Can we apply NGS (next generation sequencing) on DNA extracted from formalin fixed paraffin embedded tissues (FFPE)?

It's a little hard to tell based on your question, but it seems that you want to do Illumina sequencing of FFPE tissue samples. This is quite routine, Illumina sells kits for it.

I do not know how the FFPE process affects microbial cells, but people have published recently on doing metagenomic analysis of FFPE tissue samples. This suggests to me that it is possible.

If "any contamination" is a problem, then maybe there are additional roadblocks; low-level contamination is a routine problem in metagenomics, which is exacerbated by complicated, old, or low-input sample types. I would suggest treating it the way you would treat any other metagenomic sample, and try to exclude the possibility of contamination through methods and account for it in data analysis.