Hii,There is no scope for continuing Msc in Microbiology using the JAM rank because IIT only offers MSc in biotechnology. I myself am doing so, though i have done my graduation in microbiology. In IIT they will have related courses but not exactly pertaining to microbiology always. In IISC you can do your int-phd in a related department if you qualify as there is ample scope to do so. Rest JAM is not significant for continuing msc in microbiology. There are other entrance Exams you can give to do so.

Hope,this information will helpful for you.Goodluck.