Graduate Program in Microbiology

Challenge Yourself

UC Berkeley's graduate program in Microbiology provides an outstanding and rigorous course of study and is repeatedly ranked among the best in the world. The program is both immersive and thorough. Students take a variety of classes, teach as graduate student instructors, work with top scientists and perform research in our labs. Following is a detailed explanation of the program, including course of study, advising, lab rotation, teaching, research and more.

Admissions Process

The committee bases admissions recommendations on:
  • Grades and coursework at the undergraduate and graduate levels

  • Letters of recommendation

  • Standardized examination scores

  • Written statements of academic and professional goals

  • Other documentation of research

  • Academic potential and accomplishment

Microbiology Program Requirements
  • A basic background in chemistry, physics, mathematics and biology, roughly equivalent to the Department's undergraduate program in Microbial Biology.

  • Completed online Graduate Application for Admissions and Fellowships. ​Applications for the Fall 2017 semester are due December 1, 2016. 

  • Transcripts from each college and graduate institution attended.

  • Resume.

  • Three letters of recommendation, at least two of which should be written by science faculty. All reviewers should be familiar with the student's scholarly abilities.

  • General Aptitude test scores of the Graduate Record Examination (GRE). The Department recommends but does not require the GRE subject test in biology (B24) or biochemistry, cell and molecular biology (B22). Take the exam(s) early enough so that scores will arrive by the application deadline. To have the scores sent to the Department, note on the GRE order form the institution code R4833 (UC Berkeley) and the department code 0112 (Plant Sciences).

  • The Test of English as a Foreign Language (TOEFL) score for applicants who have received undergraduate degrees from institutions where English is not the language of instruction. With few exceptions, UC Berkeley requires a TOEFL score of at least 570 on the paper and pencil test, or 230 on the computer-based test and 90 on the Internet-based TOEFL. Take the TOEFL by November. Note on the TOEFL order form the institution code 4833 (UC Berkeley) and the department code 37 (botany). Please read the Graduate Division's Evidence of English Language Proficiency for more information.

  • If you have additional questions, please contact Graduate Student Advisor Rocío Sanchez at rocio_s@berkeley.edu or call 510-642-5167.

  • For more information regarding the application process for Fall 2017, please refer to our 2017 Graduate Application Instructions.

Graduate Group in Microbiology

The Graduate Group in Microbiology (GGM) forms the foundation of our Graduate Microbiology Program. The GGM is composed of 53 faculty from diverse departments, colleges, and schools (Plant and Microbial Biology; Molecular and Cell Biology; Public Health; Civil and Environmental Engineering; Chemical and Biomolecular Engineering; Environmental Science, Policy, and Management; Nutritional Sciences and Toxicology; Optometry; and Integrative Biology) and is administered by the Department of Plant and Microbial Biology.

The group awards the PhD degree in Microbiology. Students in the group have access to diverse disciplines through an integrated program of study that allows each student to pursue specialized interests. Students gain a breadth of understanding of microbiology from the molecular to the cellular levels of organization, as well as the interactions of microbes—beneficial and pathogenic—with other organisms.

GGM faculty have research interests in four broad areas: ecology and evolution, genetics and development, physiology and biochemistry, and host-microbe interactions. The research of many faculty spans more than one of these categories. In addition, the research goals vary from addressing fundamental questions in biology to applied studies in the control or use of microbes. Some faculty conduct research on both fundamental and applied topics.

Graduate Group in Microbiology Faculty Directory

Evaluation, Lab Rotations, Required Courses

New students will meet with Graduate Advisors before fall semester begins. The Graduate Advisor evaluates whether each student completed the courses, or equivalents, required for an undergraduate major in Microbial Biology. With a broad admissions policy, we expect that some students may need to take specific undergraduate courses in the first semesters to expand their knowledge.

Lab Rotations

Incoming students must rotate through three different laboratories during the first year, for about 10 weeks per rotation. The student may select laboratories affiliated with the Graduate Group, or select a lab outside the Group to learn a particular skill. Students explore opportunities for rotations with the relevant faculty and the Graduate Advisor. The rotations give students an opportunity to explore an area of research in which they may have an interest, but no direct experience.

