Intestinal Microbiomics

Joint action in pillar 2: Diet and Food Production

The main objectives of the Joint Action Intestinal Microbiomics (IM) are to increase knowledge on:

  • The short-term and long-term functional effects of diet, dietary patterns and dietary constituents on human intestinal microbiota
  • The impact of diet-related variations in the intestinal microbiota on health and/or on chronic disease, in order to support health promotion and prevention of non-communicable chronic disease.

This Joint Action funded 6 projects for a total amount of about 6.4 M€. The projects run for three years and will start early 2016.


Aryl hydrocarbon receptor and immunity: Activation by diet, microbiota and probiotics (ArylMUNE)

WHAT The transcription factor AhR iscrucial for maintaining intestinalhomeostasis. The aim of ArylMUNE is to assess the effects of AhR activationby microbiotica-derived componentson intestinal immunity andphysiology.

WHO ArylMUNE is a consortium ofresearch groups from 3 countries(Canada, France and TheNetherlands). The project coordinator is Harry Sokol (FR).

HOW The effects of dietaryinterventions and identified strains oflactic acid bacteria will be assessed. AhR agonist presence and activity will be evaluated in intestinal content, microbiota, host response and gastrointestinal symptoms. Novel identified microbial candidates will be tested in vitro and in mouse models to confirm their effects on AhR activation.


Diet -induced Arrangement of the gut Microbiome for improvement of Cardiometabolic health (DINAMIC)

WHAT The DINAMIC consortium investigates the interaction between diet and gut microbia and the potential of modulating these interactions for the prevention of metabolic dysfunction and cardiovascular complications in humans.

WHO The consortium consists of partners from 7 countries (France, Germany, Great Britain, Ireland, Italy and The Netherlands) and is coordinated by Thomas Clavel (DE) and Dirk Haller (DE).

HOW To gain detailed insight into associations between dietary habits, the gut microbiome and cardiometabolic health parameters, human cohorts are used. Targeted nutritional and microbiota interventions will reveal causal relationships between specific diet-responsive microbial taxa and metabolites and the development of metabolic syndrome as risk factor for cardiovascular diseases.


Impact of early life diet on microbiome development & later health (EarlyMicroHealth)

WHAT Microbial colonization of the immature gut of a new-born is essential for the development of its physiological homeostasis. The aim of the EarlyMicroHealth project is to develop early-life interventions to promote the establishment of a healthy microbiota.

WHO EarlyMicroHealth consists of a consortium of research groups of 4 countries (Ireland, Italy, Spain and The

Netherlands) and a collaboration with researchers from China. The coordinator is Miguel Gueimonde (ES).

HOW The consortium will evaluate factors that negatively impact early-life microbiota development. A dietary intervention study will determine the efficacy of early nutritional interventions in minimizing the impact of these factors.


Influence of diet on early life gut virome -  a key player in shaping the gut microbial (EarlyVir )

WHAT Bacteriophages (viruses attacking bacteria) may play a role in shaping gut microbia in early life. EarlyVir aims to investigate how the gut virome is influenced by diet, and to study its role in the origins of chronic childhood disorders.

WHO EarlyVir is a consortium consisting of research groups from 3 countries (Denmark, Canada and France) and is coordinated by Hans Bisgaard (DK).

HOW Intact viromes will be extracted from faecal samples obtained at 1 year of life from the COPSAC2010 cohort. Phage-host pairs will be established by a cultivation-based approach and the CRISPR-Cas bacterial defense mechanism will be studied in order to discover on-going phage-bacteria interactions in the gut. The study provides key information on the role of the gut virome in disease development.


From infancy to childhood: the intersect ion of gastrointestinal microbial, communities, diet and health (GI -MDH)

WHAT The GI-MDH consortium aims to study the influence of the timing and nature of solid food introduction in infancy on gastro-intestinal microbial communities and consequent health outcomes, in particular fat accretion and allergic response.
WHO The consortium consists of research groups from 3 countries (Canada, Germany and The Netherlands). The coordinator is Eileen K. Hutton (CA).

HOW From distinctly different biological, cultural and geographical areas, 4 cohorts will be brought together. Faecal samples were or will be collected and analyzed, as well as detailed information about perinatal exposures, dietary intake, medication and supplement use. In addition, GI-MDH will work to refine approaches to understanding the GI microbiome and its role on health outcomes.


Gut and blood microbiomics for studying the effect of a polyphenol-rich dietary pat tern on intestinal permeability in the elderly (MaPLE)

WHAT The MaPLEproject aims to test the hypothesis that an increased intake of polyphenol-rich foods (e.g. fruits, vegetables, nuts and seeds) reduces IP and lowers inflammogenic bacterial factors in the bloodstream, promoting a protective metabolic phenotype in the elderly.

WHO The consortium consists of research groups form 3 countries (Italy, Spain and The United Kingdom). Patrizia Riso (IT) is this project’s coordinator.

HOW Polyphenol-rich diet versus control diet will be assessed in a randomised, controlled cross-over design. Peripheral blood, urine, and faecal samples will be collected before and after each intervention period to evaluate blood bacterial and LPSloads, blood and faecal microbiota composition, short chain fatty acids and polyphenol-derived metabolites, urine metabolites, and markers of inflammation, oxidative stress and endothelial function.

Download the factsheet of Intestinal Microbiomics


Contact details of coordinators








Contact details of JPI HDHL Joint Action secretariat 
ZonMw(NL),Wilke van Ansem,


Yellow - AryIMUNE
Green - EarlyMicroHealth
Red - EarlyVir
Light Blu - GI-MDH
Pink - MaPLE



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