Identification and Characterization of Human Observational Studies in Nutritional Epidemiology on Gut Microbiomics for Joint Data Analysis

Mariona Pinart (1) , Katharina Nimptsch (2) , Sofia Forslund (3, 4, 5, 6, 7, 8) , Kristina Schlicht (9) , Miguel Gueimonde (10, 11) , Patrizia Brigidi (12) , Silvia Turroni (12) , Wolfgang Ahrens (13, 14) , Antje Hebestreit (15) , Maike Wolters (15) , Andreas Dötsch (16) , Ute Nöthlings (17) , Kolade Oluwagbemigun (17) , Rafael Cuadrat (18) , Matthias Schulze (18, 19, 20) , Marie Standl (21) , Michael Schloter (22) , Maria de Angelis (23) , Patricia Iozzo (24) , Maria Angela Guzzardi (24) , Geertrui Vlaemynck (25) , John Penders (26) , Daisy Jonkers (27) , Maya Stemmer (28) , Giulia Chiesa (29) , Duccio Cavalieri (30) , Carlotta de Filippo (31) , Danilo Ercolini (32, 32) , Francesca de Filippis (32, 32) , David Ribet (33, 34, 35) , Najate Achamrah (33, 34, 35, 36) , Marie-Pierre Tavolacci (33, 34, 35, 37) , Pierre Déchelotte (33, 34, 35, 36) , Jildau Bouwman (38) , Matthias Laudes (9) , Tobias Pischon (1, 4, 6, 39, 40)

1 Molecular Epidemiology Research Group, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany;
2 Molecular Epidemiology Research Group, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany;
3 Experimental and Clinical Research Center, A Cooperation of Charité-Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Lindenberger Weg 80, 13125 Berlin, Germany
4 HU Berlin - Humboldt-Universität zu Berlin = Humboldt University of Berlin = Université Humboldt de Berlin
5 Host-Microbiome Factors in Cardiovascular Disease Lab, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
6 German Centre for Cardiovascular Research (DZHK), Partner Site Berlin, 10785 Berlin, Germany
7 Berlin Institute of Health (BIH), 10178 Berlin, Germany
8 Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
9 Institute of Diabetes and Clinical Metabolic Research, University of Kiel, 24105 Kiel, Germany
10 Department of Microbiology and Biochemistry of Dairy Products, IPLA-CSIC, 33300 Villaviciosa, Spain;
11 Diet, Microbiota and Health Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
12 UNIBO - Alma Mater Studiorum Università di Bologna = University of Bologna
13 Leibniz Institute for Prevention Research and Epidemiology-BIPS, 28359 Bremen, Germany;
14 Institute of Statistics, Bremen University, 28359 Bremen, Germany
15 Leibniz Institute for Prevention Research and Epidemiology-BIPS, 28359 Bremen, Germany
16 Department of Physiology and Biochemistry of Nutrition, Max Rubner-Institut (MRI)-Federal Research Institute of Nutrition and Food, 76131 Karlsruhe, Germany;
17 Rheinische Friedrich-Wilhelms-Universität Bonn
18 Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, 14558 Nuthetal, Germany
19 Institute of Nutritional Science, University of Potsdam, 14558 Potsdam, Germany
20 German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
21 Institute of Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany;
22 Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany;
23 Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, 70126 Bari, Italy
24 Institute of Clinical Physiology, National Research Council, Via Moruzzi 1, 56124 Pisa, Italy
25 ILVO - Research Institute for Agricultural, Fisheries and Food
26 Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM) and Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Center, 6200 MD Maastricht, The Netherlands;
27 Department of Internal Medicine, Division Gastroenterology-Hepatology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center, 6200 MD Maastricht, The Netherlands;
28 BGU - Ben-Gurion University of the Negev
29 UNIMI - Università degli Studi di Milano = University of Milan
30 UniFI - Università degli Studi di Firenze = University of Florence = Université de Florence
31 Institute of Agricultural Biology and Biotechnology National Research Council, Via Moruzzi 1, 56124 Pisa, Italy;
32 University of Naples Federico II = Università degli studi di Napoli Federico II
33 ADEN - Nutrition, inflammation et dysfonctionnement de l'axe intestin-cerveau
34 IRIB - Institute for Research and Innovation in Biomedicine
35 UNIROUEN UFR Santé - UNIROUEN - UFR Santé
36 Service de Nutrition [CHU Rouen]
37 CIC Rouen - Centre d'Investigation Clinique [CHU Rouen]
38 Microbiology and Systems Biology Group, TNO, Utrechtseweg 48, 3704 HE Zeist, The Netherlands
39 Biobank Technology Platform, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
40 Biobank Core Facility, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, 10178 Berlin, Germany

In any research field, data access and data integration are major challenges that even large, well-established consortia face. Although data sharing initiatives are increasing, joint data analyses on nutrition and microbiomics in health and disease are still scarce. We aimed to identify observational studies with data on nutrition and gut microbiome composition from the Intestinal Microbiomics (INTIMIC) Knowledge Platform following the findable, accessible, interoperable, and reusable (FAIR) principles. An adapted template from the European Nutritional Phenotype Assessment and Data Sharing Initiative (ENPADASI) consortium was used to collect microbiome-specific information and other related factors. In total, 23 studies (17 longitudinal and 6 cross-sectional) were identified from Italy (7), Germany (6), Netherlands (3), Spain (2), Belgium (1), and France (1) or multiple countries (3). Of these, 21 studies collected information on both dietary intake (24 h dietary recall, food frequency questionnaire (FFQ), or Food Records) and gut microbiome. All studies collected stool samples. The most often used sequencing platform was Illumina MiSeq, and the preferred hypervariable regions of the 16S rRNA gene were V3–V4 or V4. The combination of datasets will allow for sufficiently powered investigations to increase the knowledge and understanding of the relationship between food and gut microbiome in health and disease.

Domaines: Alimentation et Nutrition

Mariona Pinart, Katharina Nimptsch, Sofia Forslund, Kristina Schlicht, Miguel Gueimonde, et al.. Identification and Characterization of Human Observational Studies in Nutritional Epidemiology on Gut Microbiomics for Joint Data Analysis. Nutrients, 2021, 13 (9), pp.3292. ⟨10.3390/nu13093292⟩. ⟨hal-03351389⟩