In most cases the rotations will involve laboratory work. However, sometimes a rotation could take the form of reading and discussion. Although some incoming students may have interest in particular faculty for thesis research, students need rotations for exposure to research outside their immediate area of interest. The Research Advisor gets chosen after completion of the student's third rotation. Students have the freedom to investigate different opportunities for a suitable major advisor. Whereas students may express interest in any particular laboratory at any time, they may not establish firm commitments before completing all three rotations. The student generally chooses a Research Advisor after the third rotation. In exceptional cases the student may take a fourth laboratory rotation. After formalizing the choice of a research advisor, the student initiates a research project in the Advisor's laboratory.

Required Courses

At the start of the first year, the Head Graduate Advisor sets expectations about additional course work beyond the stated requirements. Any required courses seek to ensure that each student has a strong background in the general field of microbial biology.

In the first year, students must enroll in the two-semester core course, PMB 220A-F. The core course is comprised of 6 modules, which cover the following topics: microbial genetics, genomics and computational biology, microbial diversity and evolution, cell structure and function, microbial physiology and microbial ecology. The Qualifying Examination tests these fields of knowledge near the end of the student's second year. In addition to the core course, PMB 202 and PMB 210 are required. PMB 202 "Faculty Research Review" 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. The objectives of PMB 210 “Scientific Reasoning and Logic” are to teach students to critically read and interpret scientific papers.

During the first two years, all students must enroll in two graduate-level seminar courses. 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. The Workshop on Teaching, PMB 300, must also be taken the Fall semester of a student’s second year.

Microbiology Course Requirements

Course
Title
Credit(s)
PMB 220AMicrobial Genetics1.5 Units
PMB 220BGenomics and Computational Biology1.5
PMB 220CMicrobial Diversity and Evolution1.5
PMB 220DCell Structure and Function1.5
PMB 220EMicrobial Physiology1.5
PMB 220FMicrobial Ecology1.5
PMB 202Faculty Research Review2.0
PMB 210Scientific Reasoning and Logic1.0
PMB 2902 Seminars in PMB 290 or EquivalentVariable
PMB 300Workshop on Teaching1.0

 

Program Review, Teaching

Program Review

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 academic work to full-time research. During the first year, students participate in the two-semester core course modules, PMB 220A-F, and also take PMB 202 and PMB 210. In PMB 210 “Scientific Reasoning and Logic”, 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 PMB 202 “Faculty Research Review”, 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.

Selecting a Lab

During the first year, students rotate in various labs of their choice to find a home where they can conduct their research with the guidance of a Principal Investigator. Lab rotations take place in PMB Labs and GGM Labs, giving students a wide variety of choices. By the end of the first year, students select a research laboratory in for thesis research, and assemble a thesis committee. During the 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 Graduate Student Instructors (GSIs) for undergraduate classes to develop their teaching skills.

Qualifying Exam

Normally, students take the Qualifying exam twards 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.

Teaching

The Graduate Group in Microbiology seeks to ensure that its graduate students gain instructional experience by serving as Graduate Student Instructors (GSIs). Each graduate student must serve two semesters as a Graduate Student Instructor. In addition, students must take PMB 300 “Workshop on Teaching”, a class designed to foster superior teaching by Plant and Microbial Biology graduate students, or the equivalent from another department.

 

Graduate Student Instruction (GSI)

The Department of Plant and Microbial Biology has several courses with GSI opportunities in microbial biology. Students may use teaching in other departments, such as Molecular Cell Biology, Environmental Science and Policy Management, and Integrative Biology, to fulfill the teaching requirement. The Department of Plant and Microbial Biology and a student's Research Advisors' home departments (if not PMB) also offer opportunities to teach introductory biology courses.

Graduate Review, Qualifying Exam, Dissertation

Evaluation of first year student progress occurs at the end of the first year. The faculty meet as a group to review first year student grades and core-course comments from instructors, laboratory rotation evaluations from faculty members, and any student comments the student wishes to present.  The faculty discuss each student individually and his/her progress over the course of the year which results in the student receiving a review letter which becomes part of the student’s file.  The review letter summarizes the student’s progress and may include specific recommendations or coursework requirements from the faculty.

