Microbiology and Environmental Toxicology Ph.D.


METX training includes robust critical thinking, project design, oral and written communication, and in-depth field-specific knowledge. 

Key components of METX Ph.D. training include a minimum six courses, plus BIOL 289.

  • First-quarter training introduces students to critical thinking and how to approach complex problems in environmental health: METX 200, Interdisciplinary Approaches to Problems at the Interface of Microbiology and Environmental Toxicology.

  • Second-quarter training builds expertise in their area of interest, microbiology or environmental toxicology, by taking METX 206A or METX 202. These classes build students’ foundational knowledge of microbiology or environmental toxicology, understanding of methodological approaches, and mastering experimental design and skills in research project design.

  • Second-quarter training further exposes students to multidisciplinary approaches by taking BIOL 200F, a Program in Biomedical Sciences & Engineering (PBSE) core course. This class will provide students with samples of multidisciplinary tools and approaches and an appreciation of their strengths and limitations, as well as working in teams. 

  • Third-quarter training provides in-depth field and methodology competency, project design, written communication, and research ethics. Ph.D. students will take: 

    • One of METX 210, METX 238, METX 201, or METX 250 which provides additional topic-related content and methodology, and skills at crafting and defending a research project on a non-thesis topic. 

    • METX 205. Develop student’s ability to craft grant proposals and to write clearly

    • BIOL 289, Practice of Science. Instruction in responsible conduct of research. 

  • Fourth quarter, fall quarter of 2nd year:

Oral and written presentation skills training through coursework and yearly departmental presentations and scientific writing and literature mastery through the writing of a literature review in the first year. 

Weekly seminars expose students to the breadth of our fields and provide students with opportunities to interact closely with speakers and form connections and collaborations.

Qualifying examinations designed to perfect the student’s ability to craft and defend research plans.

Extensive laboratory research training that starts immediately upon entering the program and culminates in the student’s Ph.D. dissertation or master's thesis.

Advancement to Candidacy

The student advances to candidacy after completing all coursework, completing the literature review, giving the third-year seminar and passing the Ph.D. qualifying examination.

Course Requirements

Four required core courses:

METX 200Interdisciplinary Approaches in Environmental Toxicology


METX 205Scientific Grant Writing


BIOL 200FLogic and Approaches to Scientific Discovery


BIOL 289Practice of Science


One course from the following:

METX 202Cell and Molecular Toxicology


METX 206AAdvanced Microbiology


At least one additional approved graduate-level METX course or from another department:

METX 201Sources and Fates of Pollutants


METX 210Molecular and Cellular Basis of Bacterial Pathogenesis


METX 238Pathogenesis: Molecular Mechanisms of Disease


METX 250Environmental Microbiology


METX 270
/CHEM 270/BME 270
Drug Action and Development


Any two additional courses as recommended by your first-year advising committee.

The following course each quarter:
METX 292Introductory Graduate Seminar


And one of the following as appropriate:
METX 297AIndependent Study


METX 297BIndependent Study


METX 297CIndependent Study


METX 299AThesis Research


METX 299BThesis Research


METX 299CThesis Research


Plus a topical seminar from the METX 281 series:
METX 281ATopics in Environmental Toxicology


METX 281CTopics in Environmental Microbiology


METX 281JMechanisms of Virulence and Resistance to Infectious Disease


METX 281MTopics in Molecular Toxicology


/BIOL 280O
Topics in Bacterial Pathogenesis


METX 281POrigins and Applications of Human Gut Microbial Symbiosis


METX 281RTopics in Genome-Environment Interactions


METX 281SCellular and Organismal Responses to Toxicants


METX 281VTopics in Bacterial Pathogenesis and Innate Immunity


METX 281YBiofilms: Processes and Regulation


Teaching Requirement

Doctoral students are required to work as teaching assistants (TA) for at least one quarter. Priority for TA positions is given to first-year doctoral students, then to current doctoral students who have not yet worked as a teaching assistant. Fulfilling this requirement may happen pre- or post-candidacy.

Qualifying Examination

Ph.D. qualifying examination (QE). Present and defend a dissertation research proposal to the student’s Ph.D QE committee. The student must complete Ph.D. QE no later than the end of fall quarter of the third year.

Literature Review

Under direction of the student’s advisor, write a literature review of the current state of the field of the proposed dissertation research. The written review will be handed in to the student’s advisor and the program graduate advisor by the first day of fall quarter of the second year.

Department Seminar

Give a 10-20-minute departmental seminar each academic year, and one 50-minute departmental seminar during the fall quarter of the third year. Rotation students give their rotation talks in lieu of a departmental seminar.


Dissertation and Defense

The student must submit their doctoral dissertation to the dissertation committee for tentative approval at least one month before presenting a formal, public doctoral research seminar.