Required courses seek to ensure that each student has a strong background in the general field of microbial biology. All students must enroll in the one-semester core courses: "Critical Thinking in Microbial Biology" (PMB 220), and Plant and Microbial Genetics (PMB 200A). The core course (PMB 220) lets students evaluate current research critically and to plan new research in areas of microbial biology drawn from the fields of genetics, development, physiology, ecology, evolution, and interactions with plant and animal hosts, using examples involving bacteria, archaea, viruses, algae, fungi and protists. The Qualifying Examination tests these fields of knowledge near the end of the student's second year.

In the first year Fall semester, students must enroll in PMB 202 "Outlines of Microbiology". This course exposes students to the research of members of the Graduate Group, via capsule presentations of their ongoing research and its significance to the field of Microbiology.

All students must enroll in two graduate-level seminar courses during the first two years. Seminars offer students the opportunity for oral presentation of subjects of particular interest. Seminars also let students meet individual faculty and other students in a small-group setting.

At the start of the first year, the Graduate Advisors set expectations about additional required course work. The Guidance Committee may also do so during the two first year meetings. These course requirements derive from the student's interests and background. Each student gets an individually designed program. For example, a student electing to work with a faculty member in MB whose work involved plant-microbe interactions might also be expected to enroll in a graduate course that emphasized plant biology. Alternatively, a student electing to study interactions of microbes with human hosts might be encouraged/required to take an additional graduate course on infectious diseases or epidemiology. The advisors encourage taking additional courses in plant, animal and environmental microbial biology as described in the Sample Program.