Much of the work on microbiology of the built environment focuses attention on issues relating to humans. But all those other animals that spend time in built environments are important parts of the bigger picture. Animals certainly influence what microbes are found in the built environment. And they are important customers of knowledge about the built environment. See for example this discussion: Sanitation in animal shelters | UC Davis Koret Shelter Medicine Program. Most of it focuses on pathogens/nasty microbes of course. But it does have some interesting pointers on places to find nasty microbes. Would be good to look at microbial diversity broadly in animal shelters to go along with the culturing focus on pathogens.