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Yousefi B, Melograna F, Galazzo G, van Best N, Mommers M, Penders J, Schwikowski B, Van Steen K. Capturing the dynamics of microbial interactions through individual-specific networks. Front Microbiol 2023; 14:1170391. [PMID: 37256048 PMCID: PMC10225591 DOI: 10.3389/fmicb.2023.1170391] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 04/21/2023] [Indexed: 06/01/2023] Open
Abstract
Longitudinal analysis of multivariate individual-specific microbiome profiles over time or across conditions remains dauntin. Most statistical tools and methods that are available to study microbiomes are based on cross-sectional data. Over the past few years, several attempts have been made to model the dynamics of bacterial species over time or across conditions. However, the field needs novel views on handling microbial interactions in temporal analyses. This study proposes a novel data analysis framework, MNDA, that combines representation learning and individual-specific microbial co-occurrence networks to uncover taxon neighborhood dynamics. As a use case, we consider a cohort of newborns with microbiomes available at 6 and 9 months after birth, and extraneous data available on the mode of delivery and diet changes between the considered time points. Our results show that prediction models for these extraneous outcomes based on an MNDA measure of local neighborhood dynamics for each taxon outperform traditional prediction models solely based on individual-specific microbial abundances. Furthermore, our results show that unsupervised similarity analysis of newborns in the study, again using the notion of a taxon's dynamic neighborhood derived from time-matched individual-specific microbial networks, can reveal different subpopulations of individuals, compared to standard microbiome-based clustering, with potential relevance to clinical practice. This study highlights the complementarity of microbial interactions and abundances in downstream analyses and opens new avenues to personalized prediction or stratified medicine with temporal microbiome data.
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Affiliation(s)
- Behnam Yousefi
- Computational Systems Biomedicine Lab, Institut Pasteur, University Paris City, Paris, France
- École Doctorale Complexite du vivant, Sorbonne University, Paris, France
- BIO3—Laboratory for Systems Medicine, Department of Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Federico Melograna
- BIO3—Laboratory for Systems Medicine, Department of Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Gianluca Galazzo
- Department of Medical Microbiology, Infectious Diseases and Infection Prevention, School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+, Maastricht, Netherlands
| | - Niels van Best
- Department of Medical Microbiology, Infectious Diseases and Infection Prevention, School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+, Maastricht, Netherlands
- Institute of Medical Microbiology, Rhine-Westphalia Technical University of Aachen, RWTH University, Aachen, Germany
| | - Monique Mommers
- Department of Epidemiology, Care and Public Health Research Institute (CAPHRI), Maastricht University, Maastricht, Netherlands
| | - John Penders
- Department of Medical Microbiology, Infectious Diseases and Infection Prevention, School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+, Maastricht, Netherlands
- Department of Medical Microbiology, Infectious Diseases and Infection Prevention, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Center+, Maastricht, Netherlands
| | - Benno Schwikowski
- Computational Systems Biomedicine Lab, Institut Pasteur, University Paris City, Paris, France
| | - Kristel Van Steen
- BIO3—Laboratory for Systems Medicine, Department of Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
- BIO3—Laboratory for Systems Genetics, GIGA-R Medical Genomics, University of Lièvzge, Liège, Belgium
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2
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Melograna F, Li Z, Galazzo G, van Best N, Mommers M, Penders J, Stella F, Van Steen K. Edge and modular significance assessment in individual-specific networks. Sci Rep 2023; 13:7868. [PMID: 37188794 PMCID: PMC10185658 DOI: 10.1038/s41598-023-34759-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 05/07/2023] [Indexed: 05/17/2023] Open
Abstract
Individual-specific networks, defined as networks of nodes and connecting edges that are specific to an individual, are promising tools for precision medicine. When such networks are biological, interpretation of functional modules at an individual level becomes possible. An under-investigated problem is relevance or "significance" assessment of each individual-specific network. This paper proposes novel edge and module significance assessment procedures for weighted and unweighted individual-specific networks. Specifically, we propose a modular Cook's distance using a method that involves iterative modeling of one edge versus all the others within a module. Two procedures assessing changes between using all individuals and using all individuals but leaving one individual out (LOO) are proposed as well (LOO-ISN, MultiLOO-ISN), relying on empirically derived edges. We compare our proposals to competitors, including adaptions of OPTICS, kNN, and Spoutlier methods, by an extensive simulation study, templated on real-life scenarios for gene co-expression and microbial interaction networks. Results show the advantages of performing modular versus edge-wise significance assessments for individual-specific networks. Furthermore, modular Cook's distance is among the top performers across all considered simulation settings. Finally, the identification of outlying individuals regarding their individual-specific networks, is meaningful for precision medicine purposes, as confirmed by network analysis of microbiome abundance profiles.
