut microbial community is critical for maintaining gastrointestinal health. Firmicutes, Bacteroidetes, Proteobacteria, Fusobacteria and Actinobacteria are the predominant microbial phyla in the canine and feline gut; however, their proportions vary among host species and individual studies reported in the literature.
Gut microbiota of dogs and cats under disease conditions
Similar to that observed in humans, a disrupted gut microbial community may contribute to intestinal disorders in dogs and cats, not only due to the invasion of the enteropathogens in the GIT, but also due to the participation of the gut microbiota in many processes important to host metabolism (e.g. bile acid metabolism and fermentation and utilisation of non-digestible carbohydrates and proteins).
However, when comparing the entire microbial populations among these canine studies, it is clear that they are quite variable, which may be due to many factors, including methodology (e.g. DNA extraction method and primer bias), breed, age, diet and housing environment, as well as disease stage and medication use. Although many recent studies have mainly focused on the importance of maintaining a balanced intestinal microbial ecosystem, the cause-and-effect relationships between the gut microbiota and the host health conditions are still unclear.
Dietary effects on the gut microbiota in dogs and cats
Commercial pet foods are highly variable with regard to their format, macronutrient composition, fibre content and source, and inclusion of ‘functional’ ingredients (e.g. prebiotics and probiotics, joint health modifiers, antioxidants and n-3 fatty acids). Many of these dietary factors have been investigated in canine and feline dietary studies, with emphasis on the gut microbial community in some cases. The most recent studies have investigated the effects of diet on canine and feline gut microbiota using high-throughput DNA sequencing methods. All these studies indicate that dietary interventions may affect microbial composition and activity, with potential relevance to gut health.
Many researchers have emphasised the beneficial effects of feeding non-digestible carbohydrates, prebiotics and/or probiotics to dogs and cats. While prebiotics are non-digestible food substances that increase the number or activity of specific beneficial bacteria already residing in the host, probiotics supply an exogenous source of beneficial live bacteria to the host. Prebiotic consumption often results in a greater production of fermentative end products such as SCFA in the colon that confer many benefits on the host. Probiotics may enhance intestinal health by displacing intestinal pathogens, producing antimicrobial substances or increasing immune responses. Synbiotics are preparations that contain a combination of prebiotics and probiotics.
Overall, these studies demonstrate that dietary intake may modulate the composition or activity of the gut microbiota in dogs and cats as it does in humans. However, it should be noted that most studies have focused only on faecal samples, have only evaluated genomic DNA, and have been carried out in healthy adult populations of laboratory animals and that specific microbial shifts are not universal and are often affected by the baseline composition of the host’s gut microbiota. Therefore, more research is needed in this area to gain a better understanding of dietary effects on the gut microbial community and how they may affect host health.
Future opportunities and challenges
Given their place in people’s lives, companion animals share living environment, food and microbial populations with people and serve as potential vectors for pathogen exposure. Therefore, the study of canine and feline microbiomes may not only bring benefits to the health of companion animals, but also to pet owners. Although metabolic differences exist among host species, research carried out in human subjects and other animal models may be applied to dogs and cats in many instances. Because there is often a great lack of funding sources available and the research community focused on the canine or feline microbiome is small, progress in this area has been hindered. Thus, compared with the progress made in human research, there are still many questions that remain to be answered.
With regard to disease, studies have primarily focused on specific enteropathogens associated with GI diseases rather than on the cause-and- effect relationships between microbiota and host health conditions. In some populations, for example, enteropathogens (e.g. Escherichia coli, Salmonella, Clostridium difficile, C. perfringens and Campylobacter jejuni) are present in both diseased and healthy animals. Future research needs to establish associations between microbial and host metabolism or physiology. Another issue is that the vast majority of dog- and cat-specific studies carried out thus far have focused on faecal DNA, without any indicators of microbial activity, measures of host health, and accurate dietary information. To improve the field, it will be essential to understand not only the phylogenetic structure and functional capacity of the microbiome, but the activity and responsiveness of the microbiota, identifying relevant microbe – microbe and microbe – host relationships and mechanisms by which microbes affect host GI and metabolic diseases. Finally, it will be important to determine whether and how antibiotics and other drug therapies, breed and disease affect or are affected by the gut microbiome and how this information may be used to improve diets, identify disease biomarkers and develop targeted disease therapies.