Gut microbiota of humans, dogs and cats: current knowledge and future opportunities and challenges

Abstract

High-throughput DNA sequencing techniques allow for the identification and characterisation of microbes and their genes (microbiome). Using these new techniques, microbial populations in several niches of the human body, including the oral and nasal cavities, skin, urogenital tract and gastrointestinal tract, have been described recently. Very little data on the microbiome of companion animals exist, and most of the data have been derived from the analysis of the faeces of healthy laboratory animals. High-throughput assays provide opportunities to study the complex and dense populations of the gut microbiota, including bacteria, archaea, fungi, protozoa and viruses. Our laboratory and others have recently described the predominant microbial taxa and genes of healthy dogs and cats and how these respond to dietary interventions. In general, faecal microbial phylogeny (e.g. predominance of Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria) and functional capacity (e.g. major functional groups related to carbohydrate, protein, DNA and vitamin metabolism; virulence factors; and cell wall and capsule) of the canine and feline gut are similar to those of the human gut. Initial sequencing projects have provided a glimpse of the microbial super-organism that exists within the canine and feline gut, but leaves much to be explored and discovered. As DNA provides information only about potential functions, studies that focus on the microbial transcriptome, metabolite profiles, and how microbiome changes affect host physiology and health are clearly required. Future studies must determine how diet composition, 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.

Effects of the Dietary Protein and Carbohydrate Ratio on Gut Microbiomes in Dogs of Different Body Conditions

“…However, little is known on how the dietary protein-to-carbohydrate ratio influences gut microbiotas in dogs. The five predominant bacterial phyla reported in this study, Fusobacteria , Firmicutes , Bacteroidetes , Actinobacteria , and Proteobacteria , were similar to those in previous reports (27–29), but relative abundances of each phyla can vary from study to study and likely arise from factors such as breed, sex, age, diet, or even different sampling or sequencing methodologies (27). In this study, we observed that evenness but not richness increased in response to diet manipulation; that is, the abundances of taxa present became more equal rather than community members that may have been undetected in phase 1 expanding in growth.…”

Key bacterial families (Clostridiaceae, Erysipelotrichaceae and Bacteroidaceae) are related to the digestion of protein and energy in dogs

“…Gross energy (kJ/g) was determined using bomb calorimetry. Crude fibre was determined using the gravimetric method (AOAC 978.10) and nitrogen-free extractable matter (NFE) by difference (Deng & Swanson, 2015). Dry matter (DM) was calculated as 100 less the % moisture.…”

“…Consistent with this, over the last five years much of the research in companion animal nutrition has focussed on understanding the role of diet on the composition of the faecal microbiota (Deng & Swanson, 2015). To date, diet-induced changes in faecal microbiota observed in humans and rodents have been extrapolated to dogs and cats, in spite of their very different dietary requirements.…”

“…This approach may help understand how microbial and host physiology intersect, thereby increasing the understanding of dietary effects on microbial composition in the dog, and their impact on nutrition (Deng & Swanson, 2015). …”

Isolation and Identification of the Gut Microbiota of Healthy and Diarrhoeic Dogs in Andhra Pradesh, India

“…The gastrointestinal tract of dog is a complex microbial ecosystem that mainly consists of bacteria, methanogenic archaea, yeasts, moulds and viruses (Deng and Swanson, 2015). Enterobacteriaceae was indeed the most important family of gut microbiota, causing well-defined diseases like gastroenteritis, septicaemia, reproductive and urinary tract infections (Suchodolski, 2011).…”