 

Qualifying Exam
 

The Qualifying Examination assesses the candidate's broad knowledge of microbial biology and determines in-depth knowledge in the proposed area of research. The Examination consists of a dialog between the student and the examiners to provide a forum for the student to demonstrate an ability to integrate and extrapolate from information obtained in the classroom and laboratory. The Examination provides a way to evaluate the student's preparation and potential for a research or teaching career at the professorial level. It stresses breadth, depth, and sophistication of knowledge. During the Examination the student will demonstrate:

  • Mastery of a significant body of relevant knowledge

  • The capacity to think and write critically

  • The ability to apply information learned in the classroom and laboratory to the solution of relevant biological problems

The student normally takes the Qualifying Examination normally in the third or fourth semester. The student, in consultation with the Head Graduate Advisor, will recommend a four-member Examination Committee, approved by the Graduate Division. This Committee shall have at least three regular faculty from the Graduate Group and include representatives from least two departments. Adjunct Professors may serve as members of the Committee. Non-Senate members and faculty from other campuses may serve upon approval of the Graduate Advisor and Dean of the Graduate Division.

No later than one week before the Examination the candidate will prepare and deliver to the Committee two research proposals, both of the scope and caliber appropriate for doctoral dissertation research. The student develops the topics of both the major and minor proposals in consultation with the Examination Committee Chair. To focus questioning in the candidate's proposed research area, the major proposal, in about three pages, should address the specific topic proposed for thesis research. To provide a starting point for questioning across the breadth of microbial biology, the minor proposal, in about two pages, should address a specific topic in a field that differs significantly in approach from that of the candidate's proposed dissertation research. The proposals serve as the basis for the oral examination, do not limit it.

The student, in consultation with the Research Advisor and Graduate Advisors, should ensure that Examination Committee composition's permits it to assess knowledge in both areas covered by the proposals. Any examiner may ask questions in any subject area. Thus, we strongly recommend that the student meet with each Committee member before the Examination. The professor and student may choose to focus on topics within a particular subject area and may meet regularly to discuss these topics. As long as the Committee adequately assesses the student's broad knowledge of microbial biology, the Committee may discuss additional areas by mutual agreement between the student and the examiners.

The oral examination will last approximately 3 hours. Approximately one-third of the Examination covers the major proposal, with the remaining time allocated to the minor proposal and the breadth of microbiology. Passing the Qualifying Examination requires a unanimous vote of the Committee.

Following the Examination, the Committee Chair will write a short statement about the performance of the student in each area. This summary, added to the student's file, documents that the Committee spent adequate time on Examination areas and also guides the student's future program.

Dissertation

The student invites a three-member committee to serve as the Dissertation Committee. (The student may request a four-member committee, or the Graduate Division may require one in certain circumstances). The student identifies the Committee members in consultation with the Head Graduate Advisor. The Committee must include representatives of at least two academic departments. The Chair of the Committee will be the Research Advisor, who must have faculty membership in the Graduate Group. However, an adjunct faculty member can serve as Co-Chair with a regular faculty Co-Chair. The committee must have at least one Academic Senate member from outside the Graduate Group.

At least once per year this Committee will meet with the student and evaluate progress. The Graduate Division requires that a form be sent to the Graduate Division certifying progress made by the student. The Dissertation Committee members will also advise the student about carrying out research.

All members of the Committee must approve and sign the dissertation before the Ph.D. degree gets conferred.

For the Ph.D. degree, students must complete a dissertation based on original and independent research.

The Group does not require a final examination. However, all students must present a finishing seminar to summarize the results of their dissertation project, and must respond to questions from the audience. If the faculty do not find the seminar satisfactory, they may ask the student to present the seminar again to address the concerns.

Most students take five years to complete the Ph.D. program -- two years before the Qualifying Examination and three years after.

 

Related Programs

Prospective students who wish to undertake graduate studies in microbiology at UC Berkeley may apply to one of the following three independent graduate programs:

Microbiology
The interdepartmental Microbiology Program described on this site serves students interested in all aspects of microbiology. Areas of emphasis include: microbial ecology, mycology, and plant pathogen interactions. This Program gives students access to microbiology labs in:
  • Civil & Environmental Engineering
  • Chemical Engineering
  • Chemistry
  • Environmental Science, Policy & Management
  • Molecular & Cell Biology
  • Nutrition Sciences & Toxicology
  • Optometry
  • Plant & Microbial Biology
  • School of Public Health.
  • Infectious Diseases and Immunity
Other Programs on Campus
  • The graduate program in Infectious Diseases and Immunity, in UC Berkeley's Department of Public Health, provides opportunity for the study of the biology of infectious agents, their interaction with human and other hosts, and their relationship with the environment.
  • The Molecular and Cell Biology Department offers a program for students with broad interests in biology who wish to benefit from this large department's diversity of scientific study in such areas as biochemistry, structural biology, immunology, and microbiology.  

