It depends what and how you would like to characterize.

For example, Sanger sequencing of 16S rRNA gene is very powerful tool for identification of bacteria. 

Sequencing is okay but depending on what you are interested in, you can do ale other genomic or metabolomics analysis 

Yes Dr Inetianbor is exactly wrote. The approach selection  for  molecular characterization  is always depend on your aim.  so many characterization approaches are available today in molecular biology. if you interested in only identification then 16 rRNA gene sequence is good. but your interest is in particular gene the you can used other approaches are also good like EST.

Thansk   

I totally agree with the others, it depend on what you would like to characterize and what kind of methods you have in lab. Sequencing 16S rRNA is always good if you want species/subspecies identification, sequencing of specific genes likewise. MALDI-ToF identification is also good depending on what bacteria you have. This identifies the bacteria on protein level. You can also use a lot of traditional method if you need to characterize it´s phenotype

I appreciate your contributions, Dr Marcela Krutova, J. E. Inetianbor, Dhananjay Desai and Ann-Sofi Rehnstam-Holm. They were useful.