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

HDHL INTIMIC JFA2 “Knowledge Platform on Food, Diet, Intestinal Microbiomics and Human Health” (INTIMIC KP)
Knowledge Platform on Food, Diet, Intestinal Microbiomics and Human Health
KP Intestinal Microbiomics
Dr. Jildau Bouwman
Netherlands Organisation for Applied Scientific Research (TNO)
The Netherlands


Partner Organization Partner Country
University of TurinItaly
Instituto de Productos Lácteos de AsturiasSpain
Hospital Regional Universitario de Málaga-Instituto de Investigación Biomédica de MálagaSpain
Wageningen University and ResearchThe Netherlands
Medical University of ViennaAustria
Medical University of GrazAustria
Istituto Superiore di SanitàItaly
Max Delbrueck Center for Molecular MedicineGermany
Flanders Research Institute for Agriculture, Fisheries and FoodBelgium
University of Milan, Department of Food, Environmental and Nutritional SciencesItaly
University of Barcelona, Nutrition & Food Science DepartmentSpain
Sigmund Freud University ViennaAustria
Faculty of Science and Technology, Free University of BolzanoItaly
University of Bari Aldo MoroItaly
University of Naples Federico IIItaly
Research Centre for Food and Nutrition, CREA (Council for Agricultural Research and Economics)Italy
Alma Mater Studiorum University of BolognaItaly
INRA Unité de Nutrition HumaineFrance
Max Rubner-InstituteGermany
University of Veterinary Medicine Vienna, Institute for Milk Hygiene, Milk Technology and Food ScienceAustria
Migal - Galilee Research InstituteIsrael
Amedes genetics GmbHGermany
University of Florence, NEUROFARBA DepartmentItaly
Department of Endocrinology, Diabetology and Clinical Nutrition, University of KielGermany
University of GrazAustria
Leibniz Institute for Prevention Research and Epidemiology - BIPSGermany
University of Milano, Department of Pharmacological and Biomolecular SciencesItaly
INRA/ University of Clermont AuvergneFrance
Ben-Gurion University of the NegevIsrael
Helmholtz Zentrum MünchenGermany
University Medical Center GroningenThe Netherlands
Consiglio Nazionale delle Ricerche- Istituto di Fisiologia ClinicaItaly
The Open University of IsraelIsrael
Netherlands Organisation for applied scientific research (TNO)The Netherlands
Institute of Clinical Microbiology and Hygiene, University Hospital RegensburgGermany
Institute for Laboratory Animal Science, Hannover Medical SchoolGermany
Institute of Animal Science, University of HohenheimGermany
University of GothenburgSweden
University of ViennaAustria
Unilever Research & DevelopmentThe Netherlands
NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht UniversityThe Netherlands
Bonn UniversityGermany
INSERM-University of RouenFrance
Human Nutrition Research CenterFrance
Chalmers University, Division Food and Nutrition Science, Department of Biology and Biological EngineeringSweden
Centre d'Immunologie et des Maladies InfectieusesFrance
Institute of Network Biology, Helmholtz Zentrum MünchenGermany
University Clinic RWTH Aachen, Medical Clinic IIIGermany
University of Florence, Department of BiologyItaly
Federico II University Dept Clinical Medicine and SurgeryItaly

1. Overall project description

1.1 Summary

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.


Through these efforts a network of transnational and multidisciplinary collaboration will emerge, 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.

1.2 Highlights

We identified 23 observational studies on nutrition and microbiome from INTIMIC ( that are available for future joint analyses (use case on gut microbiome composition in obese versus non-obese including data from 8 observational studies ongoing) as well that in a systematic review on gut microbiome composition in obese versus non-obese, we found that a substantial proportion of the 32 included cross-sectional studies found lower diversity and differences in gut microbiome composition in obese versus non-obese adults, but the observed heterogeneity across studies precludes clear answers (

