Program Requirements

Course Requirements

Ten credits are required for the major. All students are required to take two semesters of the 1 credit course Current Issues in Microbiology (MMI 810 & Micro 811). These 2 credits may be used for either the major or the minor, with the approval of the thesis committee.

The other credits may come from other Bacteriology or MMI courses approved by the Advising Committee or the Thesis Committee, excluding Micro. 731/MMI 901, MMI 900, and Micro. or MMI 699 and 990, or any other research, directed study, seminar or journal club course except as approved by the Steering Committee.

  • Micro 526, Physiology of Microorganisms

    3 cr. Biochemistry and genetics of microbial processes with an emphasis on learning advanced laboratory techniques.  This course is offered irregularly.  P:  Micro 303.

  • Micro 607, Advanced Microbial Genetics

    3cr. Lectures cover mutagenesis, conjugation, transformation, transduction, plasmids, cloning and transposable elements. P:Micro/Genetics/Biochem 612 or cons inst.

  • Micro 612, Prokaryotic Molecular Biology

    3cr. Molecular basis of bacterial physiology and genetics withemphasis on molecular mechanisms; topics include nucleic acid-protein interactions, transcription, translation, replication, recombination, regulation of Gene expression. P:Micro 370 or equiv &; Biochem 501 or equiv, or cons inst.

  • Micro 640, General Virology-Multiplication of Viruses

    3cr. Bacterial and animal viruses, their structure, multiplication, and genetics. P:Intro courses in Micro, biochem & genetics.

  • MMI 655, Biology and Genetics of Filamentous Fungi

    3 cr. Fungal genetics, genomics and physiology using plant pathogenic fungi and the genetic models Aspergillus nidulans and Neurospora crassa as model systems to explore the current knowledge of fungal genetics and plant/fungal interactions.

  • Micro 657, Bioinformatics for Microbiologists

    3 cr.  This course will provide a practical and fundamental introduction to sequence-based analysis focused on microbial systems.  Students will spend a significant portion of the class at the computer learning a number of skills including, but not limited to, Unix command line, installation of bioinformatics programs (e.g. standalone BLAST), databases, and introductory programming in Perl. P.  Graduate standing or consent of instructor.

  • Micro 668, Microbiology at Atomic Resolution

    3 cr. Three-dimensional protein structures form the basis for discussions of high resolution microbiology; how particular problems are solved with given protein architectures and chemistries and how themes of protein structure are modified and recycled. P: Biochem (e.g. Biochem 501), molecular biol (e.g. Micro 526 or 612) required, one semester of physical chem preferred.

  • Micro 710, Microbial Symbiosis

    3 cr. Covers the themes and diversity of plant and animal associations with microbes with an emphasis on beneficial relationships.  Examples will be drawn from recent literature.

  • MMI 740, Mechanisms of Microbial Pathogenesis

    3cr. Lecture-discussion. Host-pathogen relationships in microbial diseases. Entry level course for infectious diseases sequence (see Med Micro 760, 790). P:Cons inst, MMI 301 or equiv & a course in immunology.

  • Micro 875, Special Topics Course

    1-4 cr Of current interest to graduates. P: Variable prerequisites depending on topic.

Course Offerings

Graduate courses are offered in microbial physiology, microbial and molecular genetics, microbial regulation and development, microbial diversity, industrial microbiology and biotechnology, immunology, microbial pathogenesis, virology, food microbiology, biochemistry and microbiology of soils, and the microbiology of plant pathogens. In addition, the departments periodically offer special topics courses. Examples of past special topics courses include: regulation of transcription, eucaryotic cell cycle, bacterial DNA replication, transcription termination and anti-termination, posttranscriptional regulation of gene expression, secondary metabolism and drug production, and practical aspects of HPLC, cell biology, and microscopy.

Requirements for the Minor

The Graduate School requires that each student fulfill a Ph.D. minor program. The minor can be completed by either taking 10 graduate credits from one discipline outside of the microbiology major, or by taking 10 credit hours distributed among courses from any department related to the individual training emphasis area. This can include Bacteriology or MMI courses not used for the major.

Grade Requirement

A student must maintain a B average in all courses to meet degree requirements. Grades of S are considered to be satisfactory; an incomplete grade must be removed during the following semester of residence or it will be converted to F. A student taking minor option A must satisfy the grade requirements of the minor department.

Department Seminar and/or Journal Club

Throughout the first three years of their graduate study, students must register for and attend the weekly seminar, Micro. 731/MMI 901. Students are required to make at least one seminar presentation per academic year after achieving dissertator status. At least two of these presentations must be in Micro. 731/MMI 901.

Graduate Study Prior to Choosing a Thesis Adviser

During the week prior to the start of classes in the fall semester, each student must attend orientation activities and meet with the Advising Committee. The Committee reviews background course requirements, considers training emphasis area (if known) and devises a course of study for the first year. The Advising Committee also monitors rotations and is available for advice until a thesis advisor is identified. If a student is funded by certain training program grants, the student may also be assigned a specific adviser who represents that program until a thesis adviser is identified.

