I am doing 1st year in B.Sc microbiology from Shivaji University. Can I get admission in 2nd year B.Sc microbiology in Pune University?

Yes, you can get admission in the 2nd year of B.Sc Microbiology in Pune University. You just need to ensure whichever college you wish to apply, it should have lateral entry option. You can still get the information checked with the college/university where you wish to apply.