I'm not sure I understand the question. What is your sample exactly? Single cell suspensions of mouse intestines? Or bacteria infected cell culture?

Because if all you need to do is tell the difference between bacteria and mouse intestine cells... the FSC and SSC will do that. The mCherry can just be used as a back gating stretegy to double check.

Yes you can distinguish them by the size..

Yes, They can be distinguished on the basis of size and granularity by using FSC SSC plot. If you further want to analyze and collect them, u could do it by using PE or APC channel as bacteria is expressing a red marker.

Thanks