The basic tools and techniques to analyse the microorganisms are as follows:

1. Inspection that means microscopy

2. Identification and categorisation of microorganisms on the basis of identifying features

3. Inoculation that means biosafety

4. Incubation that means culturing of particular microorganism says a particular strain of bacteria

5. Isolation that means extraction or isolation of cultured microorganism

Go through the USFDA Bacteriological Analytical Mannual (BAM)/ISO Methods. You Can also go for training about isolation and identification of microbes from food and environmental samples.