Should samples be separated by tissue type during GTDB assignment?

I have 140 samples from jejunum (small intestine) and 140 samples from large intestine for taxonomic assignment of bacteria and archaea. I am not so interested in comparisons between tissues, but more about comparisons within each tissue (there are several treatments within each tissue that I am interested in).

I am wondering whether I should combine both tissues for taxonomy assignment using GTDB or whether I should separate the tissues?

I don’t want to bias towards homogeneity of the two tissues types by combining them, but equally I want to reduce the likelihood of the same species in each tissue being classified as different species, due to separating the two tissues during taxonomical assignment. I am a new GTDB user so I am not sure if these are even real concerns.

Whats your thoughts/advice? Thank you!!