Perhaps I am mistaken and "git" in this context is simply an acronymn for "gastro-intestinal tract". Maybe capitalization would make this more obvious to those of us not directly involved in that space or a definition of "git" somewhere in the paper that defines use of the term in that context. If that already happened then I missed it.
> For example, the git microbe Bacteroides dorei has become increasingly recognized for its role in heart conditions and T1D.
I find the word "git" perfectly appropriate here.