In recent years the gut microbiota composition of several animals has been determined. This includes the microbiome of livestock, including; cows, goats, sheep and pigs as well as domestic pets including dogs, cats, guinea pigs and rabbits. The microbiomes of numerous wildlife species have also been sequenced, for example reindeer, tasmanian devil, red panda, giant panda, buffalo, and koala.

Notably diet influences the microbiomes of all animals: herbivores can get up to 70% of their energy from microbial breakdown of plant sugars (cellulose fermentation). Within herbivores two groups are distinguished based on the location of the main fermentation: the foregut fermenters and hindgut fermenters. In foregut fermenters the fermentation takes place in the rumen and ruminants, such as cows, grind the cellulose during the fermentation. In hindgut fermenters the main fermentation chamber is the colon or the caecum. Hindgut fermenters, such as horses or elephants, are able to digest food faster which is an advantage and means that with their big body size more food can be eaten to maintain their energy needs. Also the microbiomes of wild animals can change seasonally depending on available food.

In contrast, carnivores including bears, cats, hyenas, otters, and dogs have a gut microbiome that can retrieve already-synthesized proteins and nutrients from other animals’ tissue.

This microbiome specialization for herbivorous and carnivorous animals means food sources are less limited, and allows animal species to continue to evolve and exist.