I read this short story in a science fiction anthology/collection some time before 2004. It involved what I remember to be a female "space veterinarian" needing to enter into the body of a large (worm-like?) alien organism that I believe was sick. I remember vivid descriptions of the interior of the creature - its organs and fluids as the protagonist moved from "room" to "room", even encountering smaller life forms akin to our gut flora living inside this creature.
Have searched for years to identify this story with no luck. It is not "Boojum" by Elizabeth Bear and Sarah Monette, which was released in 2012, although it has a similar feel at times.