Dog and human gut microbiomes have more similar genes and responses to diet than previously thought
Luis Pedro Coelho and colleagues from the European Molecular Biology Laboratory (EMBL), in a collaboration with Nestlé Research, evaluated the gut microbiome of two dog breeds and found that the gene content of the dogs’ microbiomes showed more similarities to the human gut microbiome than do the microbiomes of pigs or mice. These findings suggest that dogs could in future be a useful model for research into the effects of changes in diet on the human microbiome. Microbiome published the results on April 19.
The researchers mapped the gene content in the mouse, pig, and dog microbiome to a catalogue of human gut genes, and found that respectively 20%, 33%, and 63% overlapped. Computational biologist Luis Pedro Coelho, corresponding author of the study, comments: “These results suggest that we are more similar to man’s best friend than we originally thought.” Still, the authors caution that while humans and dogs host very similar microbes, they are not exactly the same, but very closely related strains of the same microbial species.
The scientists found that changes in the proportion of protein and carbohydrates in the diet had a similar effect on the microbiota of dogs and humans, regardless of the dog’s breed or sex. The microbiomes of overweight or obese dogs were found to be more responsive to a high protein diet compared to the microbiomes of lean dogs, measured as larger compositional shifts in their microbial species. This finding is consistent with the idea that microbiomes of obese organisms are easier to bring out of balance, and are therefore less resilient.
“These findings suggest that dogs could be a better model for nutrition studies than pigs or mice, and we could potentially use data from dogs to study the impact of diet on human gut microbiota,” says Coelho. Furthermore, like humans, pet dogs have a growing obesity problem. Studying how different diets affect their microbiome could, in future, help address these problems in humans.
Beagles and retrievers
The researchers investigated how diet interacted with the dog gut microbiome with a randomized controlled trial using a sample of 64 dogs, half of which were beagles and half retrievers, with equal numbers of lean and overweight dogs. All the dogs were fed the same base diet of commercially available dog food for four weeks before being randomly split into two groups: one group consumed a high protein, low carbohydrate diet and the other group consumed a high carbohydrate, low protein diet for four weeks. A total of 129 dog stool samples were collected at four and eight weeks. The researchers then extracted DNA from these samples to create a dog gut microbiome gene catalogue containing 1,247,405 genes. The resulting dog gut gene catalogue was compared to existing gut microbiome gene catalogues from humans, mice, and pigs to assess the similarities in gene content and how the dog gut microbiome responds to changes in diet.
What is a microbiome and why does it matter?
Our body is inhabited by trillions of microbes – bacteria, fungi, protozoa, and viruses. We each contain at least as many microbial cells as human ones, and maybe even more. The microbial colony living on and inside us is unique – like a fingerprint – and crucial for our well-being: they help digest food, regulate the immune system, protect us against bacteria that cause disease, and produce vitamins such as vitamin B12 or vitamin K.
The genetic material of all microbes that inhabit our body is called the microbiome. Projects such as the Human Microbiome Project aim to sequence the genome of the human microbiota – and how it changes over time. Research has shown that variations in the composition of the microbiome can determine how a person will respond to a specific treatment, and medical treatments can also alter the microbiome. These variations ripple through gene activity and metabolic processes, sometimes resulting in dysfunctions in the microbiome that can be associated with diseases such as obesity, diabetes, or fibromyalgia. This is why scientists are starting to think of humans as complex ecosystems colonised by different microbial species who collaborate or compete depending on the circumstances.
To study the effect of commonly used drugs on bacterial envelopes, EMBL scientists applied a biochemical assay using a colour reaction. The deeper the red, the stronger the disruptive effect of the drug.