Nutrients (Sep 2021)
Identification and Characterization of Human Observational Studies in Nutritional Epidemiology on Gut Microbiomics for Joint Data Analysis
- Mariona Pinart,
- Katharina Nimptsch,
- Sofia K. Forslund,
- Kristina Schlicht,
- Miguel Gueimonde,
- Patrizia Brigidi,
- Silvia Turroni,
- Wolfgang Ahrens,
- Antje Hebestreit,
- Maike Wolters,
- Andreas Dötsch,
- Ute Nöthlings,
- Kolade Oluwagbemigun,
- Rafael R. C. Cuadrat,
- Matthias B. Schulze,
- Marie Standl,
- Michael Schloter,
- Maria De Angelis,
- Patricia Iozzo,
- Maria Angela Guzzardi,
- Geertrui Vlaemynck,
- John Penders,
- Daisy M. A. E. Jonkers,
- Maya Stemmer,
- Giulia Chiesa,
- Duccio Cavalieri,
- Carlotta De Filippo,
- Danilo Ercolini,
- Francesca De Filippis,
- David Ribet,
- Najate Achamrah,
- Marie-Pierre Tavolacci,
- Pierre Déchelotte,
- Jildau Bouwman,
- Matthias Laudes,
- Tobias Pischon
Affiliations
- Mariona Pinart
- Molecular Epidemiology Research Group, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
- Katharina Nimptsch
- Molecular Epidemiology Research Group, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
- Sofia K. Forslund
- Experimental and Clinical Research Center, A Cooperation of Charité-Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Lindenberger Weg 80, 13125 Berlin, Germany
- Kristina Schlicht
- Institute of Diabetes and Clinical Metabolic Research, University of Kiel, 24105 Kiel, Germany
- Miguel Gueimonde
- Department of Microbiology and Biochemistry of Dairy Products, IPLA-CSIC, 33300 Villaviciosa, Spain
- Patrizia Brigidi
- Department of Medical and Surgical Sciences, University of Bologna, Via Massarenti 9, 40138 Bologna, Italy
- Silvia Turroni
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
- Wolfgang Ahrens
- Leibniz Institute for Prevention Research and Epidemiology-BIPS, 28359 Bremen, Germany
- Antje Hebestreit
- Leibniz Institute for Prevention Research and Epidemiology-BIPS, 28359 Bremen, Germany
- Maike Wolters
- Leibniz Institute for Prevention Research and Epidemiology-BIPS, 28359 Bremen, Germany
- Andreas Dötsch
- Department of Physiology and Biochemistry of Nutrition, Max Rubner-Institut (MRI)-Federal Research Institute of Nutrition and Food, 76131 Karlsruhe, Germany
- Ute Nöthlings
- Nutritional Epidemiology Unit, Institute of Nutrition and Food Sciences, University of Bonn, 53115 Bonn, Germany
- Kolade Oluwagbemigun
- Nutritional Epidemiology Unit, Institute of Nutrition and Food Sciences, University of Bonn, 53115 Bonn, Germany
- Rafael R. C. Cuadrat
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, 14558 Nuthetal, Germany
- Matthias B. Schulze
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, 14558 Nuthetal, Germany
- Marie Standl
- Institute of Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Maria De Angelis
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, 70126 Bari, Italy
- Patricia Iozzo
- Institute of Clinical Physiology, National Research Council, Via Moruzzi 1, 56124 Pisa, Italy
- Maria Angela Guzzardi
- Institute of Clinical Physiology, National Research Council, Via Moruzzi 1, 56124 Pisa, Italy
- Geertrui Vlaemynck
- Department Technology and Food, Flanders Research Institute for Agriculture, Fisheries and Food, 9090 Melle, Belgium
- John Penders
- 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
- Daisy M. A. E. Jonkers
- 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
- Maya Stemmer
- Department of Industrial Engineering and Management, Ben-Gurion University of the Negev, Beer-Sheva P.O. Box 653, Israel
- Giulia Chiesa
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, 20133 Milan, Italy
- Duccio Cavalieri
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Florence, Italy
- Carlotta De Filippo
- Institute of Agricultural Biology and Biotechnology National Research Council, Via Moruzzi 1, 56124 Pisa, Italy
- Danilo Ercolini
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy
- Francesca De Filippis
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy
- David Ribet
- INSERM UMR 1073 “Nutrition, Inflammation and Gut-Brain Axis Dysfunctions”, UNIROUEN, Normandie University, 76000 Rouen, France
- Najate Achamrah
- INSERM UMR 1073 “Nutrition, Inflammation and Gut-Brain Axis Dysfunctions”, UNIROUEN, Normandie University, 76000 Rouen, France
- Marie-Pierre Tavolacci
- INSERM UMR 1073 “Nutrition, Inflammation and Gut-Brain Axis Dysfunctions”, UNIROUEN, Normandie University, 76000 Rouen, France
- Pierre Déchelotte
- INSERM UMR 1073 “Nutrition, Inflammation and Gut-Brain Axis Dysfunctions”, UNIROUEN, Normandie University, 76000 Rouen, France
- Jildau Bouwman
- Microbiology and Systems Biology Group, TNO, Utrechtseweg 48, 3704 HE Zeist, The Netherlands
- Matthias Laudes
- Institute of Diabetes and Clinical Metabolic Research, University of Kiel, 24105 Kiel, Germany
- Tobias Pischon
- Molecular Epidemiology Research Group, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
- DOI
- https://doi.org/10.3390/nu13093292
- Journal volume & issue
-
Vol. 13,
no. 9
p. 3292
Abstract
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.
Keywords