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Affiliation(s)
- Federico Melograna
- BIO3 - Laboratory for Systems Medicine, Department of Human Genetics, KU Leuven, Leuven, Belgium.
| | - Zuqi Li
- BIO3 - Laboratory for Systems Medicine, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Gianluca Galazzo
- School of Nutrition and Translational Research in Metabolism (NUTRIM), Department of Medical Microbiology Infectious Diseases and Infection Prevention, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Niels van Best
- Institute of Medical Microbiology, RWTH University Hospital Aachen, RWTH University, Aachen, Germany
- Department of Epidemiology, Care and Public Health Research Institute (CAPHRI), Maastricht University, Maastricht, The Netherlands
| | - Monique Mommers
- Department of Epidemiology, Care and Public Health Research Institute (CAPHRI), Maastricht University, Maastricht, The Netherlands
| | - John Penders
- School of Nutrition and Translational Research in Metabolism (NUTRIM), Department of Medical Microbiology Infectious Diseases and Infection Prevention, Maastricht University Medical Center+, Maastricht, The Netherlands
- Care and Public Health Research Institute (CAPHRI), Maastricht University, Maastricht, The Netherlands
| | - Fabio Stella
- Department of Informatics, Systems and Communication, University of Milano-Bicocca, 20126, Milan, Italy
| | - Kristel Van Steen
- BIO3 - Laboratory for Systems Medicine, Department of Human Genetics, KU Leuven, Leuven, Belgium
- BIO3 - Laboratory for Systems Genetics, GIGA-R Medical Genomics, University of Liège, Liège, Belgium
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3
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Bervoets L, Ippel JH, Smolinska A, van Best N, Savelkoul PHM, Mommers MAH, Penders J. Practical and Robust NMR-Based Metabolic Phenotyping of Gut Health in Early Life. J Proteome Res 2021; 20:5079-5087. [PMID: 34587745 PMCID: PMC8576838 DOI: 10.1021/acs.jproteome.1c00617] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
While substantial efforts have been made to optimize and standardize fecal metabolomics for studies in adults, the development of a standard protocol to analyze infant feces is, however, still lagging behind. Here, we present the development of a hands-on and robust protocol for proton 1H NMR spectroscopy of infant feces. The influence of extraction solvent, dilution ratio, homogenization method, filtration, and duration of centrifugation on the biochemical composition of infant feces was carefully evaluated using visual inspection of 1H NMR spectra in combination with multivariate statistical modeling. The optimal metabolomics protocol was subsequently applied on feces from seven infants collected at 8 weeks, 4, and 9 months of age. Interindividual variation was exceeding the variation induced by different fecal sample preparation methods, except for filtration. We recommend extracting fecal samples using water with a dilution ratio of 1:5 feces-to-water to homogenize using bead beating and to remove particulates using centrifugation. Samples collected from infants aged 8 weeks and 4 months showed elevated concentrations of milk oligosaccharide derivatives and lactic acid, whereas short-chain fatty acids (SCFAs) and branched-chain amino acids (BCAAs) were higher in the 9 month samples. The established protocol enables hands-on and robust analyses of the infant gut metabolome. The wide-ranging application of this protocol will facilitate interlaboratory comparison of infants' metabolic profiles and finally aid in a better understanding of infant gut health.
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Affiliation(s)
- Liene Bervoets
- Department of Medical Microbiology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, 6229 HX Maastricht, The Netherlands
| | - Johannes H Ippel
- Department of Biochemistry, CARIM Cardiovascular Research Institute Maastricht, Maastricht University, 6229 HX Maastricht, The Netherlands
| | - Agnieszka Smolinska
- Department of Pharmacology and Toxicology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, 6229 HX Maastricht, The Netherlands
| | - Niels van Best
- Department of Medical Microbiology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, 6229 HX Maastricht, The Netherlands.,Institute of Medical Microbiology, RWTH University Hospital Aachen, 52074 Aachen, Germany
| | - Paul H M Savelkoul
- Department of Medical Microbiology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, 6229 HX Maastricht, The Netherlands.,Department of Medical Microbiology & Infection Control, VUMC, 1081 HV Amsterdam, The Netherlands
| | - Monique A H Mommers
- Department of Epidemiology, Maastricht University, 6229 HX Maastricht, The Netherlands
| | - John Penders
- Department of Medical Microbiology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, 6229 HX Maastricht, The Netherlands
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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 MP, 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. Nutrients 2021; 13:nu13093292. [PMID: 34579168 PMCID: PMC8466729 DOI: 10.3390/nu13093292] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/10/2021] [Accepted: 09/17/2021] [Indexed: 01/16/2023] Open
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.
