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1. Gut microbiome and atrial fibrillation—results from a large population-based study

Author

Palmu, Joonatan, Börschel, Christin S, Ortega-Alonso, Alfredo, Markó, Lajos, Inouye, Michael, Jousilahti, Pekka, Salido, Rodolfo A, Sanders, Karenina, Brennan, Caitriona, Humphrey, Gregory C, Sanders, Jon G, Gutmann, Friederike, Linz, Dominik, Salomaa, Veikko, Havulinna, Aki S, Forslund, Sofia K, Knight, Rob, Lahti, Leo, Niiranen, Teemu, and Schnabel, Renate B

Subjects
Epidemiology, Biomedical and Clinical Sciences, Clinical Sciences, Health Sciences, Cardiovascular, Heart Disease, Prevention, Genetics, 2.1 Biological and endogenous factors, Aetiology, Humans, Atrial Fibrillation, Gastrointestinal Microbiome, Heart, Bacteria, Aging, Incidence, Atrial fibrillation, Gut microbiome, Metagenomics, Public Health and Health Services, Clinical sciences
Abstract

BackgroundAtrial fibrillation (AF) is an important heart rhythm disorder in aging populations. The gut microbiome composition has been previously related to cardiovascular disease risk factors. Whether the gut microbial profile is also associated with the risk of AF remains unknown.MethodsWe examined the associations of prevalent and incident AF with gut microbiota in the FINRISK 2002 study, a random population sample of 6763 individuals. We replicated our findings in an independent case-control cohort of 138 individuals in Hamburg, Germany.FindingsMultivariable-adjusted regression models revealed that prevalent AF (N = 116) was associated with nine microbial genera. Incident AF (N = 539) over a median follow-up of 15 years was associated with eight microbial genera with false discovery rate (FDR)-corrected P

Published
2023

2. Reporting guidelines for human microbiome research: the STORMS checklist

Author

Mirzayi, Chloe, Renson, Audrey, Zohra, Fatima, Elsafoury, Shaimaa, Geistlinger, Ludwig, Kasselman, Lora J, Eckenrode, Kelly, van de Wijgert, Janneke, Loughman, Amy, Marques, Francine Z, MacIntyre, David A, Arumugam, Manimozhiyan, Azhar, Rimsha, Beghini, Francesco, Bergstrom, Kirk, Bhatt, Ami, Bisanz, Jordan E, Braun, Jonathan, Bravo, Hector Corrada, Buck, Gregory A, Bushman, Frederic, Casero, David, Clarke, Gerard, Collado, Maria Carmen, Cotter, Paul D, Cryan, John F, Demmer, Ryan T, Devkota, Suzanne, Elinav, Eran, Escobar, Juan S, Fettweis, Jennifer, Finn, Robert D, Fodor, Anthony A, Forslund, Sofia, Franke, Andre, Furlanello, Cesare, Gilbert, Jack, Grice, Elizabeth, Haibe-Kains, Benjamin, Handley, Scott, Herd, Pamela, Holmes, Susan, Jacobs, Jonathan P, Karstens, Lisa, Knight, Rob, Knights, Dan, Koren, Omry, Kwon, Douglas S, Langille, Morgan, Lindsay, Brianna, McGovern, Dermot, McHardy, Alice C, McWeeney, Shannon, Mueller, Noel T, Nezi, Luigi, Olm, Matthew, Palm, Noah, Pasolli, Edoardo, Raes, Jeroen, Redinbo, Matthew R, Rühlemann, Malte, Balfour Sartor, R, Schloss, Patrick D, Schriml, Lynn, Segal, Eran, Shardell, Michelle, Sharpton, Thomas, Smirnova, Ekaterina, Sokol, Harry, Sonnenburg, Justin L, Srinivasan, Sujatha, Thingholm, Louise B, Turnbaugh, Peter J, Upadhyay, Vaibhav, Walls, Ramona L, Wilmes, Paul, Yamada, Takuji, Zeller, Georg, Zhang, Mingyu, Zhao, Ni, Zhao, Liping, Bao, Wenjun, Culhane, Aedin, Devanarayan, Viswanath, Dopazo, Joaquin, Fan, Xiaohui, Fischer, Matthias, Jones, Wendell, Kusko, Rebecca, Mason, Christopher E, Mercer, Tim R, Sansone, Susanna-Assunta, Scherer, Andreas, Shi, Leming, Thakkar, Shraddha, Tong, Weida, Wolfinger, Russ, Hunter, Christopher, Segata, Nicola, and Huttenhower, Curtis

Subjects
Human Genome, Genetics, Computational Biology, Dysbiosis, Humans, Microbiota, Observational Studies as Topic, Research Design, Translational Science, Biomedical, Genomic Standards Consortium, Massive Analysis and Quality Control Society, Medical and Health Sciences, Immunology
Abstract

The particularly interdisciplinary nature of human microbiome research makes the organization and reporting of results spanning epidemiology, biology, bioinformatics, translational medicine and statistics a challenge. Commonly used reporting guidelines for observational or genetic epidemiology studies lack key features specific to microbiome studies. Therefore, a multidisciplinary group of microbiome epidemiology researchers adapted guidelines for observational and genetic studies to culture-independent human microbiome studies, and also developed new reporting elements for laboratory, bioinformatics and statistical analyses tailored to microbiome studies. The resulting tool, called 'Strengthening The Organization and Reporting of Microbiome Studies' (STORMS), is composed of a 17-item checklist organized into six sections that correspond to the typical sections of a scientific publication, presented as an editable table for inclusion in supplementary materials. The STORMS checklist provides guidance for concise and complete reporting of microbiome studies that will facilitate manuscript preparation, peer review, and reader comprehension of publications and comparative analysis of published results.

Published
2021

3. STEM Pride: Perspectives from transgender, nonbinary, and genderqueer scientists

Author

Armada-Moreira, Adam, Cizauskas, Carrie, Fleury, Gabriela, Forslund, Sofia Kirke, Guthman, Eartha Mae, Hanafiah, Aflah, Hope, Jen M, Jayasinghe, Izzy, McSweeney, Danny, and Young, Iris D

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Stem Cell Research - Nonembryonic - Non-Human, Stem Cell Research, Engineering, Female, Humans, Male, Mathematics, Research Personnel, Science, Sexual and Gender Minorities, Technology, Transgender Persons, Medical and Health Sciences, Developmental Biology, Biological sciences, Biomedical and clinical sciences
Abstract

In celebration of Pride Month, we asked transgender, genderqueer, and nonbinary scientists to tell us about what fascinates them, their ambitions and achievements, and how their gender identities have shaped their experiences in STEM. We owe a special thanks to 500 Queer Scientists (https://500queerscientists.com/), whose network and efforts at increasing LGBTQ+ scientists' visibility made this article possible.