Withdrawal

The Graduate Group in Microbiology (GGM) makes every effort to understand the reasons for a student's failure to meet departmental expectations. In some instances, it may recommend withdrawal from the program for one semester. In other instances, the Group asks the student to leave the program permanently. For first year students, the Head Graduate Advisor makes this recommendation, which then gets approved by vote of the entire faculty. For students who have already selected a Research Advisor, the Head Graduate Advisor in consultation with the Research Advisor and the graduate student make this recommendation to terminate the program.

Operating principles for these decisions consist of good faith and the best interests of the student. A student may appeal the decision to the Steering Committee of the Group. Normally, second year and more advanced students who get asked to leave the program may have the option of obtaining an M.S. degree according to Plan II below.

M.S. (PLAN II TYPE)

Students primarily work towards the Ph.D. In general, the Group does not admit students to the M.S. Program. The M.S. Plan II Program serves students who enter the Ph.D. degree program but for some reason cannot continue, either because their goals change or because their Guidance Committee does not recommend that they continue. This plan allows such students to show they have successfully completed a course of study in the area of microbial biology.

The Program requires a two-hour oral examination, conducted by a three-member M.S. committee. Students passing this examination obtain an M.S. degree. For the M.S. degree, Plan II, students must complete a minimum of 24 units.

FAQs

Q: Where can I find information about PMB faculty and graduate program requirements?

A:  Please visit these links:

Department of Plant and Microbial Biology
Plant Biology Program Page
Plant and Microbial Biology Faculty Page
Microbiology Program Page
Graduate Group in Microbiology Faculty Page
Graduate Admissions Brochure

Q: How many students are enrolled in the program? How many students are admitted each year?
A: As of Fall 2014, we have 40 students in our Ph.D. in Plant Biology program and 51 students in the Ph.D. in Microbiology program. The number of students we admit varies from year to year depending on funding. For the past several years, the admissions committee for each program has offered admission to 10-18 applicants.

Q: When is the deadline for admission?

A:  The deadline to apply for Fall 2017 admission is December 1, 2016.

Q: Do you offer financial support for your students?
A:  All of our admitted students receive ​five​ full years of funding contingent upon satisfactory academic progress. The annual stipend for 2016-2017 is $34,000.

pmb.berkeley.edu/funding

Q: Do you admit international students? How can international students increase their chances of being admitted?

A: We generally admit one international student per program, per year. Admissions competition is stiffer for international students. International students who have a fellowship from an outside agency that will offset their cost, such as the Fulbright, are included with domestic applicants. 

Q: I already have a Master's degree. May I transfer my coursework to UC Berkeley?
A: Although having your Master's degree may help you in the admissions process, we rarely excuse a student from any of our Ph.D. coursework for this reason. We have minimal coursework requirements, designed not only to prepare you for your qualifying exam, but also to help connect you with the other students in your cohort.

Q: I've already selected the faculty member with whom I want to work. Do I still have to do rotations, or will you admit me directly into a lab?
A: We do not admit students directly into a permanent lab. Each student must complete three required lab rotations during the first year before joining a lab.

Q: I am interested in several different programs at UC Berkeley. May I apply to all of them?
A: No. UC Berkeley allows students to apply to only one graduate program per year.

Q: Is there a minimum GRE (Graduate Record Examination) score that I need to receive in order to apply to your department? What is the average GRE score of your admitted students? 
A: We do not require a minimum GRE score to apply to our department. Your GRE scores make up only one part of your application. We view them in the context of the rest of your application materials.

Q: How do I know what materials you've already received for my file?

A: All required materials will be uploaded to the graduate application. Once you submit your application you will still be able to check for exam scores and recommendation letters via the "application status page" at grad.berkeley.edu

Q: May I submit more than three letters of recommendation?

A: Yes, you may submit additional letters of recommendation via the online application.

Q: I have submitted all my required materials and would like to update one of my transcripts. How may I do that?

A: In order to update application materials after submission, please email rocio_s@berkeley.edu

Q: I would like to tour the department. Can I drop in on a few faculty members and research labs?

A: All visitors are welcome to take a Berkeley campus tour. You can also drop in or make an appointment to meet with the Graduate Affairs Advisor Rocío Sanchez. Regrettably, the department generally cannot accommodate the many prospective students who wish to drop in to visit faculty or research labs. Students who apply for admission and are invited to our annual interview weekend in late January will meet with faculty and current graduate students, and tour our labs and facilities.