CMIT-HST Clinical Study Award

First CMIT-HST Clinical Study Award: Scope and Guidelines

The CMIT-HST Clinical Study Award is designed to challenge teams of M.D. and Ph.D. students in the HST program to test their own ideas about the human microbiome in a research study. 

The Center for Microbiome Informatics and Therapeutics (CMIT), IMES, and HST have come together to offer this unique opportunity because of the success of a prior collaboration.  In 2015, a group of HST students initiated a collaboration with CMIT researchers to investigate the effects of diet and nutrition on the human gut microbiome that culminated in the publication Predictability and persistence of prebiotic dietary supplementation in a healthy human cohort. Gurry T; HST Microbiome Consortium*, Gibbons SM, Nguyen LTT, Kearney SM, Ananthakrishnan A, Jiang X, Duvallet C, Kassam Z, Alm EJ. Sci Rep. 2018 Aug 23;8(1):12699.

We are challenging teams of M.D. and Ph.D. students in the HST program to dive into microbiome research by writing a proposal to answer a question about the human microbiome through a study. The winning proposal will be selected by committee on the basis of the study design – is it well-planned and achievable within the timeframe and budget allowed, is the team and project timeline structured for success, will the project advance our understanding of the human microbiome?

The winning team will be awarded a grant of $50,000 to conduct the research they proposed. Funds are also available to send up to 3 team members to attend the 10-day Strategies and Techniques for Analyzing Microbial Community Population Structures (STAMPS) course at the Marine Biological Labs in Woods Hole in the summer of 2020 (we will cover tuition, room, and board). This course teaches key microbiome data analysis methods that students can apply to analysis of their own data.  

Key Dates

  • Opportunity Open: September 3, 2019
  • Proposal Submission Deadline: October 4, 2019
  • Winning Proposal Selected by: November 1, 2019
  • Winning Team works with CMIT + IMES mentors to optimize study design, prepare necessary materials and kits, complete Human Subjects Training and Compliance requirements: November 2019- January 2020 
  • Study Period: February 2020 – August 2020
  • STAMPS Data Analysis Course: late July/early August 2020
  • Data Analysis: August 2020 – January 2021
  • Writing and Publishing Manuscript: Aim for mid-year of 2021

Eligibility and Team Structure

The CMIT-HST Clinical Study Award is open to all M.D. and Ph.D. students in the HST program.

This opportunity is ideal for first year HST M.D. students and anyone enrolled in the MEMP and GEMS Ph.D. programs. HST M.D.  students in other years are welcome to participate if their schedules permit. Before joining a team, each participant should give full consideration to their other commitments during the entire study period – including coursework, research, and clinical obligations – to evaluate whether they have enough time to devote to this project.

We suggest that teams consist of no more than 6 students and encourage teams with both M.D. and Ph.D. students. Most importantly, to balance the workload and ensure cooperation and collaboration, the team should be constructed so that each member has primary responsibility for one or more specific aspects of the study (eg. subject recruitment and enrollment; samples collection, processing and storage; or data analysis).One team member should take on the role of Principal Investigator and oversee all the study procedures. For data analysis in particular, each team must have 1-3 members with prior experience with programming and statistics. We will help these team members complete the application to attend the 10-day long STAMPS course in the summer of 2020. Funding for the course and lodging will be provided by CMIT upon acceptance to the course. If application to participate in STAMPS is unsuccessful we will provide support for equivalent training. 

As part of the application package, each team will submit a study plan and timeline, and outline the roles each team member will play to complete the study.


We will consider proposals that focus on any part of the human microbiome — oral, gut, respiratory, vaginal, and skin — if the study is well-thought out and addresses an open question in the field. 

When writing their research proposal, applicants should consider the time period available for completing the study (approximately 8 months), as well as their access to different patient or healthy populations, and the ease of sample collections. Proposals that rely on obtaining samples from biobanks are discouraged because it can take some time to complete the legal material transfer agreements required to obtain banked samples.

Applicants should also consider the award of $50,000 which is the funding available to conduct their research. As a rough guideline, sample processing and 16S or 18S library construction costs approximately $45 per sample for library construction and sequencing and standard metagenomic sequencing $235 per sample for library construction and sequencing. Proposals requiring a larger budget will be considered only if adequate justification for more extensive sample collection and data generation is provided.

Submission Guidelines

A complete application package will contain the following documents:

  • Cover Letter introducing your team and explaining your motivation to enter this competition
  • Proposal with the following format:

Use an Arial, Helvetica, Palatino Linotype, or Georgia typeface, a black font color, and a font size of 11 points, or larger. All figures and tables must be included in the body of the application, and count toward page limits.

Required sections and page limits:

  1.  Project Title
  2. Abstract (250 words maximum)
  3. Introduction/Project Overview (up to 2 pages): What hypothesis are you testing? Provide the scientific background for your proposal including a critical evaluation of existing knowledge, and explain how the project will address gaps in current knowledge.
  4. Project plans (up to 3 pages): List the specific aim(s) that will be completed within the funding period. Describe the approach and experimental design. Clearly describe the plan for subject recruitment, enrollment, including a description of the inclusion and exclusion criteria for the study population that will be applied. Describe which sample types will be collected, how they will be collected, and when they will be collected. State which kind(s) of data will be generated from each sample type, and what we will learn from analysis of this data.
  5. References (up to 1 page)
  6. Supplementary or Appendix material should not be included and will not be considered

Study Plan and Timeline 

  1. List the project title, the names of all team members, and their study roles. The majority of the team members must be currently enrolled in an HST program: MD, MEMP or GEMS. Teams with three to five members may include one graduate or medical student from outside HST; teams of six members may include up to two graduate or medical students from outside HST.
  2. Designate one team member as the Principal Investigator who will oversee the study
  3. For each Specific Aim in the proposal, delineate an approximate timeline for the activities related to the aim. Note which team member will be responsible for these activities.


The winning proposal will be awarded $50,000 to conduct this research. These funds are intended to cover the cost of sample processing, library construction and sequencing, and any other analyses. Funds are not intended to support salary, stipends, tuition, or travel expenses. Please submit a budget in table format showing how this work can be completed with these funds. See Scope for estimation of sample processing costs. Additional types of data can be generated and applicants can contact the Committee for more information on how to estimate these costs.

Submit the complete Application Package to Vicki Mountain at by Oct 4, 2019.

For more information, please contact the CMIT-HST Clinical Study Oversight Committee:

  • Julie Greenberg,, for questions regarding eligibility of team members.
  • Tami Lieberman,, for consultation on proposed scientific direction.  
  • Vicki Mountain,, for general matters related to the application process, study logistics, or budget.