Published
2021

4. Fasting alters the gut microbiome reducing blood pressure and body weight in metabolic syndrome patients

Author

Maifeld, András, Bartolomaeus, Hendrik, Löber, Ulrike, Avery, Ellen G., Steckhan, Nico, Markó, Lajos, Wilck, Nicola, Hamad, Ibrahim, Šušnjar, Urša, Mähler, Anja, Hohmann, Christoph, Chen, Chia-Yu, Cramer, Holger, Dobos, Gustav, Lesker, Till Robin, Strowig, Till, Dechend, Ralf, Bzdok, Danilo, Kleinewietfeld, Markus, Michalsen, Andreas, Müller, Dominik N., Forslund, Sofia K., and HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany.

Subjects
Male, Science, Medizin, Metabolic disorders, Blood Pressure, Predictive markers, Article, Body Mass Index, Feces, Desulfovibrionaceae, T-Lymphocyte Subsets, Ruminococcus, Humans, Dyslipidaemias, Aged, Metabolic Syndrome, Body Weight, Akkermansia, Fasting, Middle Aged, Diet, Gastrointestinal Microbiome, Cardiovascular diseases, Cardiovascular and Metabolic Diseases, Hypertension, Female, 600 Technik, Medizin, angewandte Wissenschaften::610 Medizin und Gesundheit::610 Medizin und Gesundheit
Abstract

Periods of fasting and refeeding may reduce cardiometabolic risk elevated by Western diet. Here we show in the substudy of NCT02099968, investigating the clinical parameters, the immunome and gut microbiome exploratory endpoints, that in hypertensive metabolic syndrome patients, a 5-day fast followed by a modified Dietary Approach to Stop Hypertension diet reduces systolic blood pressure, need for antihypertensive medications, body-mass index at three months post intervention compared to a modified Dietary Approach to Stop Hypertension diet alone. Fasting alters the gut microbiome, impacting bacterial taxa and gene modules associated with short-chain fatty acid production. Cross-system analyses reveal a positive correlation of circulating mucosa-associated invariant T cells, non-classical monocytes and CD4+ effector T cells with systolic blood pressure. Furthermore, regulatory T cells positively correlate with body-mass index and weight. Machine learning analysis of baseline immunome or microbiome data predicts sustained systolic blood pressure response within the fasting group, identifying CD8+ effector T cells, Th17 cells and regulatory T cells or Desulfovibrionaceae, Hydrogenoanaerobacterium, Akkermansia, and Ruminococcaceae as important contributors to the model. Here we report that the high-resolution multi-omics data highlight fasting as a promising non-pharmacological intervention for the treatment of high blood pressure in metabolic syndrome patients., Nutritional modification including fasting has been shown to reduce cardiometabolic risk linked to western diet. Here the authors show implementation of fasting resulted in alterations to the intestinal microbiota, and circulating immune cells, improving blood pressure and body weight in patients with metabolic syndrome.

Published
2021

5. The Gut Microbiome in Myalgic Encephalomyelitis (ME)/Chronic Fatigue Syndrome (CFS)

Author

König, Rahel S., Albrich, Werner C., Kahlert, Christian R., Bahr, Lina Samira, Löber, Ulrike, Vernazza, Pietro, Scheibenbogen, Carmen, and Forslund, Sofia K.

Subjects
Fatigue Syndrome, Chronic, Immunology, autoimmunity, microbiome, Review, antibiotics, Gastrointestinal Microbiome, gut dysbiosis, probiotics, Brain-Gut Axis, Animals, Humans, Myalgic Encephalomyelitis (ME), ME/CFS, Chronic Fatigue Syndrome (CFS), 600 Technik, Medizin, angewandte Wissenschaften::610 Medizin und Gesundheit::610 Medizin und Gesundheit
Abstract

Myalgic encephalomyelitis (ME) or Chronic Fatigue Syndrome (CFS) is a neglected, debilitating multi-systemic disease without diagnostic marker or therapy. Despite evidence for neurological, immunological, infectious, muscular and endocrine pathophysiological abnormalities, the etiology and a clear pathophysiology remains unclear. The gut microbiome gained much attention in the last decade with manifold implications in health and disease. Here we review the current state of knowledge on the interplay between ME/CFS and the microbiome, to identify potential diagnostic or interventional approaches, and propose areas where further research is needed. We iteratively selected and elaborated on key theories about a correlation between microbiome state and ME/CFS pathology, developing further hypotheses. Based on the literature we hypothesize that antibiotic use throughout life favours an intestinal microbiota composition which might be a risk factor for ME/CFS. Main proposed pathomechanisms include gut dysbiosis, altered gut-brain axis activity, increased gut permeability with concomitant bacterial translocation and reduced levels of short-chain-fatty acids, D-lactic acidosis, an abnormal tryptophan metabolism and low activity of the kynurenine pathway. We review options for microbiome manipulation in ME/CFS patients including probiotic and dietary interventions as well as fecal microbiota transplantations. Beyond increasing gut permeability and bacterial translocation, specific dysbiosis may modify fermentation products, affecting peripheral mitochondria. Considering the gut-brain axis we strongly suspect that the microbiome may contribute to neurocognitive impairments of ME/CFS patients. Further larger studies are needed, above all to clarify whether D-lactic acidosis and early-life antibiotic use may be part of ME/CFS etiology and what role changes in the tryptophan metabolism might play. An association between the gut microbiome and the disease ME/CFS is plausible. As causality remains unclear, we recommend longitudinal studies. Activity levels, bedridden hours and disease progression should be compared to antibiotic exposure, drug intakes and alterations in the composition of the microbiota. The therapeutic potential of fecal microbiota transfer and of targeted dietary interventions should be systematically evaluated.

Published
2022
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6. Impairment of gut microbial biotin metabolism and host biotin status in severe obesity:effect of biotin and prebiotic supplementation on improved metabolism

