Submission of a Ph.D. thesis containing the results of original, publishable research remains the culminating and defining event of a graduate career in Microbiology. Graduate students achieve that final event in stages, progressing from mostly academic work to full-time research.

During the first year, students participate in two Core Courses. In one course, students gain information and participate in discussions intended to provide perspective on many different areas of microbiology. Students critically review current literature to develop analytical skills needed for their graduate studies and later work. In the second course, students meet the faculty members of the Graduate Group in Microbiology. These researchers summarize their work to give students an appreciation of the breadth of Microbiology, and to help students select faculty mentors in whose laboratories they start research during 10-week rotations.

At first year's end, students select a research laboratory in for thesis research, and assemble a thesis committee. During second year, research occupies more student time, and formal academic work less. In the second year, students take more specialized courses to prepare them for research areas chosen, such as seminar classes to read and discuss relevant scientific literature. They also work as Teaching Assistants for undergraduate biology classes to develop their teaching skills.

Normally, students take the Qualifying exam towards the end of second year. This examination determines whether, through academic and independent study and research experiences, a student has successfully prepared for independent work. Students who pass the exam gain admission to formal candidacy for the Ph.D. degree. Then, students spend the most remaining graduate school time working on their research projects.