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.
Consortium
| 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 |
Highlights
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.
Products
Author: Edoardo Pasolli, Francesca De Filippis, Italia E. Mauriello, Fabio Cumbo, Aaron M. Walsh, John Leech, Paul D. Cotter, Nicola Segata, and Danilo Ercolini
Link: https://doi.org/10.1038/s41467-020-16438-8
Author: González-Domínguez R, Jáuregui O, Queipo-Ortuño MI, Andres-Lacueva C,
Link: https://doi.org/10.1021/acs.analchem.0c02008
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
Link: https://doi.org/10.1093/ajcn/nqaa204
Author: Francesca De Filippis, Edoardo Pasolli, and Danilo Ercolini.
Link: https://doi.org/10.1016/j.cub.2020.09.063
Author: Silvia Bolsega*, Andre Bleich* and Marijana Basic*
Link: https://doi.org/10.3390/nu13114173
Author: Martina Reutzel, Rekha Grewal, Carsten Esselun, Sebastian Friedrich Petry, Thomas Linn, Annette Brandt, Ina Bergheim*, Gunter P. Eckert
Link: https://doi.org/10.1080/1028415x.2021.1906392
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*
Link: https://doi.org/10.3389/fnut.2021.689084
Author: Schneider KM, Mohs A, Kilic K, Candels LS, Elfers C, Bennek E, Schneider LB, Heymann F, Gassler N, Penders J*, Trautwein C
Link: https://doi.org/10.3390/ijms20020308
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*
Link: https://doi.org/10.3390/nu13093292
Author: Mariona Pinart*, Andreas Dötsch*, Kristina Schlicht*, Matthias Laudes*, Jildau Bouwman*, Sofia K. Forslund*, Tobias Pischon* and Katharina Nimptsch*
Link: https://doi.org/10.3390/nu14010012
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.
Link: https://doi.org/10.3390/nu13082639
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*.
Link: https://doi.org/10.3390/nu13113743
Author: Matthias Laudes*, Corinna Geisler, Nathalie Rohmann, Jildau Bouwman*, Tobias Pischon*, Kristina Schlicht*
Link: https://doi.org/10.3390/nu13113866
Author: Calabrese FM, Porrelli A, Vacca M, Comte B, Nimptsch K, Pinart M, Pischon T, Pujos-Guillot E, De Angelis M*
Link: https://doi.org/10.3390/nu14010047
Author: Borrás C*, Mas-Bargues C, Román-Domínguez A, Sanz-Ros J, Gimeno-Mallench L, Inglés M, Gambini J, Viña J
Link: https://doi.org/10.3390/ijms21020418
Author: Mas-Bargues C, Borrás C*, Viña J
Link: https://doi.org/10.3390/ijms22041527
Author: Strasser B, Wolters M, Weyh C, Krüger K, Ticinesi A*
Link: https://doi.org/10.3390/nu13062045
Reports
Endreport
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 group | Authors | Means of communication |
|---|---|---|
| ECIS 2020 | Maya Stemmer, Gilad Ravid, Yisrael Parmet | Oral Presentation |
| Scientists of laboratory animal science / animal caretaker / laboratory technician / veterinaries | Silvia 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/ 2021 | scientific oral presentation |
| INTIMIC WP leaders | Presented 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 2021 | Oral presentation |
| All partners of the INTIMIC consortium | Presented 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 2021 | Oral presentation |
| All INTIMIC partners interested in healthy aging and microbiome | Presented 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 2021 | Oral 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 2021 | Oral presentation |
| DataSHIELD developers and users | Mariona 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 2021 | Oral presentation (Lightening talk) |