Author

Belda, Eugeni, Voland, Lise, Tremaroli, Valentina, Falony, Gwen, Adriouch, Solia, Assmann, Karen E., Prifiti, Edi, Aron-Wisnewsky, Judith, Debedat, Jean, Le Roy, Tiphaine, Nielsen, Trine, Amouyal, Chloe, Andre, Sebastien, Andreelli, Fabrizio, Blueher, Matthias, Chakaroun, Rima, Chilloux, Julien, Coelho, Luis Pedro, Dao, Maria Carlota, Das, Promi, Fellahi, Soraya, Forslund, Sofia, Galleron, Nathalie, Hansen, Tue H., Holmes, Bridget, Ji, Boyang, Pedersen, Helle Krogh, Phuong Le, Le Chatelier, Emmanuelle, Lewinter, Christian, Manneras-Holm, Louise, Marquet, Florian, Myridakis, Antonis, Pelloux, Veronique, Pons, Nicolas, Quinquis, Benoit, Rouault, Christine, Roume, Hugo, Salem, Joe-Elie, Sokolovska, Nataliya, Søndertoft, Nadja B., Touch, Sothea, Vieira-Silva, Sara, Galan, Pilar, Holst, Jens, Gøtze, Jens Peter, Køber, Lars, Vestergaard, Henrik, Hansen, Torben, Hercberg, Serge, Oppert, Jean-Michel, Nielsen, Jens, Letunic, Ivica, Dumas, Marc-Emmanuel, Stumvoll, Michael, Pedersen, Oluf Borbye, Bork, Peer, Ehrlich, Stanislav Dusko, Zucker, Jean-Daniel, Baeckhed, Fredrik, Raes, Jeroen, Clement, Karine, Commission of the European Communities, Medical Research Council (MRC), Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Research Unit on Cardiovascular and Metabolic Diseases [IHU ICAN], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Institut de Cardiométabolisme et Nutrition = Institute of Cardiometabolism and Nutrition [CHU Pitié Salpêtrière] (IHU ICAN), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Nutrition et obésités: approches systémiques (UMR-S 1269) (Nutriomics), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Inst Med, Dept Mol & Clin Med, Wallenberg Lab, University of Gothenburg (GU), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Centre de Recherche Épidémiologie et Statistique Sorbonne Paris Cité (CRESS (U1153 / UMR_A_1125 / UMR_S_1153)), Institut National de la Recherche Agronomique (INRA)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris Descartes - Paris 5 (UPD5)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Sorbonne Paris Cité (COMUE) (USPC), MetaGenoPolis, Institut National de la Recherche Agronomique (INRA), Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Institute of cardiometabolism and nutrition (ICAN), Université Pierre et Marie Curie - Paris 6 (UPMC)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU), Service de Nutrition [CHU Pitié-Salpétrière], Institut E3M [CHU Pitié-Salpêtrière], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Université de Bordeaux (UB), Novo Nordisk Foundation Center for Basic Metabolic Research (CBMR), Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Service de Diabétologie [CHU Pitié-Salpétrière], Laboratoire de chimie Macromoléculaire (CNRS UMR 5076), Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM), Institut Cochin (IC UM3 (UMR 8104 / U1016)), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Universität Leipzig [Leipzig], Keck School of Medicine [Los Angeles], University of Southern California (USC), Nutrition et cerveau (U1213, U855), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM), Instituto de Medicina Molecular, Metabolic functional (epi)genomics and molecular mechanisms involved in type 2 diabetes and related diseases - UMR 8199 - UMR 1283 (EGENODIA (GI3M)), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Imperial College London - National Heart and Lung Institute, and Division of Computational and Systems Medicine, Imperial College London, London, SW7 2AZ, UK

Subjects
EXPRESSION, [SDV]Life Sciences [q-bio], Biotin, Endocrinology and Diabetes, Microbiology, DIET, Mice, Humans, Animals, Obesity, CHROMIUM PICOLINATE, Inflammation, Science & Technology, OVERWEIGHT, Gastroenterology & Hepatology, Gastroenterology, 1103 Clinical Sciences, Gastrointestinal Microbiome, Obesity, Morbid, MetaCardis Consortium, Mice, Inbred C57BL, nutrition, Prebiotics, Diabetes Mellitus, Type 2, Cardiovascular and Metabolic Diseases, micronutrients, Other Clinical Medicine, diabetes mellitus, Vitamin B Complex, 1114 Paediatrics and Reproductive Medicine, intestinal bacteria, HEALTH, Life Sciences & Biomedicine
Abstract

ObjectivesGut microbiota is a key component in obesity and type 2 diabetes, yet mechanisms and metabolites central to this interaction remain unclear. We examined the human gut microbiome’s functional composition in healthy metabolic state and the most severe states of obesity and type 2 diabetes within the MetaCardis cohort. We focused on the role of B vitamins and B7/B8 biotin for regulation of host metabolic state, as these vitamins influence both microbial function and host metabolism and inflammation.DesignWe performed metagenomic analyses in 1545 subjects from the MetaCardis cohorts and different murine experiments, including germ-free and antibiotic treated animals, faecal microbiota transfer, bariatric surgery and supplementation with biotin and prebiotics in mice.ResultsSevere obesity is associated with an absolute deficiency in bacterial biotin producers and transporters, whose abundances correlate with host metabolic and inflammatory phenotypes. We found suboptimal circulating biotin levels in severe obesity and altered expression of biotin-associated genes in human adipose tissue. In mice, the absence or depletion of gut microbiota by antibiotics confirmed the microbial contribution to host biotin levels. Bariatric surgery, which improves metabolism and inflammation, associates with increased bacterial biotin producers and improved host systemic biotin in humans and mice. Finally, supplementing high-fat diet-fed mice with fructo-oligosaccharides and biotin improves not only the microbiome diversity, but also the potential of bacterial production of biotin and B vitamins, while limiting weight gain and glycaemic deterioration.ConclusionStrategies combining biotin and prebiotic supplementation could help prevent the deterioration of metabolic states in severe obesity.Trial registration numberNCT02059538.

Published
2022
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7. Identification and characterization of human observational studies in nutritional epidemiology on gut microbiomics for joint data analysis

