Ph.D in Microbiology and Immunology

General Information of Program of Study

  • A minimum of 60 post-baccalaureate credits are required for graduation. Students who already have an applicable Master’s degree may be able to apply up to 30 credits toward the 60 credits for the PhD.
  • A minimum of 25 credits of coursework as defined below in the Core Curriculum and Elective Coursework is required, which should be chosen in consultation with your research advisor and Doctoral/Masters committee.
  • A minimum of 18 dissertation credits (MB 690) are required.
  • Two-thirds of the minimum 60 credits must be at the 5XX-level or above. (Undergraduate courses at the 4XX-level are allowed, but not 3XX-level). o Credit in seminar (500), individual problem (570) and internship (576) courses may not exceed 1/3 of credits required. A maximum of 6 credits for MB570 may be applied toward the program.
  • Course work more than ten years old cannot be applied toward the program. o Transfer credits – see policy at Transferring Credits (
  • Course work taken more than six years prior to admission into the graduate program may not be applied to the program.

Core curriculum

  • All Ph.D. students who are not directly admitted into one of the MBI labs are required to conduct three laboratory rotations during their first year in the MBI graduate program. Students will be expected to balance coursework and lab work during their rotations. Students may petition the MBI Graduate Committee to be exempt from one rotation if they find a suitable lab and the PI is able to accommodate the student. All modifications from curriculum must be petitioned to the MBI Graduate Committee and Department Head for approval.
  • Students who are directly admitted will not take rotations, and these credits must be replaced by appropriate academic classes, as determine by the Doctoral Committee.
  • All Ph.D. students are required to take the two courses, which constitute the core curriculum of the MBI graduate program: MB 520 – Microbial Physiology (exceptions in particular cases may be granted; exceptions must be petitioned) and BIOB 524 – Ethical Practice of Science.

Electives Coursework (subject to change)

  • All Ph.D. students are required to take at least one course in four of the seven areas of the topic specific curriculum. See the Table below for the core groups and course opportunities to fulfill the requirements.

Teaching Assistantships

  • All Ph.D. students will complete UP TO TWO teaching assistantships, based on need and availability. This typically will be done in the student’s second year in the program. Teaching assistantships completed outside of Department of Microbiology and Immunology will not count towards this requirement unless approved ahead of time by the Department Head.
  • A Teaching Assistant (TA) workload is considered to be 19 hours per week. This consists of actual class time as well as time spent in preparation and grading.
  • Students who are acting as a TA for the first time in the Microbiology Department also must register for BIOM 497 – Educational Methods: Microbiology (2 cr.). This course is meant to give new teachers assistance in developing effective teaching techniques, training in preparing laboratory materials and help with classroom management and grading.

Doctoral Committee

  • All Ph.D. students are required to form their Doctoral Committee, and file their Program of Study, no later than the end of their first summer semester. The Doctoral Committee is expected to meet annually, at a minimum, typically after the student’s Research in Progress (RIP) presentation. Moreover, the student must meet with the Department Head annually.
  • Courses Semester Bioinformatics & Advanced Statistics MB 537 – Advances in Molecular Evolution MB 544 – Advanced Bioinformatics Fall (not 2017) Spring (Even) Biochemistry BCH 543 – Proteins BCH 544 – Molecular Biology MB 527 – Toxicology: Science of Poisons Fall (Odd) Spring (Odd) Spring Immunology MB 525 – Advanced Immunology Spring (Even) Microbial Evolution & Ecology MB 552 – Advanced Soil & Environmental Microbial. MB 591 – Precambrian Biosphere ERTH 505 – Geomicrobiology Spring (Even) Fall (Odd) Spring (Even) Microbial Genetics MB 528 – Advanced Genetics IMID 505 – Eukaryotic Gene Regulation EBIO 566 – Fundamentals of Biofilm Engineering Spring (Odd) Spring (Odd) Fall Microbial Pathogenesis MB 530 - Virology MB 505 – Host-associated Microbial Ecosystems Fall Fall Scientific Writing MB 591 – Scientific Proposal Writing Summer 15

Seminar Series and Journal Club

  • Departmental Research Seminar Series: All students are required to attend the Departmental Seminar (IMID 594) each semester in residence. For fall semester 2017, the departmental seminar will be Tuesdays from 2:00 to 2:50 PM in the Procrastinator Theater. There are limits to the number of IMID594 credits allowed in a Graduate Program (3 for Ph.D.)
  • Student Research-in-Progress (RIP) Series: All students are required to attend the Student RIP Series each year in residence, and present starting in their second year. Students may obtain credit for RIP by enrolling in MB 594 (1 credit per semester). Note that the maximum number of credits allowed on a program of study between IMID 594 and MB 594 is three.
  • Journal Clubs: All students are required to enroll in one of three MB 592 Journal Club (1 credit) sessions each semester in residence. Note that graduate students are permitted to have up to six credits of MB 592 on their program of study. o Prior to each semester, the instructors and topics of the three Journal Club will be announced. The topics will vary, but will either cover environmental or biomedical research topics or synchronize with the Departmental Research Seminar Series schedule.

