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      Effect on gut microbiota of a 1-y lifestyle intervention with Mediterranean diet compared with energy-reduced Mediterranean diet and physical activity promotion: PREDIMED-Plus Study

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          ABSTRACT

          Background

          The Mediterranean diet is a well-recognized healthy diet that has shown to induce positive changes in gut microbiota. Lifestyle changes such as diet along with physical activity could aid in weight loss and improve cardiovascular risk factors.

          Objectives

          To investigate the effect of an intensive lifestyle weight loss intervention on gut microbiota.

          Methods

          This is a substudy of the PREDIMED-Plus (Prevención con Dieta Mediterránea-Plus), a randomized controlled trial conducted in overweight/obese men and women (aged 55–75 y) with metabolic syndrome. The intervention group (IG) underwent an intensive weight loss lifestyle intervention based on an energy-restricted Mediterranean diet (MedDiet) and physical activity promotion, and the control group (CG) underwent a non-energy-restricted MedDiet for 1 y. Anthropometric, biochemical, and gut microbial 16S rRNA sequencing data were analyzed at baseline ( n = 362) and 1-y follow-up ( n = 343).

          Results

          IG participants had a weight loss of 4.2 (IQR, –6.8, –2.5) kg compared with 0.2 (IQR, –2.1, 1.4) kg in the CG ( P < 0.001). Reductions in BMI, fasting glucose, glycated hemoglobin, and triglycerides and an increase in HDL cholesterol were greater in IG than in CG participants ( P < 0.05). We observed a decrease in Butyricicoccus, Haemophilus, Ruminiclostridium 5, and Eubacterium hallii in the IG compared with the CG. Many genera shifted in the same direction within both intervention groups, indicating an overall effect of the MedDiet. Decreases in Haemophilus, Coprococcus 3, and few other genera were associated with a decrease in adiposity parameters in both intervention groups. Changes in Lachnospiraceae NK4A136 were positively associated with changes in MedDiet adherence.

          Conclusions

          Weight loss induced by an energy-restricted MedDiet and physical activity induce changes in gut microbiota. The role of MedDiet-induced changes on the host might be via short-chain fatty acid producing bacteria, whereas with energy restriction, these changes might be modulated with other mechanisms, which need to be explored in future studies. This trial was registered at http://www.isrctn.com/ISRCTN89898870 as ISRCT 89898870.

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          Most cited references61

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          phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

          Background The analysis of microbial communities through DNA sequencing brings many challenges: the integration of different types of data with methods from ecology, genetics, phylogenetics, multivariate statistics, visualization and testing. With the increased breadth of experimental designs now being pursued, project-specific statistical analyses are often needed, and these analyses are often difficult (or impossible) for peer researchers to independently reproduce. The vast majority of the requisite tools for performing these analyses reproducibly are already implemented in R and its extensions (packages), but with limited support for high throughput microbiome census data. Results Here we describe a software project, phyloseq, dedicated to the object-oriented representation and analysis of microbiome census data in R. It supports importing data from a variety of common formats, as well as many analysis techniques. These include calibration, filtering, subsetting, agglomeration, multi-table comparisons, diversity analysis, parallelized Fast UniFrac, ordination methods, and production of publication-quality graphics; all in a manner that is easy to document, share, and modify. We show how to apply functions from other R packages to phyloseq-represented data, illustrating the availability of a large number of open source analysis techniques. We discuss the use of phyloseq with tools for reproducible research, a practice common in other fields but still rare in the analysis of highly parallel microbiome census data. We have made available all of the materials necessary to completely reproduce the analysis and figures included in this article, an example of best practices for reproducible research. Conclusions The phyloseq project for R is a new open-source software package, freely available on the web from both GitHub and Bioconductor.
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            ggplot2

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              PICRUSt2 for prediction of metagenome functions

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                Author and article information