Author

Pinart, Mariona, Nimptsch, Katharina, Forslund, Sofia, Schlicht, Kristina, Gueimonde, Miguel, Brigidi, Patrizia, Turroni, Silvia, Ahrens, Wolfgang, Hebestreit, Antje, Wolters, Maike, Dötsch, Andreas, Nöthlings, Ute, Oluwagbemigun, Kolade, Cuadrat, Rafael, Schulze, Matthias, Standl, Marie, Schloter, Michael, De Angelis, Maria, Iozzo, Patricia, Guzzardi, Maria Angela, Vlaemynck, Geertrui, Penders, John, Jonkers, Daisy, Stemmer, Maya, Chiesa, Giulia, Cavalieri, Duccio, De Filippo, Carlotta, Ercolini, Danilo, De Filippis, Francesca, Ribet, David, Achamrah, Najate, Tavolacci, Marie-Pierre, Déchelotte, Pierre, Bouwman, Jildau, Laudes, Matthias, Pischon, Tobias, Pinart M., Nimptsch K., Forslund S.K., Schlicht K., Gueimonde M., Brigidi P., Turroni S., Ahrens W., Hebestreit A., Wolters M., Dotsch A., Nothlings U., Oluwagbemigun K., Cuadrat R.R.C., Schulze M.B., Standl M., Schloter M., De Angelis M., Iozzo P., Guzzardi M.A., Vlaemynck G., Penders J., Jonkers D.M.A.E., Stemmer M., Chiesa G., Cavalieri D., De Filippo C., Ercolini D., De Filippis F., Ribet D., Achamrah N., Tavolacci M.-P., Dechelotte P., Bouwman J., Laudes M., Pischon T., Molecular Epidemiology Research Group, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany, Experimental and Clinical Research Center, A Cooperation of Charité-Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Lindenberger Weg 80, 13125 Berlin, Germany, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 10117 Berlin, Germany, Host-Microbiome Factors in Cardiovascular Disease Lab, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany, German Centre for Cardiovascular Research (DZHK), Partner Site Berlin, 10785 Berlin, Germany, Berlin Institute of Health (BIH), 10178 Berlin, Germany, Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany, Institute of Diabetes and Clinical Metabolic Research, University of Kiel, 24105 Kiel, Germany, Department of Microbiology and Biochemistry of Dairy Products, IPLA-CSIC, 33300 Villaviciosa, Spain, Diet, Microbiota and Health Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain, Department of Medical and Surgical Sciences, University of Bologna, Via Massarenti 9, 40138 Bologna, Italy, Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy, Leibniz Institute for Prevention Research and Epidemiology-BIPS, 28359 Bremen, Germany, Institute of Statistics, Bremen University, 28359 Bremen, Germany, Department of Physiology and Biochemistry of Nutrition, Max Rubner-Institut (MRI)-Federal Research Institute of Nutrition and Food, 76131 Karlsruhe, Germany, Nutritional Epidemiology Unit, Institute of Nutrition and Food Sciences, University of Bonn, 53115 Bonn, Germany, Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, 14558 Nuthetal, Germany, Institute of Nutritional Science, University of Potsdam, 14558 Potsdam, Germany, German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany, Institute of Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany, Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany, Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, 70126 Bari, Italy, Institute of Clinical Physiology, National Research Council, Via Moruzzi 1, 56124 Pisa, Italy, Department Technology and Food, Flanders Research Institute for Agriculture, Fisheries and Food, 9090 Melle, Belgium, 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, 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, Department of Industrial Engineering and Management, Ben-Gurion University of the Negev, Beer-Sheva P.O. Box 653, Israel, Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, 20133 Milan, Italy, Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Florence, Italy, Institute of Agricultural Biology and Biotechnology National Research Council, Via Moruzzi 1, 56124 Pisa, Italy, Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy, Task Force on Microbiome Studies, University of Naples Federico II, 80134 Naples, Italy, Nutrition, inflammation et dysfonctionnement de l'axe intestin-cerveau (ADEN), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institute for Research and Innovation in Biomedicine (IRIB), Normandie Université (NU)-Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), UNIROUEN - UFR Santé (UNIROUEN UFR Santé), Normandie Université (NU)-Normandie Université (NU), Service de nutrition [CHU Rouen], Normandie Université (NU)-Normandie Université (NU)-CHU Rouen, Normandie Université (NU), Centre d'Investigation Clinique [CHU Rouen] (CIC Rouen), Hôpital Charles Nicolle [Rouen]-CHU Rouen, Normandie Université (NU)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Microbiology and Systems Biology Group, TNO, Utrechtseweg 48, 3704 HE Zeist, The Netherlands, Biobank Technology Platform, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany, Biobank Core Facility, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, 10178 Berlin, Germany, European Commission, Fonds de la Recherche Scientifique (Fédération Wallonie-Bruxelles), Research Foundation - Flanders, Institut National de la Santé et de la Recherche Médicale (France), Federal Ministry of Education and Research (Germany), Federal Ministry of Food and Agriculture (Germany), Ministero dell'Istruzione, dell'Università e della Ricerca, Ministero delle Politiche Agricole Alimentari e Forestali, National Institutes of Health (US), Ministero della Salute, Instituto de Salud Carlos III, Netherlands Organisation for Health Research and Development, Austrian Research Promotion Agency, Federal Ministry of Education, Science and Research (Austria), Ministry of Science, Technology and Space (Israel), Swedish Research Council for Sustainable Development, German Research Foundation, RS: CAPHRI - R4 - Health Inequities and Societal Participation, Med Microbiol, Infect Dis & Infect Prev, RS: NUTRIM - R2 - Liver and digestive health, Interne Geneeskunde, Pinart, M., Nimptsch, K., Forslund, S. K., Schlicht, K., Gueimonde, M., Brigidi, P., Turroni, S., Ahrens, W., Hebestreit, A., Wolters, M., Dotsch, A., Nothlings, U., Oluwagbemigun, K., Cuadrat, R. R. C., Schulze, M. B., Standl, M., Schloter, M., De Angelis, M., Iozzo, P., Guzzardi, M. A., Vlaemynck, G., Penders, J., Jonkers, D. M. A. E., Stemmer, M., Chiesa, G., Cavalieri, D., De Filippo, C., Ercolini, D., De Filippis, F., Ribet, D., Achamrah, N., Tavolacci, M. -P., Dechelotte, P., Bouwman, J., Laudes, M., Pischon, T., Humboldt-Universität zu Berlin, and CHU Rouen

Subjects
Nutritional Sciences, Metabolome, Metadata, Data sharing, Observational studies, Data integration, Dietary intake, Microbiome, Diet Surveys, Article, Eating, Nutritional Science, AGE, Humans, TX341-641, observational studies, Nutrition. Foods and food supply, Information Dissemination, Nutrition Survey, Nutrition Surveys, Observational studie, Gastrointestinal Microbiome, Diet Survey, Europe, Observational Studies as Topic, Cardiovascular and Metabolic Diseases, Data Integration, Data Sharing, Dietary Intake, Observational Studies, Technology Platforms, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Human
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., This research was supported by the Joint Action “European Joint Programming Initiative “A Healthy Diet for a Healthy Life” (JPI HDHL)”and the respective national/regional funding organisations: Fund for Scientific Research (FRS—FNRS, Belgium); Research Foundation—Flanders (FWO, Belgium); INSERM Institut National de la Santé et de la Recherche Médicale (France); Federal Ministry of Education and Research (BMBF, FKZ 01EA1906B, 01EA1906D); Federal Ministry of Food and Agriculture (BMEL) through the Federal Office for Agriculture and Food (BLE, Germany, grant number 2819ERA10F); Ministry of Education, University and Research (MIUR), Ministry of agricultural, food and forestry policies (MiPAAF), National Institute of Health (ISS) on behalf of Ministry of Health (Italy); National Institute of Health Carlos III (Spain); The Netherlands Organisation for Health Research and Development (ZonMw, The Netherlands), Austrian Research Promotion Agency (FFG) on behalf of the Austrian Federal Ministry for Education, Science and Research (BMBWF), Ministry of Science and Technology (Israel), Formas (Sweden). This research was also supported by the German Research Foundation (DFG, KFO339: “food@”).

Published
2021
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8. Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology

