The Graduate Program


The Microbiology Graduate PhD Program is an MIT-wide program that is designed to provide students with broad exposure to modern areas of microbiology and depth in the chosen area of thesis work. The first incoming class of students for this program arrived Fall 2008. These students will join a vibrant, thriving microbiology community on the MIT campus. There are more than 50 faculty in 10 different departments and divisions that study microbes. Graduate students admitted to the new Microbiology Graduate Program will be integrated into this extensive community and will receive training in a broad range of areas in microbiology.

The major components of the training program are described in detail below along with information on life as a graduate student at MIT.


Required course work (4):

Students with a particularly strong background in any of the below areas may have the option of placing out of the related course; approval of the Graduate Education Committee is required.

  1. Methods and Problems in Microbiology - 7.492J (Fall) (12 units) L. Samson, M. Polz
    Limited to graduate students in the microbiology program. This is the only course with this restriction. Students will read and discuss primary literature covering key areas of microbial research with emphasis on methods and approaches used to understand and manipulate microbes.
  2. Microbial Genetics and Evolution - 7.493J (Fall) (12 units) A. Grossman, E. Alm
    Required of students in program, but open to others. Will cover aspects of microbial genetic and genomic analyses, central dogma, horizontal gene transfer, and evolution.
  3. Quantitative Biology of Molecular Systems - 7.57 (Spring) (12 units) P. Gupta, A. Regev Introduces the fundamental concepts and tools of quantitative approaches to molecular and cellular biology. Covers a wide range of mathematical, computational, and statistical methods, although no previous expertise in these areas is required. Focus is on understanding quantitative approaches through the analysis of particular problems and examples drawn from classical genetics, molecular biology, cell biology, genomics, and systems biology.
  4. Biochemistry.
    of the following courses:
    Principles of Biochemical Analysis - 7.51 (Fall) (12 units) A. Keating,R. Sauer, F. Solomon
    Fundamental principles of biochemistry. Analysis of the structure and mechanism of catalytic and regulatory macromolecules.
    Biological Chemistry II - 7.80 (Spring) (12 units) A. Y. Ting, E. Nolan
    Advanced treatment of biochemical mechanisms that underlie biological processes. Topics include macromolecular machines such as the ribosome, the proteosome, fatty acid synthases as a paradigm for polyketide synthases and non-ribosomal polypeptide synthases, metal cluster assembly and oxidative stress. Emphasis is on experimental methods used to unravel these processes and how these processes fit into the cellular context and coordinate regulation.

     Research Rotations in Microbiology - 7.499 (Fall, IAP, Spring) (12 units) Staff
           Introduction to faculty participating in the Interdepartmental Microbiology graduate program and
           a series of lab rotations. During the first year, students will rotate through three labs of MIT faculty
           that participate in the Microbiology Graduate Program. These rotations will help provide students
           a broad exposure to microbiology research and will be used to select a lab for their thesis
           research by the end of the first year. Given the interdisciplinary nature of the program
           and many research programs, students may be able to work jointly with more than one research
           supervisor. Required and limited to graduate students in the microbiology program.

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Elective course work (3):

Students must take three elective courses, totaling 36 units, from the following list. Electives can be chosen to provide depth in a specific area of interest or additional breadth in training. Courses from some other areas may also fulfill the requirement, with the approval of the Graduate Education committee.

Fall Electives:

Environmental Microbiology1.89 (Fall) (12 units)
Principles of Bioinorganic Chemistry5.062 (Fall) (6 units) (Part I)
Enzymes: Structure and Function5.50 (Fall) (12 units)
Advanced Biological Chemistry5.52 (Fall) (12 units)
Microbial Physiology7.62 (Fall) (12 units)
Topics in Metabolic Biochemistry7.75J/5.77J (Fall) (12 units) Staff
Systems Biology8.591J/7.81J (Fall) (12 units)
Metabolic and Cell Engineering10.544 (Fall) (9 units)
Statistical Thermodynamics 10.546J/5.70J (Fall) (12 units)
Systems Microbiology20.106J (Fall) (12 units)
Biomolecular Kinetics and Cellular Dynamics 20.420J(Fall) (12 units)
Analysis of Biological Networks20.440 (Fall) (12 units)
Quantitative Genomics HST508 (Fall) (12 units)

