Research Programs


2012-2019 Financed by the french initiative "Investissements d'Avenir"

Coordinator: S.D. Ehrlich (INRA - France) Partners: INRA-MICALIS, Université Catholique de Lyon (Thierry Magnin), Cardiometabolism and Nutrition Institute (Karine Clément)

MetaGenoPolis (MGP) has a strategic goal to demonstrate the impact of the human gut microbiota on health and disease, by making available cutting-edge metagenomics technology, quantitative and functional, to the medical, academic and industrial communities. The approach is built upon the knowledge gathered by the EC FP7 MetaHIT project, such as the establishment of a broad gene catalogue of the human intestinal metagenome, discovery of the three human enterotypes, characterization of microbiota in two chronic diseases, obesity and inflammatory bowel disease and the pilot high-throughput functional metagenomics screens.

International Human Microbiome Standards - IHMS

2011-2015. Financed by the European Commission (FP7) -

Principal investigators : S.D Ehrlich (INRA, France) - Coordinator; J. Doré (INRA, France); F. Guarner (HUVH, Spain); J. Versalovic (BCM, USA); L. Zhao (SJTU, China); E. Pelletier (CEA genoscope, France); Wang Jun (BGI, China); P. Bork (EMBL, Germany); B. Singh (Western, Canada).

Final aim : Optimization of methods for the assessment of the effects of the gut microbiome on human health through the standardization of procedures and protocols.

Korean Microbiome Diversity Using Korean Twin Cohort Project

Project funded from 2010 at level of 2 million dollars for the next 5 years by National Research Foundation of Korea.

Principal Investigator: Prof. GwangPyo Ko, Seoul National University

The aim of this program is to determine the microbiomes present in various epithelial sites of the human body by using Korean Twin Cohort, investigate the relationship between human microbiomes and the relevant diseases on their respective sites and develop the database to cover the diversity of Korean microbiomes and their related data. This research should determine the disease targets for early diagnosis and prevention, and help establishing a dedicated center for Korean microbiome information and analysis.

The success of this project shall lead to identification of the target microbiome and genes associated with human diseases (particularly for metabolic and immune response disorders), provide the basis of disease prevention using chemical or biological agents for manipulating the composition of human microbiome and lead to the development of NGS bioinformatics pipelines and microbiome database.  It should also help train the researchers with various life science expertises and strengthen the collaboration with the leading groups in the field of microbiome research across the International Human Microbiome Consortium.

NIH Human Microbiome Project

The NIH Human Microbiome Project (HMP) is a five year initiative that has been funded at a level of $115 million over five years by the NIH Roadmap Program. The goal of the HMP is to extensively characterize the microbes that live in an on the human body, and to assess the ability to demonstrate correlations of changes of the human microbiome with human healthThere are a number of initiatives that will be funded as part of the NIH HMP that will contribute to achieving this goal; RFAs for those initiatives have been published and applications will funded in September 2008 and March 2009.   The NIH provided preliminary funding ($8.2 million for one year) in September, 2007 for the NIH HMP to “jumpstart” the program.  The jumpstart year is followed by four additional years of funding that will be awarded competitively for sequencing of additional bacteria, viral and eukaryotic microbial genomes and metagenomic sequence sampling of body regions.  A Data Analysis and Coordination Center (DACC) was funded in September 2008 at the University of Maryland.  A set of grants with the goals of developing new technologies and software tools for the HMP and studying Ethical, Legal and Social Issues have also been funded.  In June 2009, the NIH will announce the support of the large-scale sequencing centers and demonstration projects to study changes in the human microbiome on health and disease that will be funded for the final four years of the HMP.

Further information on the NIH HMP program may be found at

The Australian Jumpstart Human Microbiome Project

Project funded from 2009 by the Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australia

Principal investogator : Mark Morrison

Canadian Human Microbiome Initiative

Projects funded from 2009 by the Canadian Institutes of Health Research (CIHR). Information about funding opportunities can be found on the CIHR website as well as a description of the Canadian Microbiome Initiative call.

Principal investigators:

  • Emma Allen-Vercoe (University of Guelph) "Investigating the potential effects of host-derived stress hormones on the human gut microflora"
  • Barton B. Finlay (University of British Columbia) "The role of the gastrointestinal microbiota in asthma"
  • Rob Holt (University of British Columbia) "Linking infectious agents to cancer : a metagenomics approach"
  • David M. Hwang (University Health Network) "Assessing the impact of polymicrobial pulmonary infections in cystic fibrosis via metagenomics"
  • Anita L. Kozyrskyj (University of Alberta) "The impact of antibiotics on intestinal microbiota of infants"
  • Amee R. Manges (The Research Institute of the McGill UNiversity Health Centre) "Microbial metagenomics of the intestinal microbiota and the etiology of Clostridium difficile - associated disease in hospitalized patients"
  • Deborah M. Money (University of British Columbia) "Metagenomics characterization of the human vaginal microbiome"
  • Josh D. Neufeld (University of Waterloo, Ontario) "Establishing a complete taxonomic baseline for the human microbiome"
  • Kieran C. O'Doherty (University of British Columbia) "Developing ethical and regulatory guidelines for research on the human microbiome and its applications: speaking to the experts and stakeholders"
  • Kevin P. Rioux (University of Calgary) "Characterizing the fecal microbiome and bacteria-derived volatile organic compounds in patients with nonalcoholic fatty liver disease (NAFLD)"
  • Alain Stinzi (University of Ottawa) "Role of the gut microbiome in pediatric gastrointestinal illnesses"
  • Michael G. Surette (University of Calgary) "Elusive respiratory pathogens in the oropharyngeal flora"

DACC - Data Analysis and Coordination Center

2008-2013. Funded by the NIH Human Microbiome Project (HMP).

Principal investigator : Owen White (Institute for Genome Sciences, USA)

MicroObes, Human Intestinal Microbiome in Obesity and Nutritional Transition

2008-2010. Financed in part by the French National Agency for Research (ANR).

Principal investigators : J. Doré (INRA, FR) - Coordinator; K. Clément & A. Basdevant (UPMC, FR); D. Le Paslier & J. Weissenbach (CEA Genoscope, FR); Jean-François Gibrat & Philippe Bessières (INRA, FR); Jean-Pierre Gauchi & Alain Trubuil (INRA, FR); E. Maguin, P. Renault & S.D. Ehrlich (INRA, FR)

MetaHIT, Metagenomics of the Human Intestinal Tract

2008-2011. Financed in part by the European Commission (FP7).

Principal investigators : S.D. Ehrlich (INRA, FR) - Coordinator; J. Weissenbach (CEA Genoscope, FR); S. Brunak (DTU, DK); R. Oozeer (Danone, FR); P. Bork (EMBL, D); F. Guarner (HUVH, Spain); M. Rescignio (IEO, I); O. Pederson (NN, DK); K. Kristiansen (SDU, DK); E. Caldwell (UCB Pharma, SP); W. de Vos (WU, NL); J. Parkhill (WTSI, UK); WangJun (BGI, PRC)

NIH Jumpstart Program

2007-2008. Financed by the NIH.

Principal investigators : Sarah Highlander (sequencing centers at Baylor College of Medicine, USA); Bruce Birren (the Broad Institute, USA), Robert Strausberg (The J. Craig Venter Institute) and George Weinstock (Washington University School of Medicine).

The HMP Jumpstart aims at the following goals: 1. Generation of the complete genome sequences of 200 bacterial strains isolated from the human body; 2. Recruitment of donors for and securing samples from five body regions; and 3. Performing 16S rRNA metagenomic sequence analysis of the sampled body regions.