species can be both singular and plural, afaik.

species can definitely be plural or singular, but in your examples, the singular vs. plural of "guinea pig" is what is driving the verb agreement..? So I'm a little confused at the question, because in both of these sentences "species" in singular, since it's only in reference to the species of "guinea pig."

... found in guinea pigs. The species is often used as a model in biomedicine. <-singular, one species<br/>
... found in the guinea pig and the rabbit. These species are often used as models in biomedicine. <- plural, two species

But does "..pigs" go with "which frequently serve as a model species" ?
or rather
"in the guinea pig, which frequently serves as"

Since it's one species (there are not several species of guinea pigs as far as I'm aware) it would be much less ambiguous to put "guinea pig" in singular.

But does "..pigs" go with "which frequently serve as a model species" ?
or rather
"in the guinea pig, which frequently serves as"

Edit: @Lara Chu (AmE)
Missed your comment, while I was replying. Yes, I realize it's more a question of verb agreement with guinea pig/guinea pigs. I was not sure if I may use "in the guinea pig"

I certainly think you can use "in the guinea pig," just as you can use the singular form of any particular species. Lara's example with "the rabbit" is also fine.