INTIMIC Knowledge Platform

Knowledge Platform on Food, Diet, Intestinal Microbiomics and Human Health

Background and aim:

Studies suggest that the intestinal microbiome modulates the risk of several chronic diseases, including type 2 diabetes, allergy, cardiovascular disease, and colorectal cancer (CRC). Dietary factors are related to chronic disease risk, and they have been suggested to modulate the composition and function of the gut microbiome. However, detailed knowledge on the relationship of diet, the microbiome, and chronic disease risk is still limited.

The overarching aim of the knowledge platform is to foster studies on the microbiome, nutrition and health by  assembling available information in the field of microbiome research in food, nutrition and health in a comprehensive way, which also includes other disciplines (e.g. food science, metabolomics) that are relevant in the context of microbiome research. The goal is to make this information findable, accessible, interoperable and reusable (FAIR) to the scientific community and to link and provide in-depth information to various stakeholders.

The platform has made relevant human and non-human studies on food, diet and intestinal microbiomics avaibale in a FAIR way. Moreover, it has delivered a clear overview of the SOPs used within the microbiome community and the sources of the inter- and intra-individual variation of a healthy microbiome both at a taxonomic and functional level has been specified by the platform. In addition an overview of the standards developed for (omics) analysis platforms relevant for this platform, like metabolomics, dietary intake and physical activity has been made. The project results were disseminated in a coordinated way by amongst others publications in a special issue of Nutrients and a final meeting in Vienna.  An inventory of available models, resources and strategies that can be utilized inanalysing and validating cause-effect mechanisms was delivered and benefits, drawbacks and limitations of these models/ strategies assessed.

Through these efforts a network of transnational and multidisciplinary collaboration has emerged, that will further develop and increase the impact of microbiome research in human health. Urgent areas of research in this KP were identified to be the roles of microbiome in early infancy, during ageing and in subclinical and clinically manifest disease.

Expected impact

The platform has ensured a solid basis of data and standards to bring the scientific field on the interaction between microbiome, nutrition and health further. This knowledge may lead to healthier food, and functional food products.This initiative has consolidated (open access) nutritional mechanistic, intervention and epidemiological studies related to studies on the relation between microbiome, nutrition and health via the DASH-IN infrastructure. For this development standardisation is crucial as combining studies depends on mapping of similar data and design.We have developed a system that allows generalized data sharing and our impact will be the fulfilment of these needs and a much better use of nutritional study data for future analyses across datasets and study types. The work on standard operating procedures will have a large impact on future data sharing also outside of the IKP consortium by linking to initiatives such as ELIXIR. Datasets may be used by the law makers, medical doctors, funding institutions. The outcome has made it easier to access medically and nutritionally relevant datasets and exploitation of previously unreleased datasets as well as published ones to the benefit of the wider EU based scientific community . On the longer term, this platform will help to form better and more informed hypotheses in future studies and make it possible to actually test new hypotheses without having to conduct additional studies. The use cases have shown that new research is possible on the collected data. DASH-IN developed by ENPADASI is used as platform to collect the data.


Partner Organization Partner Country
University of Turin Italy
Instituto de Productos Lácteos de Asturias Spain
Hospital Regional Universitario de Málaga-Instituto de Investigación Biomédica de Málaga Spain
Wageningen University and Research The Netherlands
Medical University of Vienna Austria
Medical University of Graz Austria
Istituto Superiore di Sanità Italy
Max Delbrueck Center for Molecular Medicine Germany
Flanders Research Institute for Agriculture, Fisheries and Food Belgium
University of Milan, Department of Food, Environmental and Nutritional Sciences Italy
University of Barcelona, Nutrition & Food Science Department Spain
Sigmund Freud University Vienna Austria
Faculty of Science and Technology, Free University of Bolzano Italy
University of Bari Aldo Moro Italy
University of Naples Federico II Italy
Research Centre for Food and Nutrition, CREA (Council for Agricultural Research and Economics) Italy
Alma Mater Studiorum University of Bologna Italy
INRA Unité de Nutrition Humaine France
Max Rubner-Institute Germany
University of Veterinary Medicine Vienna, Institute for Milk Hygiene, Milk Technology and Food Science Austria
Migal - Galilee Research Institute Israel
Amedes genetics GmbH Germany
University of Florence, NEUROFARBA Department Italy
Department of Endocrinology, Diabetology and Clinical Nutrition, University of Kiel Germany
University of Graz Austria
Leibniz Institute for Prevention Research and Epidemiology - BIPS Germany
University of Milano, Department of Pharmacological and Biomolecular Sciences Italy
INRA/ University of Clermont Auvergne France
Ben-Gurion University of the Negev Israel
Helmholtz Zentrum München Germany
University Medical Center Groningen The Netherlands
Consiglio Nazionale delle Ricerche- Istituto di Fisiologia Clinica Italy
The Open University of Israel Israel
Netherlands Organisation for applied scientific research (TNO) The Netherlands
Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg Germany
Institute for Laboratory Animal Science, Hannover Medical School Germany
Institute of Animal Science, University of Hohenheim Germany
University of Gothenburg Sweden
University of Vienna Austria
Unilever Research & Development The Netherlands
NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University The Netherlands
Bonn University Germany
INSERM-University of Rouen France
Human Nutrition Research Center France
Chalmers University, Division Food and Nutrition Science, Department of Biology and Biological Engineering Sweden
Centre d'Immunologie et des Maladies Infectieuses France
Institute of Network Biology, Helmholtz Zentrum München Germany
University Clinic RWTH Aachen, Medical Clinic III Germany
University of Florence, Department of Biology Italy
Federico II University Dept Clinical Medicine and Surgery Italy



