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Department of Microbiology
Thesis Research

UW Microbiology

Thesis Research

Laboratory Rotations

Overview of First-Year Laboratory Rotations

Graduate students generally rotate through three laboratories during the first year. Each rotation lasts one quarter (registered as MICROM 500). The primary purpose of the rotations is to acquaint students with faculty members and their labs to provide the basis for choosing a Thesis Advisor. The first year is a time to explore, and students are encouraged to consider labs beyond their current knowledge base or “comfort zone.”

Exploration and Resources

Students are not required to arrange a Fall rotation prior to arrival, nor is it recommended to arrange all three rotations before Fall Quarter. In addition to the Departmental Website, the Department of Microbiology Annual Retreat (see above) is an excellent place to meet faculty and discuss their work. Incoming students should also contact current students who have joined laboratories of interest or speak with them during orientation or at the retreat.

A series of bi-weekly meetings (MICROM 599) in Autumn Quarter will introduce first-year students to faculty research. At each meeting, two faculty members present their research projects, providing an overview of lab opportunities and serving as a basis for making rotation decisions for Winter and Spring Quarters.

Arranging Rotations and Scheduling Deadlines

It is the student’s responsibility to contact faculty members among the Graduate Training Faculty to arrange rotations. Faculty are polled each Summer Quarter for their interest in taking rotation or thesis students; however, this decision is often based on funding, which changes throughout the year. Therefore, the most straightforward way to find out if a faculty member is available for a rotation is to contact them directly.

The deadline for scheduling the Fall rotation is the Friday before the start of classes. Deadlines for Winter and Spring are one month before the start of classes. Students should notify the GPA of their rotation choices by these deadlines. Students are encouraged to meet individually with the GPAC as needed to discuss their academic progress, rotations, and future plans. 

Evaluation

At the end of each rotation, students will give a 15-minute presentation to the Department in a mini-symposium (Rotation Talks) during Finals Week. The faculty supervisor will write a brief evaluation of the student's performance during their rotation, which will be collected by the GPA, made available to the student, and kept in the student's file.

Choosing a Thesis Advisor

The choice of a Thesis Advisor is important and worthy of considerable care and thought both during and after the rotations. It should be emphasized that the selection of an Advisor depends on numerous factors and is not a unilateral decision on either the student’s or faculty member’s part. First-year students should plan to discuss thesis research opportunities and available funding with those faculty members with whom they rotate. Students should meet with potential Thesis Advisors on a regular basis throughout the rotation to explore the kinds of research projects available and to get a sense for the way the faculty member approaches research problems and mentoring. First-year students should plan to choose their Thesis Advisor in the last three weeks of Spring quarter, and the deadline for making a decision is the last day of instruction of Spring Quarter. Although the possibility of joining the lab should be discussed during each rotation, no commitments are to be made by either the students or the faculty before this time. Students should convey their choices to the GPA by this deadline, and both the student and Thesis Advisor will sign a contract ensuring their awareness of Departmental expectations and requirements for completing the Ph.D. One metric for satisfactory academic progress in the first year is to successfully join a thesis lab.  Accordingly, failure to secure a thesis lab by the end of Spring Quarter may result in immediate drop from the program. Students encountering challenges in securing a place in a lab should contact the GPAC or GPA as early as possible. Note that each Microbiology student can have only a single primary mentor who is responsible for training and financial support. There are no formal “co-mentor” arrangements. However, collaborators may play a strong role in the trajectory of the thesis project, may serve on the thesis committee, and may be asked to contribute to the support of a student, at the discretion of the primary mentor.

Ph.D. Supervisory Committee

A well-balanced committee is of tremendous benefit to the students and their advisors. By the end of Autumn Quarter of the second year, a five person Ph.D. Supervisory Committee is appointed as follows:

  1. Chair (Advisor) must be Microbiology Graduate Teaching Faculty*
  2. Member Microbiology Graduate Teaching Faculty*
  3. Member Microbiology Graduate Teaching Faculty*
  4. Member Microbiology Graduate Teaching Faculty or Faculty member outside of the department
  5. Graduate School Representative (GSR) - cannot have a Primary, Joint, or Affiliate appointment in the Microbiology Department but can have an Adjunct Appointment. Please see here for more information from the Graduate School on this policy. 