                Contributors
                Journal
                Am J Clin Nutr
                Am J Clin Nutr
                ajcn
                The American Journal of Clinical Nutrition
                Oxford University Press
                0002-9165
                1938-3207
                September 2021
                21 May 2021
                21 May 2021
                : 114
                : 3
                : 1148-1158
                Affiliations
                Universitat Rovira i Virgili, Department of Biochemistry and Biotechnology, Hospital Universitari de Sant Joan de Reus, Institut d’Investigacions Sanitàries Pere i Virgili, Human Nutrition Unit , Reus, Spain
                CIBER de Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III , Madrid, Spain
                CIBER de Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III , Madrid, Spain
                Unidad de Gestion Clínica de Endocrinología y Nutrición, Laboratorio del Instituto de Investigación Biomédica de Málaga (IBIMA), Hospital Universitario de Málaga (Virgen de la Victoria) , Universidad de Málaga, Málaga, Spain
                Universitat Rovira i Virgili, Department of Biochemistry and Biotechnology, Hospital Universitari de Sant Joan de Reus, Institut d’Investigacions Sanitàries Pere i Virgili, Human Nutrition Unit , Reus, Spain
                CIBER de Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III , Madrid, Spain
                Instituto de Investigación Sanitaria y Biomédica de Alicante, ISABIAL-UMH, Alicante , Spain
                CIBER Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III (ISCIII) , Madrid, Spain
                CIBER de Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III , Madrid, Spain
                Department of Preventive Medicine, University of Valencia , Valencia, Spain
                CIBER de Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III , Madrid, Spain
                Cardiovascular Risk and Nutrition (Regicor Study Group), Hospital del Mar Research Institute (IMIM) , Barcelona, Spain
                Endocrinology and Nutrition Department, Hospital Clinic Universitari , Barcelona, Spain
                August Pi i Sunyer Biomedical Research Institute (IDIBAPS) , Barcelona, ​​Spain
                Universitat Rovira i Virgili, Department of Biochemistry and Biotechnology, Hospital Universitari de Sant Joan de Reus, Institut d’Investigacions Sanitàries Pere i Virgili, Human Nutrition Unit , Reus, Spain
                CIBER de Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III , Madrid, Spain
                CIBER de Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III , Madrid, Spain
                Unidad de Gestion Clínica de Endocrinología y Nutrición, Laboratorio del Instituto de Investigación Biomédica de Málaga (IBIMA), Hospital Universitario de Málaga (Virgen de la Victoria) , Universidad de Málaga, Málaga, Spain
                Instituto de Investigación Sanitaria y Biomédica de Alicante, ISABIAL-UMH, Alicante , Spain
                CIBER Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III (ISCIII) , Madrid, Spain
                CIBER de Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III , Madrid, Spain
                Department of Preventive Medicine, University of Valencia , Valencia, Spain
                CIBER de Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III , Madrid, Spain
                Cardiovascular Risk and Nutrition (Regicor Study Group), Hospital del Mar Research Institute (IMIM) , Barcelona, Spain
                August Pi i Sunyer Biomedical Research Institute (IDIBAPS) , Barcelona, ​​Spain
                CIBER de Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III , Madrid, Spain
                Unidad de Gestion Clínica de Endocrinología y Nutrición, Laboratorio del Instituto de Investigación Biomédica de Málaga (IBIMA), Hospital Universitario de Málaga (Virgen de la Victoria) , Universidad de Málaga, Málaga, Spain
                Universitat Rovira i Virgili, Department of Biochemistry and Biotechnology, Hospital Universitari de Sant Joan de Reus, Institut d’Investigacions Sanitàries Pere i Virgili, Human Nutrition Unit , Reus, Spain
                CIBER de Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III , Madrid, Spain
                CIBER de Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III , Madrid, Spain
                UGC Medicina Interna, Hospital Regional Universitario de Málaga , Malaga, Spain
                CIBER de Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III , Madrid, Spain
                University of Navarra, Department of Preventive Medicine and Public Health , IdiSNA, Pamplona, Spain
                Department of Nutrition, Harvard T. H. Chan School of Public Health , Boston, MA, USA
                Universitat Rovira i Virgili, Department of Biochemistry and Biotechnology, Hospital Universitari de Sant Joan de Reus, Institut d’Investigacions Sanitàries Pere i Virgili, Human Nutrition Unit , Reus, Spain
                CIBER de Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III , Madrid, Spain
                CIBER de Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III , Madrid, Spain
                Unidad de Gestion Clínica de Endocrinología y Nutrición, Laboratorio del Instituto de Investigación Biomédica de Málaga (IBIMA), Hospital Universitario de Málaga (Virgen de la Victoria) , Universidad de Málaga, Málaga, Spain
                Author notes
                Address correspondence to IM-I (e-mail: isabel.moreno@ 123456ibima.eu )
                Address correspondence to MB (e-mail: monica.bullo@ 123456urv.cat )
                Author information
                https://orcid.org/0000-0003-2700-7459
                Article
                nqab150
                10.1093/ajcn/nqab150
                8408861
                34020445
                243968f0-0dd0-4875-bf31-c2ad555ea3d5
                © The Author(s) 2021. Published by Oxford University Press on behalf of the American Society for Nutrition.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License ( https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@ 123456oup.com

                History
                : 24 November 2020
                : 09 April 2021
                Page count
                Pages: 11
                Funding
                Funded by: Spanish institutions for funding Scientific Biomedical Research;
                Funded by: >CIBER Fisiopatología de la Obesidad y Nutrición;
                Funded by: Instituto de Salud Carlos III, DOI 10.13039/501100004587;
                Funded by: Fondo de Investigación para la Salud;
                Funded by: European Regional Development Fund, DOI 10.13039/501100008530;
                Award ID: PI13/00462
                Award ID: PI16/00501
                Award ID: PI19/00576
                Award ID: PI17/01441
                Award ID: PI14/01206
                Funded by: Implementación y evaluación de una intervención intensiva sobre la actividad física Cohorte;
                Award ID: OBN16PE01
                Award ID: 2013ACUP00194
                Funded by: Generalitat Valenciana, DOI 10.13039/501100003359;
                Award ID: PROMETEO 2017/17
                Funded by: Ministry of Science and Innovation, DOI 10.13039/501100004837;
                Award ID: PI19/00781
                Funded by: European Union’s Horizon 2020 Research and Innovation Program;
                Award ID: 728018
                Funded by: Radboud University Medical Center, DOI 10.13039/501100006209;
                Funded by: Fondo de Investigacion Sanitaria;
                Award ID: PI16/00516
                Funded by: FEDER, DOI 10.13039/501100002924;
                Funded by: Miguel Servet Type I;
                Award ID: CP15/00028
                Funded by: Fondo Europeo de Desarrollo Regional-FEDER;
                Funded by: Comissió Executiva d'Ajuts de Recerca de l'Agència de Gestió d'Ajuts Universitaris i de Recerca de la Generalitat de Catalunya;
                Award ID: 2018FI_B_00444
                Funded by: Universitat Rovira i Virgili, DOI 10.13039/501100007512;
                Funded by: Fundació Catalunya La Pedrera;
                Funded by: Patrimonio Comunal Olivarero;
                Categories
                Original Research Communications
                Nutritional Status, Dietary Intake, and Body Composition
                AcademicSubjects/MED00060
                AcademicSubjects/MED00160

                Nutrition & Dietetics
                weight loss,gut microbiota,mediterranean diet,energy restriction,obesity
                Nutrition & Dietetics
                weight loss, gut microbiota, mediterranean diet, energy restriction, obesity

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