We have shown that the microbiome is heavily affected by the diet, including the food microbiome and that the microbiome is clinically relevant to many diseases and from a diagnosis and intervention point of view.

We have expended the DASH-IN standards of ENPADASI with (microbiome) standards for observational study data, intervention study data, microbiome data and other omics data (food, processing, fermentation, Food-Biomarker, physical activity, metagenomics, metabolomics). Many datasets available in a standardized way (also for studies focusing on prebiotic) and some data of some open data sources is made FAIR.

We have shown that there are  still large issues with biological and technical variance (shown by ring trials), although a lot of initiatives are working on development of standards. We have gained better insight in the background of the variation in the measures (of which sample collection is the origin of the largest technical variation).

On the website training material and other material is made available.


Title: Large-scale genome-wide analysis links lactic acid bacteria from food with the gut microbiome
Author: Edoardo Pasolli, Francesca De Filippis, Italia E. Mauriello, Fabio Cumbo, Aaron M. Walsh, John Leech, Paul D. Cotter, Nicola Segata, and Danilo Ercolini
Title: Characterization of the human exposome by a comprehensive and quantitative large scale multi-analyte metabolomics platform.
Author: González-Domínguez R, Jáuregui O, Queipo-Ortuño MI, Andres-Lacueva C,
Title: Recommendations for standardizing nomenclature for dietary (poly)phenol catabolites.
Author: Colin D Kay, Michael N Clifford, Pedro Mena, Gordon J McDougall, Cristina Andres-Lacueva, Aedin Cassidy, Daniele Del Rio, Nikolai Kuhnert, Claudine Manach, Gema Pereira-Caro, Ana Rodriguez-Mateos, Augustin Scalbert, Francisco Tomás-Barberán, Gary Williamson, David S Wishart, and Alan Crozier
Title: Newly explored Faecalibacterium diversity is connected to age, lifestyle, geography, and disease
Author: Francesca De Filippis, Edoardo Pasolli, and Danilo Ercolini.
Title: Synthetic Microbiomes on the Rise—Application in Deciphering the Role of Microbes in Host Health and Disease
Author: Silvia Bolsega*, Andre Bleich* and Marijana Basic*
Title: Effects of different standard and special diets on cognition and brain mitochondrial function in mice
Author: Martina Reutzel, Rekha Grewal, Carsten Esselun, Sebastian Friedrich Petry, Thomas Linn, Annette Brandt, Ina Bergheim*, Gunter P. Eckert
Title: Colonization Ability and Impact on Human Gut Microbiota of Foodborne Microbes From Traditional or Probiotic-Added Fermented Foods: A Systematic Review
Author: Marianna Roselli, Fausta Natella, Paola Zinno, Barbara Guantario, Raffaella Canali, Emily Schifano, Maria De Angelis*, Olga Nikoloudaki, Marco Gobbetti*, Giuditta Perozzi and Chiara Devirgiliis*
Title: Intestinal Microbiota Protects against MCD Diet-Induced Steatohepatitis
Author: Schneider KM, Mohs A, Kilic K, Candels LS, Elfers C, Bennek E, Schneider LB, Heymann F, Gassler N, Penders J*, Trautwein C
Title: Identification and Characterization of Human Observational Studies in Nutritional Epidemiology on Gut Microbiomics for Joint Data Analysis
Author: Pinart M, Nimptsch K, Forslund SK, Schlicht K, Gueimonde M, Brigidi P, Turroni S, Ahrens W, Hebestreit A, Wolters M, Dötsch A, Nöthlings U, Oluwagbemigun K, Cuadrat RRC, Schulze MB, Standl M, Schloter M, De Angelis M, Iozzo P, Guzzardi MA, Vlaemynck G, Penders J, Jonkers DMAE, Stemmer M, Chiesa G, Cavalieri D, De Filippo C, Ercolini D, De Filippis F, Ribet D, Achamrah N, Tavolacci M-P, Déchelotte P, Bouwman J, Laudes M, Pischon T*
Title: Gut microbiome composition in obese and non-obese persons: a systematic review and meta-analysis
Author: Mariona Pinart*, Andreas Dötsch*, Kristina Schlicht*, Matthias Laudes*, Jildau Bouwman*, Sofia K. Forslund*, Tobias Pischon* and Katharina Nimptsch*
Title: Infants’ First Solid Foods: Impact on Gut Microbiota Development in Two Intercontinental Cohorts.
Author: Homann C-M, Rossel CAJ, Dizzell S, Bervoets L, Simioni J, Li J, Gunn E, Surette MG, de Souza RJ, Mommers M*, Hutton EK, Morrison KM, Penders J*, van Best N, Stearns JC.
Title: BMI, Alcohol Consumption and Gut Microbiome Species Richness Are Related to Structural and Functional Neurological Abnormalities
Author: Geisler C, Pankoke J, Schlicht K*, Knappe C, Rohmann N, Hartmann K, Settgast U, Türk K, Seoudy AK, Franke A, Schreiber S, Schulte DM, Laudes M*.
Title: Microbiota in Health and Disease-Potential Clinical Applications
Author: Matthias Laudes*, Corinna Geisler, Nathalie Rohmann, Jildau Bouwman*, Tobias Pischon*, Kristina Schlicht*
Title: Metaproteomics Approach and Pathway Modulation in Obesity and Diabetes: A Narrative Review
Author: Calabrese FM, Porrelli A, Vacca M, Comte B, Nimptsch K, Pinart M, Pischon T, Pujos-Guillot E, De Angelis M*
Title: BCL-xL, a Mitochondrial Protein Involved in Successful Aging: From C. elegans to Human Centenarians
Author: Borrás C*, Mas-Bargues C, Román-Domínguez A, Sanz-Ros J, Gimeno-Mallench L, Inglés M, Gambini J, Viña J
Title: Bcl-xL as a Modulator of Senescence and Aging
Author: Mas-Bargues C, Borrás C*, Viña J
Title: The Effects of Lifestyle and Diet on Gut Microbiota Composition, Inflammation and Muscle Performance in Our Aging Society
Author: Strasser B, Wolters M, Weyh C, Krüger K, Ticinesi A*