Author

Bel Lassen, Pierre, Nielsen, Trine, Bergh, Per-Olof, Rouault, Christine, André, Sébastien, Marquet, Florian, Andreelli, Fabrizio, Salem, Joe-Elie, Assmann, Karen, Bastard, Jean-Philippe, Forslund, Sofia, Le Chatelier, Emmanuelle, Falony, Gwen, Pons, Nicolas, Prifti, Edi, Quinquis, Benoit, Roume, Hugo, Vieira-Silva, Sara, Hansen, Tue, Pedersen, Helle Krogh, Lewinter, Christian, Sønderskov, Nadja, Vestergaard, Henrik, Raes, Jeroen, Nielsen, Jens, Bork, Peer, Ehrlich, S. Dusko, Pedersen, Oluf, Aron-Wisneswky, Judith, Clément, Karine, Bäckhed, Fredrik, Molinaro, Antonio, Lassen, Pierre, Henricsson, Marcus, Wu, Hao, Adriouch, Solia, Belda, Eugeni, Chakaroun, Rima, Nielse, Trine, Bergh, Christine, Rouault, Sébastien, Andr, Florian, Marquet, Fabrizio, Andreelli, Joe-Elie, Salem, Karen, Assmann, Jean-Philippe, Bastard, Sofia, Forslund, Emmanuelle, Le Chatelier, Gwen, Falon, Nicolas, Pons, Edi, Prift, Benoit, Quinquis, Hugo, Roume, Sara, Vieira-Silv, Tue, Hansen, Krogh, Pedersen, Christian, Lewinter, Nadja, The, Metacardis, Køber, Lars, Vestergaar, Henrik, Hansen, Torben, Zucker, Jean-Daniel, Galan, Pilar, Dumas, Marc-Emmanuel, Rae, Jeroen, Oppert, Jean-Michel, Letunic, Ivica, Nielse, Jens, Ehrlic, S, Stumvoll, Michael, Pederse, Oluf, Aron-Wisnewsky, Judith, Bäckhe, Fredrik, Sahlgrenska Center for Cardiovascular and Metabolic Research, Partenaires INRAE, Sahlgrenska University Hospital, Nutrition et obésités: approches systémiques (nutriomics) (UMR-S 1269 INSERM - Sorbonne Université), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Centre de Recherche en Nutrition Humaine d'Ile-de-France (CRNH-IDF), Institut de Veille Sanitaire (INVS)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Institut National Agronomique Paris-Grignon (INA P-G)-CETAF-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Sorbonne Paris Nord, Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Institute of cardiometabolism and nutrition (ICAN), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université-Sorbonne Université (SU), Medical Department III – Endocrinology, Nephrology, Rheumatology, Universität Leipzig [Leipzig], Novo Nordisk Foundation Center for Basic Metabolic Research (CBMR), Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Centre d'Investigation Clinique de Paris Est, Institut National de la Santé et de la Recherche Médicale (INSERM), AP-HP Hôpital Tenon [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Experimental and Clinical Research Center [Berlin, Germany], Max Delbrück Center for Molecular Medicine [Berlin] (MDC), Helmholtz-Gemeinschaft = Helmholtz Association-Helmholtz-Gemeinschaft = Helmholtz Association-Charité - Universitätsmedizin Berlin / Charite - University Medicine Berlin, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, Université Catholique de Louvain (UCL), VIB-KU Leuven Center for Microbiology [Belgium], Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Sorbonne Université (SU)-Universtié Yaoundé 1 [Cameroun]-Université Cadi Ayyad [Marrakech] (UCA)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Institut de Recherche pour le Développement (IRD [France-Nord]), Equipe 3: EREN- Equipe de Recherche en Epidémiologie Nutritionnelle (CRESS - U1153), Centre de Recherche Épidémiologie et Statistique Sorbonne Paris Cité (CRESS (U1153 / UMR_A_1125 / UMR_S_1153)), Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Metabolism, Digestion and Reproduction, Imperial College London, National Heart and Lung Institute [London] (NHLI), Royal Brompton and Harefield NHS Foundation Trust-Imperial College London, Centre de Recherche en Nutrition Humaine - Ile de France (CRNH - IDF), Biobyte Solutions GMBH, Nutrition et obésités: approches systémiques (UMR-S 1269) (Nutriomics), Institut de Veille Sanitaire (INVS)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Institut National Agronomique Paris-Grignon (INA P-G)-CETAF-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Sorbonne Paris Nord, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Sahlgrenska Academy at University of Gothenburg [Göteborg], CHU Tenon [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Helmholtz-Gemeinschaft = Helmholtz Association-Helmholtz-Gemeinschaft = Helmholtz Association-Charité - UniversitätsMedizin = Charité - University Hospital [Berlin], Helmholtz-Gemeinschaft = Helmholtz Association, Charité - UniversitätsMedizin = Charité - University Hospital [Berlin], Rega Institute for Medical Research [Leuven, België], Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Research Unit on Cardiovascular and Metabolic Diseases (ICAN), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Institut de Cardiométabolisme et Nutrition = Institute of Cardiometabolism and Nutrition [CHU Pitié Salpêtrière] (IHU ICAN), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-CHU Pitié-Salpêtrière [AP-HP], Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA)-Sorbonne Université (SU)-Institut de Recherche pour le Développement (IRD [France-Nord]), Chalmers University of Technology [Göteborg], European Molecular Biology Laboratory [Heidelberg] (EMBL), Université Sorbonne Paris Nord-Centre de Recherche Épidémiologie et Statistique Sorbonne Paris Cité (CRESS (U1153 / UMR_A_1125 / UMR_S_1153)), Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Imperial College London-Royal Brompton and Harefield NHS Foundation Trust, HAL-SU, Gestionnaire, Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Institut de Veille Sanitaire (INVS)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Sorbonne Paris Nord-Institut National Agronomique Paris-Grignon (INA P-G)-Sorbonne Université (SU)-CETAF-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de la Santé et de la Recherche Médicale (INSERM), Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU), Institut de Recherche pour le Développement (IRD [France-Nord])-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Sorbonne Université (SU), Charité - Universitätsmedizin Berlin / Charite - University Medicine Berlin, Auteur indépendant, Commission of the European Communities, and Universität Leipzig

Subjects
0301 basic medicine, Male, ACCURATE METHOD, endocrine system diseases, Metabolite, [SDV]Life Sciences [q-bio], General Physics and Astronomy, Type 2 diabetes, GUT MICROBIOME, GLUCOSE, Cohort Studies, chemistry.chemical_compound, 0302 clinical medicine, Endocrinology, [CHIM] Chemical Sciences, Prediabetes, lcsh:Science, 2. Zero hunger, RISK, Multidisciplinary, biology, INSULIN SENSITIVITY, Imidazoles, HOMEOSTASIS MODEL ASSESSMENT, Middle Aged, 3. Good health, Multidisciplinary Sciences, [SDV] Life Sciences [q-bio], 030220 oncology & carcinogenesis, Science & Technology - Other Topics, Enterotype, Female, Adult, medicine.medical_specialty, Science, Carbohydrate metabolism, Microbiology, digestive system, Article, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, INTESTINAL MICROBIOTA, Internal medicine, medicine, Humans, [CHIM]Chemical Sciences, Histidine, Author Correction, PHYSIOLOGY, Aged, Science & Technology, Bacteria, General Chemistry, Metabolism, medicine.disease, biology.organism_classification, Gastrointestinal Microbiome, MetaCardis Consortium, METAGENOME, INDIVIDUALS, 030104 developmental biology, chemistry, Diabetes Mellitus, Type 2, Cardiovascular and Metabolic Diseases, lcsh:Q, Bacteroides
Abstract

Microbiota-host-diet interactions contribute to the development of metabolic diseases. Imidazole propionate is a novel microbially produced metabolite from histidine, which impairs glucose metabolism. Here, we show that subjects with prediabetes and diabetes in the MetaCardis cohort from three European countries have elevated serum imidazole propionate levels. Furthermore, imidazole propionate levels were increased in subjects with low bacterial gene richness and Bacteroides 2 enterotype, which have previously been associated with obesity. The Bacteroides 2 enterotype was also associated with increased abundance of the genes involved in imidazole propionate biosynthesis from dietary histidine. Since patients and controls did not differ in their histidine dietary intake, the elevated levels of imidazole propionate in type 2 diabetes likely reflects altered microbial metabolism of histidine, rather than histidine intake per se. Thus the microbiota may contribute to type 2 diabetes by generating imidazole propionate that can modulate host inflammation and metabolism., Gut microbial metabolism of nutrients contributes to metabolic diseases, and the histidine metabolite imidazole propionate (ImP) is produced by type 2 diabetes (T2D) associated microbiome. Here the authors report that circulating ImP levels are increased in subjects with prediabetes or T2D in three European populations, and this increase associates with altered gut microbiota rather than dietary histidine.

