Microbe-Host Interactions Ph.D. Program

Through new discoveries and state-of-the-science training of future scientists, the Microbe-Host Interactions Ph.D. graduate program strives to be a world-class center of excellence in biomedical research. The program’s mission evolved from the realization that while we cannot imagine our global village without germs, we can imagine a world without preventable and treatable microbial diseases. Our focus is to train students to define the interactions between microbes—specifically, bacteria and viruses—and their host organisms that lead to disease or promote health.

Researchers in the Microbe-Host Interactions (MHI) program, supported by the Department of Pathology, Microbiology and Immunology, have developed innovative in vivo and in vitro systems to study basic mechanisms of bacterial and viral pathogenesis. A key direction in the Department is to use the information garnered from mammalian and microbial genomes projects to identify new genes that control the infection process and affect clinical outcomes.

The MHI program is designed to equip each student with an in-depth understanding of their particular discipline (e.g. bacterial pathogenesis or virus replication), while imparting a knowledge of host biology sufficient for understanding pathogen-host interactions. As a research training program, MHI emphasizes training in the fundamental principles that underlie hypothesis-driven research. The program also offers numerous opportunities to attend seminars by world-class researchers and to discuss recent scientific developments in various journal clubs.

The Microbe-Host Interactions (MHI) Ph.D. program was conceived in 2016, with its inaugural class joining in 2017. MHI was born out of the former Microbiology and Immunology Ph.D. program, which operated since its founding in the early 1990s. The goal of the MHI program is to train aspiring scientists with interests in the area of the biochemistry and molecular and cell biology of microbes, including bacteria and viruses. While much of the research in faculty laboratories is on interactions of pathogens with their hosts, the program also encompasses research in microbiomes, including normal host flora. The program also trains students whose research interests include immune control of infections. Students interested aspects of immunology and pathology distinct from microbial infections are encouraged to undertake their training in our sister program, Molecular Pathology and Immunology (MPI).

Students enter the MHI program following completion of one year of studies in the Interdisciplinary Graduate Program (IGP) or the Quantitative and Chemical Biology Program (QCB), or completion of 1-2 years of coursework in the Medical Scientist Training Program (MSTP).

The MHI recognizes the rotation guidelines of the IGP, QCB and MSTP and encourages students to select rotations that suit their needs, either in exploring the laboratory environment of a potential mentor or in gaining exposure to a technology or conceptual framework of interest. The main purpose of flexible lab rotations is to gain first-hand experience in state-of-the-art methodologies applied to the solution of research problems. In addition, students have the opportunity to gain insight into the working environment and personalities of potential Ph.D. thesis advisors so that a satisfactory match can be made between student and advisor.

After students complete the required rotations, they select an advisor's laboratory for their dissertation research by late spring or early summer of their first year. This is probably the most important decision made by a student at this stage of their professional education. The choice of a faculty mentor should be based on an informed analysis of the student's intellectual needs and preferences. This choice may therefore be discussed with the MHI Program (DGS), the Division Chief and Department Chair, and the IGP, QCB, or MSTP Director. The final selection of a mentor for Ph.D. dissertation research must be approved by the Graduate Education Committee (GEC) in the Department of Pathology, Microbiology and Immunology (PMI). The proposed mentor must submit formal notification to the Director of Graduate Studies of his/her intention to train a graduate student. The notification letter should include: 1) the nomination of a specific student, 2) a proposed research project for the student (3-4 sentences), and 3) a source of funding for the student’s stipend and tuition.

Another avenue exists for students to enter the MHI Program of Study. Faculty may recruit a student to enter his/her laboratory directly. Such students participate in the graduate program offered to each IGP student but may bypass the rotation period and enter the sponsoring faculty member's laboratory immediately upon the student's arrival at Vanderbilt. In this case, the mentor shall provide full financial support for the student’s tuition and stipend costs.

Ph.D. Program Schedule Overview
Requirement Year 1 Year 2 Year 3 Year 4 Year 5
IGP X        
Required Courses X X      
Electives   X      
Reading List   Due 04/01      
Annotated Reading List   Due 06/01      
PreQual Meeting   By 08/01      
Selection of Thesis Committee & Submission of Specific Aims   By 08/15      
Approval of Abstract & Aims by Thesis Committee     Due 09/15    
Set Date for QE     By 09/15    
Take QE     By 11/01                                  
Give RIP     X X X
Teach Med Micro       X  
Thesis Committee Meetings          X X   X X   X

 

24 Didactic Hours

All Vanderbilt Ph.D. students must complete 24 didactic (coursework) hours and maintain a 3.0 or better GPA in order to take the Ph.D. Qualifying Exam.

72 Total Hours

To be awarded the Ph.D. degree, students must complete total of 72 credit hours. This includes the total didactic hours with the remainder comprised of M&IM 8999 and 9999 (Non-Candidate Research and Ph.D. Dissertation Research, respectively).

Upon completion of 72 total credit hours, students register for 0 hours of Research (9999).


Required Courses



Year 1 Required Coursework

IGP Requirements
(does not apply to MSTP)

IGP 300A, Bioregulation I – Core Curriculum, FALL [8]
IGP 300B, Modules and Electives [4-8]

MSTP Requirements
1-2 years of Medical School, with corresponding transfer credits

Summer of 1st year:

M&IM 332 Foundations in Microbiology and Immunology I, SUMMER [2] Cassat
*Not required for students entering via the MSTP*
The objective of this course is to familiarize learners with core concepts in immunology, microbiology, and virology. The course is divided into 10 week-long sessions in which a core component of mammalian immunity is introduced, followed by an examination of how microbial pathogens evade or dismantle the immune response.