4. Impact

4.1 List of publications

AuthorsTitleYear, Issue, PPPartners NumberDoiPdf
Edoardo Pasolli, Francesca De Filippis, Italia E. Mauriello, Fabio Cumbo, Aaron M. Walsh, John Leech, Paul D. Cotter, Nicola Segata, and Danilo ErcoliniLarge-scale genome-wide analysis links lactic acid bacteria from food with the gut microbiome
González-Domínguez R, Jáuregui O, Queipo-Ortuño MI, Andres-Lacueva C, Characterization of the human exposome by a comprehensive and quantitative large scale multi-analyte metabolomics platform.DOI:10.1021/acs.analchem.0c02008.
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 CrozierRecommendations for standardizing nomenclature for dietary (poly)phenol catabolites.
Francesca De Filippis, Edoardo Pasolli, and Danilo Ercolini. Newly explored Faecalibacterium diversity is connected to age, lifestyle, geography, and disease
Silvia Bolsega*, Andre Bleich* and Marijana Basic*Synthetic Microbiomes on the Rise—Application in Deciphering the Role of Microbes in Host Health and Disease10.3390/nu13114173
Martina Reutzel, Rekha Grewal, Carsten Esselun, Sebastian Friedrich Petry, Thomas Linn, Annette Brandt, Ina Bergheim*, Gunter P. EckertEffects of different standard and special diets on cognition and brain mitochondrial function in mice10.1080/1028415X.2021.1906392
Marianna Roselli, Fausta Natella, Paola Zinno, Barbara Guantario, Raffaella Canali, Emily Schifano, Maria De Angelis*, Olga Nikoloudaki, Marco Gobbetti*, Giuditta Perozzi and Chiara Devirgiliis*Colonization Ability and Impact on Human Gut Microbiota of Foodborne Microbes From Traditional or Probiotic-Added Fermented Foods: A Systematic Review10.3389/fnut.2021.689084
Schneider KM, Mohs A, Kilic K, Candels LS, Elfers C, Bennek E, Schneider LB, Heymann F, Gassler N, Penders J*, Trautwein CIntestinal Microbiota Protects against MCD Diet-Induced Steatohepatitis10.3390/ijms20020308
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*Identification and Characterization of Human Observational Studies in Nutritional Epidemiology on Gut Microbiomics for Joint Data Analysis
Mariona Pinart*, Andreas Dötsch*, Kristina Schlicht*, Matthias Laudes*, Jildau Bouwman*, Sofia K. Forslund*, Tobias Pischon* and Katharina Nimptsch*Gut microbiome composition in obese and non-obese persons: a systematic review and meta-analysis
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. Infants’ First Solid Foods: Impact on Gut Microbiota Development in Two Intercontinental Cohorts.
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*.BMI, Alcohol Consumption and Gut Microbiome Species Richness Are Related to Structural and Functional Neurological Abnormalities10.3390/nu13113743
Matthias Laudes*, Corinna Geisler, Nathalie Rohmann, Jildau Bouwman*, Tobias Pischon*, Kristina Schlicht*Microbiota in Health and Disease-Potential Clinical Applications10.3390/nu13113866
Calabrese FM, Porrelli A, Vacca M, Comte B, Nimptsch K, Pinart M, Pischon T, Pujos-Guillot E, De Angelis M*Metaproteomics Approach and Pathway Modulation in Obesity and Diabetes: A Narrative Review
Borrás C*, Mas-Bargues C, Román-Domínguez A, Sanz-Ros J, Gimeno-Mallench L, Inglés M, Gambini J, Viña JBCL-xL, a Mitochondrial Protein Involved in Successful Aging: From C. elegans to Human Centenarians10.3390/ijms21020418
Mas-Bargues C, Borrás C*, Viña JBcl-xL as a Modulator of Senescence and Aging10.3390/ijms22041527
Strasser B, Wolters M, Weyh C, Krüger K, Ticinesi A*The Effects of Lifestyle and Diet on Gut Microbiota Composition, Inflammation and Muscle Performance in Our Aging Society

4.2 Presentation of the project

Target groupAuthorsMeans of communicationHyperlinkPdf
ECIS 2020Maya Stemmer, Gilad Ravid, Yisrael ParmetOral Presentation

4.3 List of submitted patents and other outputs

Patent licencePartners involvedYearInternational eu or national patentCommentPdf

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This project has received funding from the European Union’s
H2020 Research and Innovation Programme under grant agreement n.696300

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