Published
2020
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9. Gut Microbiome Composition in Obese and Non-Obese Persons: A Systematic Review and Meta-Analysis.

Author

Pinart, Mariona, Dötsch, Andreas, Schlicht, Kristina, Laudes, Matthias, Bouwman, Jildau, Forslund, Sofia K., Pischon, Tobias, and Nimptsch, Katharina

Abstract

Whether the gut microbiome in obesity is characterized by lower diversity and altered composition at the phylum or genus level may be more accurately investigated using high-throughput sequencing technologies. We conducted a systematic review in PubMed and Embase including 32 cross-sectional studies assessing the gut microbiome composition by high-throughput sequencing in obese and non-obese adults. A significantly lower alpha diversity (Shannon index) in obese versus non-obese adults was observed in nine out of 22 studies, and meta-analysis of seven studies revealed a non-significant mean difference (−0.06, 95% CI −0.24, 0.12, I2 = 81%). At the phylum level, significantly more Firmicutes and fewer Bacteroidetes in obese versus non-obese adults were observed in six out of seventeen, and in four out of eighteen studies, respectively. Meta-analyses of six studies revealed significantly higher Firmicutes (5.50, 95% 0.27, 10.73, I2 = 81%) and non-significantly lower Bacteroidetes (−4.79, 95% CI −10.77, 1.20, I2 = 86%). At the genus level, lower relative proportions of Bifidobacterium and Eggerthella and higher Acidaminococcus, Anaerococcus, Catenibacterium, Dialister, Dorea, Escherichia-Shigella, Eubacterium, Fusobacterium, Megasphera, Prevotella, Roseburia, Streptococcus, and Sutterella were found in obese versus non-obese adults. Although a proportion of studies found lower diversity and differences in gut microbiome composition in obese versus non-obese adults, the observed heterogeneity across studies precludes clear answers. [ABSTRACT FROM AUTHOR]

Published
2022
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10. Towards the biogeography of prokaryotic genes

Author

Luis Pedro Coelho, Renato Alves, Álvaro Rodríguez del Río, Pernille Neve Myers, Carlos P. Cantalapiedra, Joaquín Giner-Lamia, Thomas Sebastian Schmidt, Daniel R. Mende, Askarbek Orakov, Ivica Letunic, Falk Hildebrand, Thea Van Rossum, Sofia K. Forslund, Supriya Khedkar, Oleksandr M. Maistrenko, Shaojun Pan, Longhao Jia, Pamela Ferretti, Shinichi Sunagawa, Xing-Ming Zhao, Henrik Bjørn Nielsen, Jaime Huerta-Cepas, Peer Bork, European Commission, European Research Council, Helmut Horten Foundation, National Key Research and Development Program (China), Shanghai Municipal Education Commission, International Development Research Centre (Canada), Fundación 'la Caixa', Agencia Estatal de Investigación (España), Innovation Fund Denmark, Coelho, Luis Pedro, Alves, Renato, Del Río, Álvaro Rodríguez, Myers, Pernille Neve, Cantalapiedra, Carlos P, Giner-Lamia, Joaquín, Mende, Daniel R, Orakov, Askarbek, Letunic, Ivica, Hildebrand, Falk, Van Rossum, Thea, Forslund, Sofia K, Khedkar, Supriya, Maistrenko, Oleksandr M, Pan, Shaojun, Jia, Longhao, Ferretti, Pamela, Sunagawa, Shinichi, Nielsen, Henrik Bjørn, Huerta-Cepas, Jaime, Bork, Peer, Coelho, Luis Pedro [0000-0002-9280-7885], Alves, Renato [0000-0002-7212-0234], Del Río, Álvaro Rodríguez [0000-0003-3907-3904], Myers, Pernille Neve [0000-0002-1824-3305], Cantalapiedra, Carlos P [0000-0001-5263-533X], Giner-Lamia, Joaquín [0000-0003-1553-8295], Mende, Daniel R [0000-0001-6831-4557], Orakov, Askarbek [0000-0001-6823-5269], Letunic, Ivica [0000-0003-3560-4288], Hildebrand, Falk [0000-0002-0078-8948], Van Rossum, Thea [0000-0002-3598-5001], Forslund, Sofia K [0000-0003-4285-6993], Khedkar, Supriya [0000-0001-6606-2202], Maistrenko, Oleksandr M [0000-0003-1961-7548], Pan, Shaojun [0000-0002-5270-5614], Jia, Longhao [0000-0002-3490-840X], Ferretti, Pamela [0000-0002-1707-9013], Sunagawa, Shinichi [0000-0003-3065-0314], Nielsen, Henrik Bjørn [0000-0003-2281-5713], Huerta-Cepas, Jaime [0000-0003-4195-5025], and Bork, Peer [0000-0002-2627-833X]

Subjects
Multidisciplinary, Humans, Metagenome, Drug Resistance, Microbial, Metagenomics, Ecosystem, Article, Anti-Bacterial Agents
Abstract

Funding was provided by the European Union’s Horizon 2020 Research and Innovation Programme (grant 686070: DD-DeCaF to P.B.) and Marie Skłodowska-Curie Actions (grant 713673 to A.R.d.R.), the European Research Council (ERC) MicrobioS (ERC-AdG-669830 to P.B.), JTC project jumpAR (01KI1706 to P.B.), a BMBF Grant (grant 031L0181A: LAMarCK to P.B.), the European Molecular Biology Laboratory (P.B.), the ETH and Helmut Horten Foundation (S.S.), the National Key R&D Program of China (grant 2020YFA0712403 to X.-M.Z.), (grant 61932008 to X.-M.Z.; grant 61772368 to X.-M.Z.; grant 31950410544 to L.P.C.), the Shanghai Municipal Science and Technology Major Project (grant 2018SHZDZX01 to X.-M.Z. and L.P.C.) and Zhangjiang Lab (X.-M.Z. and L.P.C.), the International Development Research Centre (grant 109304, EMBARK under the JPI AMR framework; to L.P.C.), la Caixa Foundation (grant 100010434, fellowship code LCF/BQ/DI18/11660009 to A.R.d.R.), the Severo Ochoa Program for Centres of Excellence in R&D from the Agencia Estatal de Investigación of Spain (grant SEV-2016-0672 (2017–2021) to C.P.C.), the Ministerio de Ciencia, Innovación y Universidades (grant PGC2018-098073-A-I00 MCIU/AEI/FEDER to J.H.-C. and J.G.-L.), the Innovation Fund Denmark (grant 4203-00005B, PNM), the Biotechnology and Biological Sciences research Council (BBSrC) Gut MicroInstitute Strategic Programmebes and Health BB/r012490/1 and its constituent project BBS/e/F/000Pr10355 (F.H.). R.A. is a member of the Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences.

