The department of bacteriology was established in 1943 with Prof. R. N. Naik as Bacteriologist. The Bacteriological research scheme was sanctioned with Assistant Bacteriologist, Assistant Pathologist and Research Assistants to study Haemorrhagic Septicaemia, Black Quarter and Mastitis. Later on, the staff were absorbed as teaching staff. In 1955, Prof. D. T. Parnaik became Professor of Bacteriology. He held the charge of Principal of the college till 1963 and contributed greatly for the development of the Department. Dr. S. L. Manjrekar was Professor for a short period (1963-1964) and Prof. S. P. Kaduskar held the post from 1964-1966. Later Prof. V. B. Kukarni was Head of the Department till 1974 followed by Dr. V. L. Paranjape (1974-1989).

The following scientists who also contributed to the department were Dr. D. S. Gorhe who was instrumental in starting the virology laboratory and worked on African Horse Sickness virus. Dr. J. B. Khot worked on calf mortality and mucosal disease, Dr. V. L. Paranjape and Dr. A. V. Manda worked on Canine Distemper, Infectious Canine hepatitis and Foot and mouth disease. Further Dr. V. G. Patil-Kulkarni worked on poultry diseases, Dr. S. R. Kulkarni on Mastitis and Dr. A. N. Mulbagal carried out pioneering work on buffalo immunoglobulin. Dr. A. N. Mulbagal became Professor in 1989 followed by Dr. (Mrs.) A. A. Sherikar from 1993 to 2007. Dr. Sherikar contributed immensely in the development of department through ICAR project on Surveillance of Viral Encephalitis and Application of Deuterated water as Thermostabilizer in vaccine and other funding agency projects. Dr. A. M. Das remained Professor during 2007 to 2008. Dr. A.S. Bannalikar was Professor during 2008-2015 and significantly contributed for department by working on Rabies Pilot project and strengthen the research activities of department. Dr. (Mrs.) R.S. Gandge took over the charge of Professor for the period of 2015-18 and later by Dr. S.B. Majee looked after the duties of Professor from 2018 -2021 who improved the teaching and research activities and conducted various extramural projects. At present Dr. (Mrs.) R.S. Gandge has taken over again as Professor from 2021 onwards and has ongoing ICMR sponsored project and contributed in the infrastructure development and revenue generation.

The department achieved the various milestones as first-time study in India viz. detection of South African Horse sickness virus, isolation, identification and characterization of Gumboro disease virus & Inclusion body hepatitis virus SMAM-1 strain, CPV/AAS/85strain, Bordetella bronchoseptica etc.

Till date total 133 MVSc and 10 Ph.D. students completed their degree in Veterinary Microbiology subject. The department has completed many research projects sponsored by ICAR, ICMR, DBT, BARC in addition to various agency or industry funded projects. The staff of department have contributed in patents and have been received various awards at national and international levels, published >170 research publications, obtained > 100 NCBI gene accession nos.

The department has separate Bacteriology, Virology, Tissue culture and Molecular laboratory and laboratory animal experimentation facility. The specialized staff, all having PhD degree in various fields of Microbiology are working on the thrust area of Rabies, Brucellosis, Mastitis, and Poultry Mycoplasmosis. Various diagnostic services are offered.

The Department of Microbiology is routinely testing samples for some important zoonotic disease such as brucellosis and rabies. Rabies antibody titre testing is regularly carried out for detecting vaccinal antibodies in rabies vaccinated dogs & cats, as per the requirement from pet owner who are traveling with their pets abroad. Thus, department has achieved many milestones and engaged in teaching, research extension activity including societal services.