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Affiliation(s)
- Mariona Pinart
- Molecular Epidemiology Research Group, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; (M.P.); (T.P.)
| | - Katharina Nimptsch
- Molecular Epidemiology Research Group, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; (M.P.); (T.P.)
- Correspondence: ; Tel.: +49-30-9046-4573
| | - 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;
- 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 (MDC), 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
| | - Kristina Schlicht
- Institute of Diabetes and Clinical Metabolic Research, University of Kiel, 24105 Kiel, Germany; (K.S.); (M.L.)
| | - Miguel Gueimonde
- 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
| | - 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; (W.A.); (A.H.); (M.W.)
- Institute of Statistics, Bremen University, 28359 Bremen, Germany
| | - Antje Hebestreit
- Leibniz Institute for Prevention Research and Epidemiology-BIPS, 28359 Bremen, Germany; (W.A.); (A.H.); (M.W.)
| | - Maike Wolters
- Leibniz Institute for Prevention Research and Epidemiology-BIPS, 28359 Bremen, Germany; (W.A.); (A.H.); (M.W.)
| | - 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; (U.N.); (K.O.)
| | - Kolade Oluwagbemigun
- Nutritional Epidemiology Unit, Institute of Nutrition and Food Sciences, University of Bonn, 53115 Bonn, Germany; (U.N.); (K.O.)
| | - Rafael R. C. Cuadrat
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, 14558 Nuthetal, Germany; (R.R.C.C.); (M.B.S.)
| | - Matthias B. Schulze
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, 14558 Nuthetal, Germany; (R.R.C.C.); (M.B.S.)
- Institute of Nutritional Science, University of Potsdam, 14558 Potsdam, Germany
- German Center for Diabetes Research (DZD), 85764 Neuherberg, 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; (P.I.); (M.A.G.)
| | - Maria Angela Guzzardi
- Institute of Clinical Physiology, National Research Council, Via Moruzzi 1, 56124 Pisa, Italy; (P.I.); (M.A.G.)
| | - 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; (D.E.); (F.D.F.)
- Task Force on Microbiome Studies, University of Naples Federico II, 80134 Naples, Italy
| | - Francesca De Filippis
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy; (D.E.); (F.D.F.)
- Task Force on Microbiome Studies, University of Naples Federico II, 80134 Naples, Italy
| | - David Ribet
- INSERM UMR 1073 “Nutrition, Inflammation and Gut-Brain Axis Dysfunctions”, UNIROUEN, Normandie University, 76000 Rouen, France; (D.R.); (N.A.); (M.-P.T.); (P.D.)
| | - Najate Achamrah
- INSERM UMR 1073 “Nutrition, Inflammation and Gut-Brain Axis Dysfunctions”, UNIROUEN, Normandie University, 76000 Rouen, France; (D.R.); (N.A.); (M.-P.T.); (P.D.)
- Department of Nutrition, CHU Rouen, 76000 Rouen, France
| | - Marie-Pierre Tavolacci
- INSERM UMR 1073 “Nutrition, Inflammation and Gut-Brain Axis Dysfunctions”, UNIROUEN, Normandie University, 76000 Rouen, France; (D.R.); (N.A.); (M.-P.T.); (P.D.)
- INSERM CIC-CRB 1404, CHU Rouen, 76000 Rouen, France
| | - Pierre Déchelotte
- INSERM UMR 1073 “Nutrition, Inflammation and Gut-Brain Axis Dysfunctions”, UNIROUEN, Normandie University, 76000 Rouen, France; (D.R.); (N.A.); (M.-P.T.); (P.D.)
- Department of Nutrition, CHU Rouen, 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; (K.S.); (M.L.)
| | - Tobias Pischon
- Molecular Epidemiology Research Group, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; (M.P.); (T.P.)