*At least one, and preferably two, members of the committee (including the Advisor) must be Primary or Joint members of the Department of Microbiology.

The composition of the committee, including a recommendation for the GSR, is determined by the student and her/his advisor with final approval by the GPAC. All students will submit their committee choices to the GPA (microgpa@uw.edu) one week before the start of Autumn quarter. Names of two alternative faculty to fulfill the “core or joint member” requirement should also be submitted at this time. The GPAC will review all committees for composition, with the criteria described above. Once permission has been granted by the GPAC, students will then contact faculty to form the committee by the end of Autumn Quarter.

Individual Development Plan (IDP)

An IDP is a self-assessment that will help trainees define and pursue their short- and long-term career goals. The Department of Microbiology requires that all students complete an IDP, in consultation with their thesis advisor, and discuss the IDP annually with their Ph.D. Supervisory Committee. This will ensure that students have considered their future plans, receive training, and have access to resources that will prepare them for diverse career paths. There is no required format for the IDP, although one that requires both short- and long-term planning is preferred. An excellent tool is available from Science (https://www.science.org/content/article/myidp). An example IDP form is available on the website under Graduate Student Resources. Once the annual IDP has been completed, a copy should be forwarded to the GPA for inclusion in the student’s file. The IDP should also be sent to the Ph.D. Supervisory Committee with other written materials before each meeting.

Guidelines for Ph.D. Supervisory Committee Meetings

The time limit for completing all requirements for the Microbiology Ph.D. degree is 6 years (24 quarters). Time on leave does not count towards this limit, but aggregate time on and off leave cannot exceed 10 years. Below is a series of guidelines to provide both students and faculty with a set of benchmarks against which student progress can be measured. Note that it is the policy of the Department of Microbiology that students do not bring refreshments (food or drink) to committee meetings. This includes the Topic Exam, the General Exam, and annual committee meetings starting in year 4.

Second Year

One Week Before Autumn Quarter – deadline for submitting suggestions for the composition of the Ph.D. Supervisory Committee to the chair of the GPAC.

End of Autumn Quarter – deadline for finalizing the Ph.D. Supervisory Committee

January 31 – deadline for scheduling a date and time for the Topic Exam with the Ph.D. Supervisory Committee. The exam must take place by the end of Spring Quarter. When2Meet (when2meet.com) polls or similar services facilitate scheduling. 

6 weeks prior to the Topic Exam – deadline to submit Topic Exam proposals to GPAC. (see Topic Exam under Didactic Curriculum and Exams below). 

End of Spring Quarter – deadline for completion of the Topic Exam.

Third Year

Last Day of Fall Quarter (mid-December) – deadline for scheduling a date and time for the General Exam. When2Meet (when2meet.com) polls or similar services facilitate scheduling. The student must enter the date, time, and location of the exam on MyGrad (https://grad.uw.edu/for-students-and-post-docs/mygrad-program/) under “Schedule a doctoral general or final exam”. Once this is completed, inform the GPA (microgpa@uw.edu), who will then officially approve the date in MyGrad.

Last Day of Winter Quarter (mid-March) – deadline for completion of the General Exam (see General Exam under Didactic Curriculum and Exams below).

Fourth and Fifth Years 

At least one meeting with the Ph.D. Supervisory Committee is required in every academic year in graduate school beginning in Year 2. This requirement is fulfilled in Year 2 by the meeting for the Topic Exam and in Year 3 by the meeting for the General Exam. In Year 4 and subsequent years, the time of year in which the meeting occurs is at the discretion of the student and the advisor. The advisor and at least three additional members of the committee must be present. The GSR is not required to attend though should be invited. It is the responsibility of both the student and advisor to ensure that annual meetings are scheduled. Note that depending on progress, more than one meeting per year may be suggested by the Ph.D. Supervisory Committee.

As summarized in the Microbiology Thesis Committee Meeting Guidelines (available on the website under Graduate Student Resources), one week prior to each meeting, the student will provide the committee with a 2-3 page written progress report and a copy of their most recent IDP. This concise report should include progress since the previous meeting, news of publications or anticipated timelines for publications, and a summary of plans for the next year. Students will receive much better guidance if the committee is aware of what will be presented at the meeting in advance.