Ph.D. Qualifying Exam

  • The qualifying exam allows the student’s graduate advisory committee to assess the development of the dissertation research plan and evaluate the student’s capabilities for the comprehensive exam. This exam will consist of two parts: 1) A written proposal on your future dissertation research, 2) A 30-to-50 minute chalk talk for the student’s committee. Students will be expected to complete the qualifying exam by the end of the 4th semester in the program.
  • It is suggested that students write-up their dissertation proposal in the form of an appropriate Pre-doctoral Fellowship application, and disseminate to their graduate committee a minimum of one week before the chalk talk presentation. The written dissertation proposal should follow guidelines of a national funding agency, with the intent that suitable proposals will be submitted. For the qualifying exam, the proposals should focus on the research component required in some pre-doctoral fellowships. Suggested application guidelines can be found from NIH, USDA, DOD, NSF, among others.
  • The student’s graduate committee will agree upon a format based on the topic and applicability of research. It is expected that the student will develop and write the majority of the dissertation proposal, with input and guidance from their faculty mentor.
  • The student will then present a chalk-talk style presentation of the dissertation proposal to the committee. This presentation should summarize the stated goals of the dissertation proposal and provide context for the research plans, expected outcomes and alternative strategies. During the chalk-talk, the committee will evaluate and challenge the student’s capacity to present their research plan, their comprehension of relevant background material, and the rigor of their hypotheses. The graduate committee will then decide whether: A) The student has passed the qualifying exam. B) The student must revise their written dissertation proposal, but can continue toward the Comprehensive Exam. C) The student must significantly revise and re-present their dissertation proposal and/or needs further classwork prior to taking the Comprehensive exam.
  • Upon successful completion of the Qualifying Exam, the graduate committee and the student will generate a timeline for the completion of the Comprehensive Exam.

Ph.D. Comprehensive Exam

  • All Ph.D. students must successfully complete a comprehensive examination no later than the 5th semester (excluding summers) after enrollment in the Ph.D. program. The Department of Microbiology & Immunology utilizes a comprehensive examination involving written and oral components to assess breadth of knowledge in their Ph.D. training. The exam design evaluates a student's ability to generate and organize scientific concepts, present those concepts in a written and oral format, and support and defend the proposal from external critical analysis.
  • The comprehensive exam will consist of an off-topic (different from dissertation project) written research proposal (6 pages, single spaced), which serves as the written exam portion, and an oral defense and exam of off-topic proposal and general knowledge by the graduate committee.
  • For the off-topic research proposal, the student will develop three potential topics and present them to the committee with the dissertation research proposal. These topics will be written up as a one-two paragraph proposal that briefly summarizes the important background information, question(s) to be asked and an overall strategy that will be taken in putting together the proposed work. These topics will be written up and presented to the graduate committee. The graduate committee will review and discuss the three topics and decide on the most acceptable one to serve as the written portion of the comprehensive exam. Once decided, the student will have 3 weeks to thoroughly and independently research and design a research proposal to address the problem(s). The proposal will be a six-page research proposal. The student cannot seek advice or input on the off-topic proposal from their mentor, members of the graduate committee or other departmental faculty.
  • The student will provide the committee with the written off-topic proposal 1 week in advance of the examination date. The student will present a 15 to 20 minute presentation of the proposed research to the committee, at which point the oral examination begins. Questions will pertain to the proposed research as well as general knowledge pertinent to the student’s class background and proposed dissertation research areas. When evaluating the performance of the student, the graduate committee can choose to: 1) Pass the student on both written and oral aspects. 2) Request written revisions to the off-topic proposal or a new oral presentation be provided. In the event of re-write or re-take of oral questioning, the committee decides format and timing to address the student’s needs. 3) The student has summarily failed both the written and oral examination. In which case, the committee will provide feedback as to what will be required of the student prior to retaking the exam. The student has a single chance to re-take the exam within a 6- month time frame. A second failure will result in dismissal from the academic program.


  • All Ph.D. students must have one manuscript accepted and at least one manuscript submitted for publication in peer-reviewed journals before the dissertation defense. The Ph.D. student must be first author on at least one of the two manuscripts.

Dissertation & Defense

  • The student is required to present a public, oral defense of their dissertation research, followed by a critical examination by their Doctoral Committee. Please refer to for all timelines, requirements and paperwork.
  • The primary role of the major professor and Doctoral Committee is to guide the student throughout their dissertation research. It is required that the student's Doctoral Committee meet at least once each year following a formal presentation of the student's research to discuss the student's progress.
  • A student’s dissertation must be prepared and submitted electronically in the format described in the latest version of the Electronic Thesis and Dissertation (ETD) Initiative ( Previously published electronic theses and dissertations may be viewed through the MSU Library.
  • A dissertation draft must be approved by the major professor before it is submitted to the Doctoral Committee. The student must defend the dissertation orally no sooner than two weeks after submission of the dissertation to the Doctoral Committee. The oral defense consists of a public seminar followed by a detailed examination of the student and dissertation by the Doctoral Committee.
  • Notification of the oral defense must be to The Graduate School and the MBI Department at least two weeks prior, so that proper posting can be made well in advance. Final approval of the dissertation rests with The Graduate School. That office reads the dissertation for formatting, grammar and content.
  • A dissertation approved by the Doctoral Committee, Department Head, and the Dean of The Graduate School is required. This must be submitted as an electronic dissertation no later than 14 days before the end of the semester. A hardbound copy of the dissertation is appreciated, but not required, by the MBI Department. 
Core Courses
MB 520Microbial Physiology3
BIOB 524Ethical Practice of Science3
Elective Courses (must take at least one course in four of the seven topic areas below)
Bioinformatics & Adv. Statistics
MB 5373
MB 544Advanced Bioinformatics4
BCH 543Proteins3
BCH 544Molecular Biology3
MB 527Toxicology3
MB 525Advanced Immunology3
Microbial Evolution & Ecology
MB 552Adv Soil & Env Microbiology3
MB 591Precambian Biosphere1-4
ERTH 505Geomicrobiology3
Microbial Genetics
MB 528Advanced Genetics3
IMID 505Gene Regulation in Human Development, Disease, and Immunity3
EBIO 566Fundamentals of Biofilm Engr3
Microbial Pathogenesis
MB 530Virology3
MB 505Host-Associated Microbiomes4
Scientific Writing
MB 591Precambian Biosphere1-4
Total Credits49-55