During the initial 6 months of graduate study, students complete at least 3 research rotations with 3 different program faculty or trainers. The length and timing of rotations will be decided by the individual student in consultation with the faculty with whom they are rotating, although 3-4 rotations of 1-2 months each is appropriate. Students may select a thesis adviser as early as Dec. 15, but no later than Feb. 21 of the first year. Deviation from the minimal number of rotations or dates for selection of a thesis adviser requires approval of the Advising Committee. A student who fails to select a thesis advisor by July 1 of the first year may be dismissed from the Program.

Graduate Study after Choosing a Thesis Adviser

Formulation of the Thesis Committee. A committee consisting of five faculty members guides the student's progress towards the degree. At least one member must be outside the thesis adviser's department. Students form their committees at the end of their second semester and submit the names of the committee members to the Steering Committee for approval. At least 2 members of a student's thesis committee besides the thesis advisor must be members of the core faculty of the Bacteriology or Medical Microbiology and Immunology departments. Initial Meeting. The student may write a brief description of research planned for the next year (1-2) pages is sufficient by June 15 of the first year, distribute the write-up to the committee and meet with the committee prior to August 15. At the meeting, the student's coursework for completion of degree requirements will be approved. Annual Meetings with Thesis Committee. Students are required to prepare a brief progress report and hold an annual meeting with the committee. The student is responsible for obtaining committee member signatures and turning these in to the Program Office.

Completion of Graduate Studies

Teaching Requirement. As part of their training, students are required to perform one semester of teaching. Waivers be granted for special circumstances by the Steering Committee in consultation with the appropriate departmental administrator.

Preliminary Examination. Before the first day of fall semester classes in the third year in the Microbiology Ph.D. program, students will complete the requirements of the qualifying exam, which is centered around a research proposal. The exam consists of two parts, the written proposal and an oral defense by the student before the members of the Thesis Committee.

The Written Proposal (Part A). The student will write and submit the research proposal to the Thesis Committee. The subject matter of the proposal will coincide with the student's anticipated thesis research. The proposal should be written as a research proposal divided into five sections: 1) Abstract, 2) Sepecific Aims, 3) Background and Significance, 4) Prelimanary Results, and 5) Experimental Plan. The proposal will have an upper limit of 15 double-spaced text pages including embedded tables and figures. References are not included in the page limit. The student should consult with others, including the thesis adviser and committee members, before and during the writing process. At least 4 weeks prior to the anticipated oral defense, the student will submit the proposal to the members of the committee. The committee will have two weeks to evaluate the proposal. During the third week, the student should meet with each member of the committee to learn his/her appraisal. Based on the these comments, the student will revise the proposal and resubmit it at least one week prior to the oral defense. If a committee member has reservations about the original or the revised proposal that are serious enough to make voting to "pass" unlikely, that member should notify the student and the thesis adviser of his/her concerns immediately. In such cases, the thesis adviser, after consultation with the other committee members may delay the defense to allow time for corrective actions.

The Oral Defense (Part B). The student will give a brief (20-30 min.) oral presentation describing the research proposal and then respond to questions raised by the members of the Thesis Committee. The questions will center around the research proposal, but may include any question relevant to it or to the expected proficiencies in microbiology enumerated by the Steering Committee. Following the examination, the Thesis Committee will decide whether the student (i) passes the exam unconditionally and proceeds to candidacy, (ii) passes the exam conditionally and is instructed to complete additional work to satisfy a perceived deficiency, or (iii) fails the exam.


After the student has passed the Preliminary Examination and all other degree requirements have been met, the Graduate School warrant certifying candidacy for the Ph.D. will be signed by the Thesis Committee and returned to the Graduate School.

Procedure for Appeal

A student who fails the Preliminary Examination may be offered a second opportunity to pass the qualifying examination or may be dismissed from the program. Appeals of a decision by the Thesis Committee must be made to the Steering Committee within two weeks or they will be final. The Steering Committee will make the final decision on an appeal. A student who has not satisfied the qualifying examination requirement within 36 months of entering the Ph.D. program will be dropped from the program, except by appeal in writing to the Steering Committee, which will make the final decision.

Thesis and Final Defense

Prior to graduation, every student must submit a thesis based on original and significant observations. Six months prior to the expected defense date, the student will meet with the Thesis Committee and obtain approval of the thesis prospectus. Students are required to present a seminar on his/her dissertation research, which is followed directly by the final examination. The final examination will be an oral defense of the thesis to the Thesis Committee. One month prior to the scheduled oral defense, the student must obtain the Ph.D. warrant from the Graduate School. For the students to pass the final exam, four of the five committee members must sign to affirm passage.

Career Opportunities for Program Graduates

UW-Madison Microbiology graduates compete successfully for positions in the nation's most prestigious academic institutions, industrial and clinical laboratories, and government agencies.