Year 2 Required Coursework

Fall of 2nd year:

Students must complete one or both of the following courses:
M&IM 328-2. Molecular Virology. FALL. [2] Ruley
This course focuses on interactions of animal viruses with their host cells, discussed at the molecular and cellular level as model systems. Special emphasis is placed on current literature and methodology.

M&IM 8350. Bacterial Pathogenesis FALL. [2] Hadjifrangiskou
The objective of this course is to provide learners with in-depth knowledge on core concepts of bacterial physiology in the context of pathogenesis. Students will become acquainted with core bacterial processes and how these processes are engaged and altered during the course of infection, as well as changes in the environment (manmade and not).

Spring of 2nd year:

M&IM 8334 Foundations in Microbiology and Immunology III, SPRING [2] Aiken, Lacy
This course aims to equip learners with high level knowledge of their respective areas of research, with an emphasis on the primary research literature and experimental approaches. The course is organized in a series of topic modules from which the student selects to generate a learning plan that is tailored to their specific research interests. Self-directed study is emphasized.

M&IM 8335 Research Proposals: Preparation & Critical Review, SPRING. [2] (Ruley)
An essential skill for scientists in an academic setting is the ability to obtain extramural research funding through peer reviewed grant applications. This course will offer didactic sessions in which the process of preparing and reviewing grant applications is discussed. Each student will write a grant application using the NRSA format for postdoctoral fellowships. The student should propose research in one of the four major emphasis areas of the department: molecular pathology, virology, immunology, or microbial pathogenesis. A student and a faculty member will provide a written review for each of the final grants. The course will conclude with a mock NIH study section in which each grant is reviewed orally and scored.

Students who earn a grade lower than a B in a required course may be required to retake the course to be approved to take the Qualifying Exam. In this event, the student’s mentor will meet with the Program Director to make this determination. Students must review their didactic coursework hours with the Program Director prior to registration for the Fall semester. Students who have an insufficient number of credit hours from the IGP will be required to take additional electives to be approved to take the Qualifying Exam.


Elective Courses

Elective courses are chosen by the student and advisor to best fit their research program. Graduate level courses outside of the Department that fit the student's research program may fulfill the 24 didactic hour requirement. Please consult with your advisor and the Director of Graduate Studies prior to registration if you wish to take an elective course outside of the Department.

M&IM 8334: Special Topics in Molecular Pathogenesis

The interaction of animal viruses with their host cells, discussed at the molecular and cellular level as model systems. Special emphasis on current literature and methodology. Prerequisite: A course in biochemistry

Aiken/Jerome/2/Spring

M&IM 328-3: Molecular and Cellular Immunology

The cellular and molecular foundations of the immune response system and the humoral and cellular reactions that result from immunologic interactions. Two to three lectures per week and seminars presented by students. Prerequisite: IGP 300a, 300b, and 301, or equivalent.

Joyce(Director)/2-3/Fall

M&IM 332:Foundations of Microbiology and Immunology I

The objectives of this course are to alert students to important original research articles in the area of microbial genetics and pathogenesis, to apply methods of scientific logic for critical analysis of the knowledge presented in the articles, and to help students present complex data and conclusions to an audience.

Skaar/2/Summer

M&IM 333: Foundations of Microbiology and Immunology II

Second semester of required course work. The objectives of this course are to alert students to important original research articles in the area of molecular virology and immunology, to apply methods of scientific logic for critical analysis of the knowledge presented in the articles, and to help students present complex data and conclusions to an audience. Prerequisite: M&IM 332.

Ruley/3/Fall

M&IM 334: Foundations of Microbiology and Immunology III

Third semester of required course work. The objectives of this course are to alert students to important original research articles in the area of molecular immunology, to apply methods of scientific logic for critical analysis of the knowledge presented in the articles, and to help students present complex data and conclusions to an audience. Prerequisite: M&IM 333.

Boothby/2/Spring

M&IM 335: Research Proposals - Preparation & Critical Review

An essential skill for scientists in an academic setting is the ability to obtain extramural research funding through peer reviewed grant applications. This course will offer didactic sessions in which the process of preparing and reviewing grant applications is discussed. Each student will write a grant application using the NRSA format for postdoctoral fellowships. The student should propose research in one of the four major emphasis areas of the department: microbial genetics, virology, immunology, or microbial pathogenesis. The initial grant submission will be reviewed by a faculty mentor. The student will amend the application according to the reviewer’s comments and submit a final version. Procedures for reviewing grant applications will then be discussed. Two students and the original faculty mentor will provide a written review for each of the final grants. The course will conclude with a mock NIH study section in which grants are reviewed orally and scored

Crowe(Director)/Thomas/Cover/1/Spring

M&IM 369: Master's Thesis Research

Staff/0-13/All

M&IM 8999/PhD Dissertation Research

Non qualifying hour course for students in the Ph.D. program who have not yet passed their qualifying exam. Prequisite: IGP 300b or equivalent.

Staff/0-12/All

M&IM 9999: PhD Dissertation Research

Staff/0-13/All  

MICROBE-HOST INTERACTIONS HANDBOOK

MHI Hand book.jpg