Dear Karthika,

Live/dead kit will determine live and dead bacterial cells only. They are not specific as well. I suggest you can use specific bacterial probes people generally use for FISH. As, I am not aware of bacterial groups you are targeting but it is possible to design probes as well in addition to literature search..

I hope this helps.

You can use DNA stains like DAPI or Hoechst 33258. They would perfectly work on fixed material. If you are looking into infected material of lets say animal tissue you should also expect staining of nuclei and mitochondria, but you can discriminate bacteria by shape and size. Alternatively you can use a combination of acridine orange and fluorescein for differential gram negative and positive bacteria (

European Journal of Clinical Microbiology and Infectious Diseases

May 2002, Volume 21, Issue 5, pp 373-378

Differential Fluorescent Staining Method for Detection of Bacteria in Blood Cultures, Cerebrospinal Fluid and Other Clinical Specimens). I hope this helps

FISH is a great way of labeling specific taxonomic groups. Use this database to find a specific probe sequence for genus/species level

http://www.microbial-ecology.net/probebase/

Check out this publication http://www.sciencedirect.com/science/article/pii/S0045653511007648

Thank you all for your valuable answers. I will try with universal bacterial probes. EUB338