Microbiome Human Intervention Core

The Human Intervention Core offers a wide array of services to assist with the design and implementation of microbiome studies.  The core can assist with longitudinal studies as well as pilot studies.  Pilot studies can be rapidly implemented with human intervention core staff, project managers and research coordinators, to conduct these studies.


  1. Design resources-observational and interventional
    1. Study design consultation
      1. 2 hours of free consultation with Penn researchers expert in microbiome study design
      2. Additional time at a nominal charge
    2. Study organization consultation.
      1. 2 hours of free consultation with a project manager who has extensive experience in  microbiome study implementation
      2. Additional time at a nominal charge
  2. Study organization resources
    1. Logistical planning
    2. Sample collection methods and tools
    3. Case report form templates
    4. Recruitment methods
    5. Budgeting
  3. Implementation of pilot studies
    1. Human Intervention Core staff to implement studies (subject to availability)
    2. Regulatory submissions and document maintenance (dependent upon funding)
    3. Potential to expand staffing, if funding is obtained for full studies

Previous Projects

Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes
Gary D. Wu, Jun Chen, Christian Hoffmann, Kyle Bittinger, Ying-Yu Chen, Sue A. Keilbaugh, Meenakshi Bewtra, Dan Knights, William A. Walters, Rob Knight, Rohini Sinha, Erin Gilroy, Kernika Gupta, Robert Baldassano, Lisa Nessel, Hongzhe Li, Frederic D. Bushman, James D. Lewis. Science. 2011 October 7; 334(6052): 105–108. Published online 2011 September 1. doi: 10.1126/science.1208344

Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production.
Wu GD, Compher C, Chen EZ, Smith SA, Shah RD, Bittinger K, Chehoud C, Albenberg LG, Nessel L, Gilroy E, Star J, Weljie AM, Flint HJ, Metz DC, Bennett MJ, Li H, Bushman FD, Lewis JD. Gut. 2014 Nov 26. pii: gutjnl-2014-308209. doi: 10.1136/gutjnl-2014-308209.

Comparative Effectiveness of Nutritional and Biological Therapy in North American Children with Active Crohn's Disease.
Lee D, Baldassano RN, Otley AR, Albenberg L, Griffiths AM, Compher C, Chen EZ, Li H, Gilroy E, Nessel L, Grant A, Chehoud C, Bushman FD, Wu GD, Lewis JD. Inflamm Bowel Dis. 2015 May 12. [Epub ahead of print]

For further information or to request assistance from the Microbiome Human Intervention Core, please fill out this form and send to: nessel@pennmedicine.upenn.edu and uroy@pennmedicine.upenn.edu

Operational Information

Dr. James Lewis
Core Director

Dr. Charlene Compher
Director, Microbiome-related Diet Assessment Research & Professor of Nutrition Science

Lisa Nessel
Project Manager

Unmesha Roy Paladhi
Research Coordinator



Pricing: Under development

© The Trustees of the University of Pennsylvania | Site best viewed in a supported browser. | Site Design: PMACS Web Team.