Progress in Microbiology program requirements and the IDP will be discussed briefly at the beginning of each committee meeting. The remaining time should be spent on a student presentation and committee discussion. The student presentation should include a brief background and key pieces of new data obtained since the last meeting as well as an experimental rationale that supports future plans. Towards the end of the meeting, the committee should meet briefly with the student while the advisor is out of the room to provide an opportunity for the student to convey any confidential concerns pertaining to mentoring. Similarly, the committee should meet briefly with the advisor while the student is out of the room to inform the committee of any concerns. Committee discussion while both the student and advisor are out of the room is at the discretion of the committee.

At the conclusion of the meeting, all present should complete and sign the Annual Thesis Committee Meeting Report (available on the website under Graduate Student Resources). In addition, the faculty advisor will prepare a short summary of the discussion within 2 weeks of the meeting that is distributed to the members of the committee and to the student. A copy of this report is also sent to the GPA (microgpa@uw.edu) to be placed in the student's file. It is very important to document any problems that have been identified in the report. If progress is unsatisfactory, the student may be placed on Academic Alert, and the committee should clearly describe what must be accomplished over a defined time frame for the student to be removed from Academic Alert. If these expectations are not met after one quarter, Academic Alert may be extended, or the student may be placed on Final Academic Alert. A student on Final Academic Alert for one quarter who fails to meet the expectations of the advisor and committee may be recommended for Academic Drop per UW Graduate School Policy 3.7.

If the student plans to finish in 1-2 quarters following a committee meeting, the student should provide an outline of the proposed thesis and seek approval from the committee to begin writing the thesis. A timeline for completion of the thesis and for the Final Exam (Thesis Defense) should be presented. Approval of the committee is required prior to the writing of the thesis and must be documented on the Annual Thesis Committee Meeting Report. Although the expectation is that a student's thesis research will be published in 2-3 (or more) peer-reviewed papers, the formal requirement of the Microbiology graduate program is for the student to be the first author on at least one paper that is published (or in press) in a refereed journal prior to the Final Exam (see Final Exam and Format for the Ph.D. Thesis under Didactic Curriculum and Exams below).

Sixth Year

Because the Microbiology program requires that students earn their doctoral degree within 6 years (24 quarters) of entering the program, students nearing or past the program’s limit will be placed on Academic Alert (potentially leading to Final Academic Alert and Academic Drop; Graduate School Policy 3.7). To extend their graduate studies into year 7, the following must be completed no later than the end of Spring Quarter of year 6:

  1. Ph.D. Supervisory Committee Meeting: The student must convene a Ph.D. Supervisory Committee meeting during which they present a milestone-driven plan that will allow them to complete all degree requirements by the end of Summer Quarter of year 7. This plan generally includes an outline of a manuscript with supporting figures and should be presented in writing to the committee one week prior to the meeting as a supplement to the usual progress report.
  2. Plan Evaluation: During the meeting, Committee members should provide feedback on the suitability and feasibility of the plan. If the student and advisor are not in agreement, the Committee will mediate to develop a final plan for completion of the student's research program. This discussion must be documented in the meeting summary submitted as part of the Annual Thesis Committee Meeting Report.
  3. Submission of the Plan: The finalized plan, signed by both the student and thesis advisor, must be submitted to the Chair of GPAC and filed by the GPA. The written plan should include detailed and frequent milestones for interim progress monitoring.

Year 7 Monitoring: 

Ph.D. Supervisory Committee meetings must be held at least quarterly to review student progress. Zoom meetings are acceptable. If student progress is unsatisfactory, the student may be placed on Academic Alert and Final Academic Alert pursuant to Graduate School Policy 3.7 . If program requirements have not been met by the end of Winter Quarter of year 7, the student is automatically placed on Academic Alert for Spring Quarter. During the first faculty meeting of Spring Quarter, the GPAC Chair will present the student's situation for discussion in executive session. All Ph.D. Supervisory Committee members, including those who are not Microbiology Faculty, will be invited. The Microbiology Graduate Training faculty will then vote by confidential ballot, and a simple majority of non-abstaining votes will determine the outcome:

  1. The student will be permitted to immediately begin scheduling their thesis defense, which must take place before the end of Autumn Quarter, even though program requirements have not been met.
  2. The student will be placed on Final Academic Alert in Summer Quarter. Failure to meet program requirements by the end of Summer Quarter will result in the student being removed from enrollment. Students at this point are generally eligible for a non-thesis master's degree (see Appendix 3).