Published
2021

11. Salt Transiently Inhibits Mitochondrial Energetics in Mononuclear Phagocytes.

Author

Geisberger, Sabrina, Bartolomaeus, Hendrik, Neubert, Patrick, Willebrand, Ralf, Zasada, Christin, Bartolomaeus, Thomas, McParland, Victoria, Swinnen, Dries, Geuzens, Anneleen, Maifeld, András, Krampert, Luka, Vogl, Marion, Mähler, Anja, Wilck, Nicola, Markó, Lajos, Tilic, Ekin, Forslund, Sofia K., Binger, Katrina J., Stegbauer, Johannes, and Dechend, Ralf

Subjects
*MACROPHAGES, *MITOCHONDRIA, *CELL physiology, *CELL migration, *PLASMA displays, *PHAGOCYTE metabolism, *DIETARY sodium
Abstract

Background: Dietary high salt (HS) is a leading risk factor for mortality and morbidity. Serum sodium transiently increases postprandially but can also accumulate at sites of inflammation affecting differentiation and function of innate and adaptive immune cells. Here, we focus on how changes in extracellular sodium, mimicking alterations in the circulation and tissues, affect the early metabolic, transcriptional, and functional adaption of human and murine mononuclear phagocytes.Methods: Using Seahorse technology, pulsed stable isotope-resolved metabolomics, and enzyme activity assays, we characterize the central carbon metabolism and mitochondrial function of human and murine mononuclear phagocytes under HS in vitro. HS as well as pharmacological uncoupling of the electron transport chain under normal salt is used to analyze mitochondrial function on immune cell activation and function (as determined by Escherichiacoli killing and CD4+ T cell migration capacity). In 2 independent clinical studies, we analyze the effect of a HS diet during 2 weeks (URL: http://www.clinicaltrials.gov. Unique identifier: NCT02509962) and short-term salt challenge by a single meal (URL: http://www.clinicaltrials.gov. Unique identifier: NCT04175249) on mitochondrial function of human monocytes in vivo.Results: Extracellular sodium was taken up into the intracellular compartment, followed by the inhibition of mitochondrial respiration in murine and human macrophages. Mechanistically, HS reduces mitochondrial membrane potential, electron transport chain complex II activity, oxygen consumption, and ATP production independently of the polarization status of macrophages. Subsequently, cell activation is altered with improved bactericidal function in HS-treated M1-like macrophages and diminished CD4+ T cell migration in HS-treated M2-like macrophages. Pharmacological uncoupling of the electron transport chain under normal salt phenocopies HS-induced transcriptional changes and bactericidal function of human and murine mononuclear phagocytes. Clinically, also in vivo, rise in plasma sodium concentration within the physiological range reversibly reduces mitochondrial function in human monocytes. In both a 14-day and single meal HS challenge, healthy volunteers displayed a plasma sodium increase of [Formula: see text] and [Formula: see text] respectively, that correlated with decreased monocytic mitochondrial oxygen consumption.Conclusions: Our data identify the disturbance of mitochondrial respiration as the initial step by which HS mechanistically influences immune cell function. Although these functional changes might help to resolve bacterial infections, a shift toward proinflammation could accelerate inflammatory cardiovascular disease. [ABSTRACT FROM AUTHOR]

Published
2021
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12. Reporting guidelines for human microbiome research: the STORMS checklist

Author

Dermot P.B. McGovern, Suzanne Devkota, Eran Segal, Rimsha Azhar, Thomas Sharpton, Douglas S Kwon, Massive Analysis, Elizabeth Grice, Eran Elinav, Jonathan Braun, Louise B. Thingholm, Paul Wilmes, Benjamin Haibe-Kains, Wendell D. Jones, Sofia Forslund, David Casero, Russell D. Wolfinger, Kirk Bergstrom, Ramona L Walls, Rebecca Kusko, Pamela Herd, Viswanath Devanarayan, Fatima Zohra, Brianna Lindsay, Aedin Culhane, Francesco Beghini, Heidi E. Jones, Maria Carmen Collado, Mingyu Zhang, Wenjun Bao, Robert D. Finn, Liping Zhao, Jonathan P Jacobs, Andreas Scherer, Xiaohui Fan, Omry Koren, Jennifer Fettweis, Morgan G. I. Langille, Weida Tong, Jordan E Bisanz, Malte Rühlemann, Curtis Huttenhower, Scott Handley, Rob Knight, Susanna-Assunta Sansone, Shannon McWeeney, Gregory A Buck, Sujatha Srinivasan, Jennifer B Dowd, Ekaterina Smirnova, Amy Loughman, Janneke van de Wijgert, Audrey Renson, Frederic D. Bushman, John F. Cryan, Christopher E. Mason, Levi Waldron, Harry Sokol, Susan Holmes, Andre Franke, Leming Shi, Anthony A. Fodor, Nicola Segata, Matthew R. Redinbo, Matthew Olm, Jeroen Raes, David A MacIntyre, Luigi Nezi, Joaquin Dopazo, Shaimaa Elsafoury, Kelly Eckenrode, Francine Z Marques, Peter J. Turnbaugh, Ni Zhao, Christopher Hunter, Lynn Schriml, Georg Zeller, Jack Gilbert, Ami Bhatt, Noah Palm, Ludwig Geistlinger, Juan S Escobar, Michelle Shardell, Dan Knights, Tim R Mercer, Vaibhav Upadhyay, Shraddha Thakkar, Noel T. Mueller, Manimozhiyan Arumugam, Paul D. Cotter, Gerard Clarke, Alice C. McHardy, Lisa Karstens, Cesare Furlanello, Edoardo Pasolli, Chloe Mirzayi, Justin L Sonnenburg, Ryan T Demmer, Patrick D. Schloss, Lora J. Kasselman, Takuji Yamada, Matthias Fischer, Hector Corrada Bravo, R Balfour Sartor, Consortium, Genomic Standards, Society, Massive Analysis and Quality Control, Mirzayi, Chloe, Renson, Audrey, Furlanello, Cesare, Sansone, Susanna-Assunta, Zohra, Fatima, Elsafoury, Shaimaa, Geistlinger, Ludwig, Kasselman, Lora J., Eckenrode, Kelly, van de Wijgert, Janneke, Loughman, Amy, Marques, Francine Z., Macintyre, David A., Arumugam, Manimozhiyan, Azhar, Rimsha, Beghini, Francesco, Bergstrom, Kirk, Bhatt, Ami, Bisanz, Jordan E., Braun, Jonathan, Bravo, Hector Corrada, Buck, Gregory A., Bushman, Frederic, Casero, David, Clarke, Gerard, Collado, Maria Carmen, Cotter, Paul D., Cryan, John F., Demmer, Ryan T., Devkota, Suzanne, Elinav, Eran, Escobar, Juan S., Fettweis, Jennifer, Finn, Robert D., Fodor, Anthony A., Forslund, Sofia, Franke, Andre, Gilbert, Jack, Grice, Elizabeth, Haibe-Kains, Benjamin, Handley, Scott, Herd, Pamela, Holmes, Susan, Jacobs, Jonathan P., Karstens, Lisa, Knight, Rob, Knights, Dan, Koren, Omry, Kwon, Douglas S., Langille, Morgan, Lindsay, Brianna, Mcgovern, Dermot, Mchardy, Alice C., Mcweeney, Shannon, Mueller, Noel T., Nezi, Luigi, Olm, Matthew, Palm, Noah, Pasolli, Edoardo, Raes, Jeroen, Redinbo, Matthew R., Rühlemann, Malte, Balfour Sartor, R., Schloss, Patrick D., Schriml, Lynn, Segal, Eran, Shardell, Michelle, Sharpton, Thoma, Smirnova, Ekaterina, Sokol, Harry, Sonnenburg, Justin L., Srinivasan, Sujatha, Thingholm, Louise B., Turnbaugh, Peter J., Upadhyay, Vaibhav, Walls, Ramona L., Wilmes, Paul, Yamada, Takuji, Zeller, Georg, Zhang, Mingyu, Zhao, Ni, Zhao, Liping, Bao, Wenjun, Culhane, Aedin, Devanarayan, Viswanath, Dopazo, Joaquin, Fan, Xiaohui, Fischer, Matthia, Jones, Wendell, Kusko, Rebecca, Mason, Christopher E., Mercer, Tim R., Scherer, Andrea, Shi, Leming, Thakkar, Shraddha, Tong, Weida, Wolfinger, Ru, Hunter, Christopher, Segata, Nicola, Huttenhower, Curti, Dowd, Jennifer B., Jones, Heidi E., and Waldron, Levi