Spring Electives

Biophysical Chemistry5.64 (Spring) (6 units; second half of semester) Staff
Biophysical Chemistry Techniques5.78 (6 units first half) or 7.71 (12 units whole semester) (Spring) (6 or 12 units)
Foundations of Algorithms and Computational Techniques in Systems Biology6.581J/20.482J (Spring) (12 units)
Computational Systems Biology6.874J (Spring) (12 units)
Molecular Biology7.58 (Spring) (12 units)
Immunology7.63 (Spring) (12 units)
Molecular Basis of Infectious Disease Graduate - 7.66 (Spring) (12 units)
Regulation of Gene Expression7.70 (Spring) (12 units)
Nucleic Acids, Structure, Function, Evolution and Their Interactions with Proteins 7.77 (Spring) (12 units)
Foundations of Computational and Systems Biology7.91J/20.490J (Spring) (12 units)
Biochemical Engineering10.542 (Spring) (12 units)
Molecular and Cellular Pathophysiology20.450 (Fall) (12 units)

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Rotations and thesis research

During the first year, students will rotate through three labs of MIT faculty that participate in the Microbiology Graduate Program. These rotations will help provide students broad exposure to microbiology research and will be used to select a lab for their thesis research by the end of the first year. Given the interdisciplinary nature of the program and many research programs, students may be able to work jointly with more than one research supervisor.

Teaching experience

Learning to effectively communicate scientific ideas is an important skill. Students in the Microbiology program will have an opportunity to improve their communication skills through teaching. Each student will serve as a teaching assistant for one semester in an undergraduate or graduate subject related to microbiology. This will typically take place in the second year.

Training in ethical conduct of research

All students will participate in a course on the ethical conduct of research. This will typically take place during the first year.

Qualifying exams

Students will proceed to Ph.D. candidacy after successful completion of a qualifying exam, typically during the second year. Students will submit a written research proposal in the style of a grant or fellowship application based on their planned thesis project. Students will then present and discuss the research proposal with a small committee of faculty.

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Student advising

In the first year, students will be advised by members of the graduate committee. Once students join a thesis lab, the research mentor will be the primary advisor. Early in the second year, students will form a thesis committee and meet at least annually. The committee will consist of faculty with expertise in the student's area of research and collectively provide the breadth expected by the program. The thesis committee will primarily provide advice on research. In addition, in the student's early years the thesis committee will also provide advice on course-work to ensure that students have the appropriate breadth and depth for his or her educational program. In later years, the graduate and thesis committees will also provide students with advice on career options.


All students in the program will receive a stipend that is sufficient to support living in the Cambridge/Boston area. The stipend will be approximately the same as for graduate students in other MIT departments, which is ~$33,000 in 2013-2014.

Financial Support and Fellowships

Students in the program will be financially supported throughout their training. This support includes tuition, stipend, and health insurance.

During the first year, students are supported by funds from the School of Science, the School of Engineering, the Provost's Office, and the Departments of Biological Engineering, Biology, Chemical Engineering, and Chemistry. In subsequent years, students will be supported as Research Assistants in their thesis lab.

Although students will be supported, they are strongly encouraged to apply for fellowships. Students applying to the Microbiology program are eligible for many of these fellowships, including those detailed on the following websites:

National Science Foundation (NSF)

Environmental Protection Agency (EPA)

National Defense Science & Engineering Graduate Fellowship (NDSEG)

Under-represented minorities should also see these websites:

Howard Hughes Medical Institute (HHMI)

Ford Foundation

Additionally, student can visit the Graduate Students Office website which has a comprehensive listing.

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Life at MIT

Living in the Boston/Cambridge area offers students a wide range of activities and opportunities outside the lab. MIT has a number of community and student groups, sponsors an extensive intramural sports program, and provides access to excellent athletic facilities. Boston and Cambridge are also rich in cultural activities, the arts, museums, theater, sports, and more. Cape Cod, New Hampshire, and Vermont are all just a couple of hours and less away, offering fantastic skiing, hiking, beach, and other outdoor activities. For more information about life at MIT, visit some of these websites:

MIT Mind & Handbook
Graduate Student Council
Community and Student Groups
MIT Athletics and Intramural Sports
Cambridge Information
Boston Information

Housing and Transportation

Graduate students have the option of living on-campus or off-campus. Upon admission to the program, students will receive housing information. In addition, see the Housing at MIT website.

Boston and Cambridge offer excellent public transportation options for getting around, commuting, and accessing Boston's Logan International Airport. The MBTA runs an extensive subway and bus system and MIT offers subsidized T-passes. For more information, see the MIT Parking and Transportation website.

Application Procedure

See this separate section for complete information on applying to the MIT Microbiology Graduate Program.

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