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, 10117 Berlin, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Berlin, 10785 Berlin, Germany
- 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
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5
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Homann CM, 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. Nutrients 2021; 13:nu13082639. [PMID: 34444798 PMCID: PMC8400337 DOI: 10.3390/nu13082639] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 12/11/2022] Open
Abstract
The introduction of solid foods is an important dietary event during infancy that causes profound shifts in the gut microbial composition towards a more adult-like state. Infant gut bacterial dynamics, especially in relation to nutritional intake remain understudied. Over 2 weeks surrounding the time of solid food introduction, the day-to-day dynamics in the gut microbiomes of 24 healthy, full-term infants from the Baby, Food & Mi and LucKi-Gut cohort studies were investigated in relation to their dietary intake. Microbial richness (observed species) and diversity (Shannon index) increased over time and were positively associated with dietary diversity. Microbial community structure (Bray–Curtis dissimilarity) was determined predominantly by individual and age (days). The extent of change in community structure in the introductory period was negatively associated with daily dietary diversity. High daily dietary diversity stabilized the gut microbiome. Bifidobacterial taxa were positively associated, while taxa of the genus Veillonella, that may be the same species, were negatively associated with dietary diversity in both cohorts. This study furthers our understanding of the impact of solid food introduction on gut microbiome development in early life. Dietary diversity seems to have the greatest impact on the gut microbiome as solids are introduced.
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Affiliation(s)
- Chiara-Maria Homann
- Department of Medicine, McMaster University, Hamilton, ON L8N 3Z5, Canada; (C.-M.H.); (S.D.); (M.G.S.)
- Department of Pediatrics, McMaster University, Hamilton, ON L8S 4K1, Canada; (E.G.); (K.M.M.)
- Centre for Metabolism, Obesity and Diabetes Research, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Connor A. J. Rossel
- Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, 6229 ER Maastricht, The Netherlands; (C.A.J.R.); (L.B.); (J.P.)
| | - Sara Dizzell
- Department of Medicine, McMaster University, Hamilton, ON L8N 3Z5, Canada; (C.-M.H.); (S.D.); (M.G.S.)
| | - Liene Bervoets
- Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, 6229 ER Maastricht, The Netherlands; (C.A.J.R.); (L.B.); (J.P.)
| | - Julia Simioni
- Department of Obstetrics & Gynecology, McMaster University, Hamilton, ON L8S 4K1, Canada; (J.S.); (J.L.); (E.K.H.)
| | - Jenifer Li
- Department of Obstetrics & Gynecology, McMaster University, Hamilton, ON L8S 4K1, Canada; (J.S.); (J.L.); (E.K.H.)
- McMaster Midwifery Research Centre, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Elizabeth Gunn
- Department of Pediatrics, McMaster University, Hamilton, ON L8S 4K1, Canada; (E.G.); (K.M.M.)
- Centre for Metabolism, Obesity and Diabetes Research, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Michael G. Surette
- Department of Medicine, McMaster University, Hamilton, ON L8N 3Z5, Canada; (C.-M.H.); (S.D.); (M.G.S.)
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Russell J. de Souza
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, ON L8S 4K1, Canada;
- Population Health Research Institute, Hamilton Health Sciences Corporation, Hamilton, ON L8L 2X2, Canada
| | - Monique Mommers
- Department of Epidemiology, Care and Public Health Research Institute (CAPHRI), Maastricht University, 6229 ER Maastricht, The Netherlands;
| | - Eileen K. Hutton
- Department of Obstetrics & Gynecology, McMaster University, Hamilton, ON L8S 4K1, Canada; (J.S.); (J.L.); (E.K.H.)
- McMaster Midwifery Research Centre, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Katherine M. Morrison
- Department of Pediatrics, McMaster University, Hamilton, ON L8S 4K1, Canada; (E.G.); (K.M.M.)
- Centre for Metabolism, Obesity and Diabetes Research, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - John Penders
- Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, 6229 ER Maastricht, The Netherlands; (C.A.J.R.); (L.B.); (J.P.)
- InVivo Planetary Health: An Affiliate of the World Universities Network (WUN), West New York, NJ 10704, USA
- Department of Medical Microbiology, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Centre, 6229 ER Maastricht, The Netherlands
| | - Niels van Best
- Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, 6229 ER Maastricht, The Netherlands; (C.A.J.R.); (L.B.); (J.P.)
- InVivo Planetary Health: An Affiliate of the World Universities Network (WUN), West New York, NJ 10704, USA
- Institute of Medical Microbiology, RWTH University Hospital Aachen, RWTH University, 52074 Aachen, Germany
- Correspondence: (N.v.B.); (J.C.S.)
| | - Jennifer C. Stearns
- Department of Medicine, McMaster University, Hamilton, ON L8N 3Z5, Canada; (C.-M.H.); (S.D.); (M.G.S.)
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON L8S 4K1, Canada
- Correspondence: (N.v.B.); (J.C.S.)
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