Subjects
Biomedical, Microbiota, Human microbiome, MEDLINE, Translational medicine, Computational Biology, Dysbiosis, Humans, Observational Studies as Topic, Translational Science, Biomedical, Research Design, General Medicine, Data science, General Biochemistry, Genetics and Molecular Biology, Checklist, Comprehension, Genetic epidemiology, Observational study, Translational Science, Microbiome
Abstract

The particularly interdisciplinary nature of human microbiome research makes the organization and reporting of results spanning epidemiology, biology, bioinformatics, translational medicine and statistics a challenge. Commonly used reporting guidelines for observational or genetic epidemiology studies lack key features specific to microbiome studies. Therefore, a multidisciplinary group of microbiome epidemiology researchers adapted guidelines for observational and genetic studies to culture-independent human microbiome studies, and also developed new reporting elements for laboratory, bioinformatics and statistical analyses tailored to microbiome studies. The resulting tool, called ‘Strengthening The Organization and Reporting of Microbiome Studies’ (STORMS), is composed of a 17-item checklist organized into six sections that correspond to the typical sections of a scientific publication, presented as an editable table for inclusion in supplementary materials. The STORMS checklist provides guidance for concise and complete reporting of microbiome studies that will facilitate manuscript preparation, peer review, and reader comprehension of publications and comparative analysis of published results.

Published
2021
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13. Skin Sodium Accumulates in Psoriasis and Reflects Disease Severity

Author

Marcus Kelm, Andreas Krause, Peter Linz, Vladimir-Andrey Gimenez-Rivera, Florian C. Kurschus, Joanna Wegner, András Maifeld, Elisa Wistorf, Lajos Markó, Dominik N. Müller, Theda Bartolomaeus, Anna Brand, Ralf Dechend, Susanne Karbach, Georgios Kokolakis, Nicola Wilck, Johannes Wild, Natalia Rakova, Ari Waisman, Tine V. Karlsen, Markus Kleinewietfeld, Sandra Philipp, Michael Boschmann, Anna Birukov, Helge Wiig, Björn E. Clausen, Sofia K. Forslund, Michael Schultheis, Titus Kuehne, Friedrich C. Luft, Rebecca Jung, Wild, Johannes/0000-0002-1446-8101, Wilck, Nicola/0000-0003-3189-5364, Birukov, Anna/0000-0002-8306-3351, Karlsen, Tine, Veronica/0000-0002-1512-2479, Gimenez RIvera, Vladimir, Andrey/0000-0001-5055-208X, Maifeld, Andras, Wild, Johannes, Karlsen, Tine, V, Rakova, Natalia, Wistorf, Elisa, Linz, Peter, Jung , Rebecca, Birukov, Anna, Gimenez-Rivera, Vladimir-Andrey, Wilck, Nicola, Bartolomaeus, Theda, Dechend, Ralf, KLEINEWIETFELD, Markus, Forslund, Sofia K., Krause, Andreas, Kokolakis, Georgios, Philipp, Sandra, Clausen, Bjoern E., Brand , Anna, Waisman, Ari, Kurschus, Florian C., Wegner, Joanna, Schultheis, Michael, Luft, Friedrich C., Boschmann, Michael, Kelm, Marcus, Wiig, Helge, Kuehne, Titus, Muller, Dominik N., Karbach, Susanne, and Marko, Lajos

Subjects
Male, medicine.medical_specialty, Sodium, chemistry.chemical_element, Inflammation, Imiquimod, Dermatology, Sodium Chloride, Lymphocyte Activation, Severity of Illness Index, Biochemistry, Article, Mice, Internal medicine, Psoriasis, medicine, Extracellular, Animals, Humans, T helper 17 cell, Molecular Biology, Cells, Cultured, Skin, integumentary system, business.industry, Spectrophotometry, Atomic, Spectrum Analysis, Interleukin-17, Cell Differentiation, Cell Biology, medicine.disease, Pathophysiology, Mice, Inbred C57BL, Endocrinology, chemistry, Cardiovascular and Metabolic Diseases, Th17 Cells, medicine.symptom, business, Intracellular, medicine.drug
Abstract

Sodium can accumulate in the skin at concentrations exceeding serum levels. A high sodium environment can lead to pathogenic T helper 17 cell expansion. Psoriasis is a chronic inflammatory skin disease in which IL-17. producing T helper 17 cells play a crucial role. In an observational study, we measured skin sodium content in patients with psoriasis and in age-matched healthy controls by Sodium-23 magnetic resonance imaging. Patients with PASI > 5 showed significantly higher sodium and water content in the skin but not in other tissues than those with lower PASI or healthy controls. Skin sodium concentrations measured by Sodium-23 spectroscopy or by atomic absorption spectrometry in ashed-skin biopsies verified the findings with Sodium-23 magnetic resonance imaging. In vitro T helper 17 cell differentiation of naive CD4(+) cells from patients with psoriasis markedly induced IL-17A expression under increased sodium chloride concentrations. The imiquimod-induced psoriasis mouse model replicated the human findings. Extracellular tracer Chromium-51-EDTA measurements in imiquimod- and sham-treated skin showed similar extracellular volumes, rendering excessive water of intracellular origin. Chronic genetic IL-17A-driven psoriasis mouse models underlined the role of IL-17A in dermal sodium accumulation and inflammation. Our data describe skin sodium as a pathophysiological feature of psoriasis, which could open new avenues for its treatment.

Published
2022
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