The project found that reference standards in the field of human microbiome research needed to be further developed in order to improve quality management. It was also concluded that the stability of measures needed to be improved in order to fully implement the microbiome in practice. Defining the core human microbiome was identified as an important step in this process, but it was acknowledged that the road towards this goal was long. The project also recommended removing false positives and negatives from analysis in order to increase the societal impact of the research. Finally, the project suggested exploring the gnotobiotic microbiome as a new possibility in the field.

We propose the development of a expert centre, for instance within a research instructure. This expert centre can help with the coordination for further standardization of the human microbiome field.

Communication & Dissemination Activities

Target groupAuthorsMeans of communication
ECIS 2020Maya Stemmer, Gilad Ravid, Yisrael ParmetOral Presentation
Scientists of laboratory animal science / animal caretaker / laboratory technician / veterinariesSilvia Bolsega*, Lisa Osbelt, Anna Smoczek, Till Strowig, Andre Bleich*, and Marijana Basic* / Microbiota composition influences the colitis phenotype in an interleukin 10-deficient mouse model / 59. Wissenschaftliche Tagung der Gesellschaft für Versuchstierkunde GV-SOLAS / online conference/ 2021scientific oral presentation
INTIMIC WP leadersPresented by Mariona Pinart on behalf of MDC partners, Kristina Schlicht on behalf of CAU partners, and Martin Larsen (INSERM), Title: “WP6: Human association studies”, WP leader meeting, online meeting, 11 Nov 2020 and 25 March 2021Oral presentation
All partners of the INTIMIC consortiumPresented by Mariona Pinart on behalf of MDC partners, Kristina Schlicht on behalf of CAU partners, and Martin Larsen (INSERM), Title: “WP6: Human association studies”, General assembly, online meeting, 27 Nov 2020 and 06 September 2021Oral presentation
All INTIMIC partners interested in healthy aging and microbiomePresented by Mariona Pinart on behalf of Tobias Pischon (WG2 leader), Title: “WG2: Healthy ageing”, Thematic working group (WG) meeting, online meeting, 11 Jan 2021 and 10 June 2021Oral presentation
Molecular Epidemiology Research group at MDC (aim was to set a collaboration in the Use Case 3)Prof Juan Ramón González (Barcelona ISGlobal), Title of the presentation: “Orchestrating privacy-protected non-disclosive omic data analyses in multi-cohort studies using DataSHIELD”, Episeminar at the Molecular Epidemiology Research Group, online meeting hosted by MDC, 24 September 2021Oral presentation
DataSHIELD developers and usersMariona Pinart on behalf of MDC, Title of the presentation: “Investigating differences in the microbiome composition in obese and non-obese individuals and its relationship to diet using DataSHIELD”, 2021 DataSHIELD conference, online meeting hosted by the Newcastle University, 11 November 2021Oral presentation (Lightening talk)


Project number:
HDHL-INTIMIC Knowledge Platform
Duration: 100%
Duration: 100 %
Project lead and secretary:
Dr. Jildau Bouwman
Responsible organisation:
Netherlands Organisation for Applied Scientific Research (TNO), The Netherlands