I'm having great success using Cell Tracker red with Lactobacillus. Cell Tracker Blue CMHC and Green CM-H2DCFDA aren't working. I'm doing some trouble-shooting but I'd appreciate any insights from people who have tried these dyes on bacteria.
If I get it right, it seems that the CytoTrace (CMTPX) work fine while the acetylated fluorophores like fluorescein diacetate and other lipophilic fluorophores do not. Due to the fundamentally different structures, I would therefore suggest to try other fluorophores based on the CytoTrace technology.