{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,7]],"date-time":"2026-05-07T17:58:23Z","timestamp":1778176703477,"version":"3.51.4"},"reference-count":41,"publisher":"MDPI AG","issue":"14","license":[{"start":{"date-parts":[[2025,7,18]],"date-time":"2025-07-18T00:00:00Z","timestamp":1752796800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Farmodi\u00e9tica S.A"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Nutrients"],"abstract":"<jats:p>Background: The gut microbiota is increasingly recognized as a key modulator in obesity management, influencing host energy balance, lipid metabolism, and inflammatory pathways. With obesity prevalence continuing to rise globally, dietary interventions that promote beneficial microbial shifts are essential for enhancing weight loss outcomes and long-term health. Objective: This study investigated the effects of the multicomponent Weight Loss Maintenance 3 Phases Program (WLM3P), which integrates caloric restriction, a high-protein low-carbohydrate diet, time-restricted eating (10h TRE), dietary supplementation (prebiotics and phytochemicals), and digital app-based support on gut microbiota composition compared to a standard low-carbohydrate diet (LCD) in adults with obesity. The analysis focused exclusively on the 6-month weight loss period corresponding to Phases 1 and 2 of the WLM3P intervention. Methods: In this sub-analysis of a randomized controlled trial (ClinicalTrials.gov Identifier: NCT04192357), 58 adults with obesity (BMI 30.0\u201339.9 kg\/m2) were randomized to the WLM3P (n = 29) or LCD (n = 29) groups. Stool samples were collected at baseline and 6 months for 16S rRNA sequencing. Alpha and beta diversity were assessed, and genus-level differential abundance was determined using EdgeR and LEfSe. Associations between microbial taxa and clinical outcomes were evaluated using regression models. Results: After 6-month, the WLM3P group showed a significant increase in alpha diversity (p = 0.03) and a significant change in beta diversity (p &lt; 0.01), while no significant changes were observed in the LCD group. Differential abundance analysis revealed specific microbial signatures in WLM3P participants, including increased levels of Faecalibacterium. Notably, higher Faecalibacterium abundance was associated with greater reductions in fat mass (kg, %) and visceral adiposity (cm2) in the WLM3P group compared to LCD (p &lt; 0.01). Conclusions: These findings suggest a potential microbiota-mediated mechanism in weight loss, where Faecalibacterium may enhance fat reduction effectiveness in the context of the WLM3P intervention.<\/jats:p>","DOI":"10.3390\/nu17142360","type":"journal-article","created":{"date-parts":[[2025,7,18]],"date-time":"2025-07-18T12:09:53Z","timestamp":1752840593000},"page":"2360","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Gut Microbiota Shifts After a Weight Loss Program in Adults with Obesity: The WLM3P Study"],"prefix":"10.3390","volume":"17","author":[{"given":"Vanessa","family":"Pereira","sequence":"first","affiliation":[{"name":"NOVA Medical School, Faculty of Medical Sciences, NMS, FCM, Nova University of Lisbon, 1169-056 Lisbon, Portugal"},{"name":"Nutrition Department Farmodi\u00e9tica, Farmodi\u00e9tica, 2785-723 Lisbon, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2631-2566","authenticated-orcid":false,"given":"Amanda","family":"Cuevas-Sierra","sequence":"additional","affiliation":[{"name":"NOVA Medical School, Faculty of Medical Sciences, NMS, FCM, Nova University of Lisbon, 1169-056 Lisbon, Portugal"},{"name":"Precision Nutrition and Cardiometabolic Health, IMDEA-Alimentaci\u00f3n Institute (Madrid Institute for Advanced Studies), Campus of International Excellence (CEI), Universidad Aut\u00f3noma de Madrid (UAM), Spanish National Research Council (Consejo Superior de Investigaciones Cient\u00edficas, CSIC), 28049 Madrid, Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9916-275X","authenticated-orcid":false,"given":"Victor","family":"de la O","sequence":"additional","affiliation":[{"name":"Precision Nutrition and Cardiometabolic Health, IMDEA-Alimentaci\u00f3n Institute (Madrid Institute for Advanced Studies), Campus of International Excellence (CEI), Universidad Aut\u00f3noma de Madrid (UAM), Spanish National Research Council (Consejo Superior de Investigaciones Cient\u00edficas, CSIC), 28049 Madrid, Spain"},{"name":"Faculty of Health Sciences, International University of La Rioja (UNIR), 26006 Logro\u00f1o, Spain"}]},{"given":"Rita","family":"Salvado","sequence":"additional","affiliation":[{"name":"NOVA Medical School, Faculty of Medical Sciences, NMS, FCM, Nova University of Lisbon, 1169-056 Lisbon, Portugal"},{"name":"Primary Care Research Unit of Salamanca (APISAL), Salamanca Primary Healthcare Management, Castilla y Le\u00f3n Regional Health Authority (SACyL), Institute of Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain"}]},{"given":"In\u00eas","family":"Barreiros-Mota","sequence":"additional","affiliation":[{"name":"NOVA Medical School, Faculty of Medical Sciences, NMS, FCM, Nova University of Lisbon, 1169-056 Lisbon, Portugal"},{"name":"Comprehensive Health Research Center (CHRC), NOVA Medical School, Faculty of Medical Sciences, NMS, FCM, NOVA University Lisbon, 1169-056 Lisbon, Portugal"}]},{"given":"In\u00eas","family":"Castela","sequence":"additional","affiliation":[{"name":"NOVA Medical School, Faculty of Medical Sciences, NMS, FCM, Nova University of Lisbon, 1169-056 Lisbon, Portugal"},{"name":"Comprehensive Health Research Center (CHRC), NOVA Medical School, Faculty of Medical Sciences, NMS, FCM, NOVA University Lisbon, 1169-056 Lisbon, Portugal"}]},{"given":"Alexandra","family":"Camelo","sequence":"additional","affiliation":[{"name":"CATAA\u2014Agro-Food Technological Support Center, Industrial Zone of Castelo Branco, Rua A, 6000-459 Castelo Branco, Portugal"},{"name":"Center for Functional Ecology Science for People & the Planet, TERRA Associated Laboratory, Department of Life Sciences, University of Coimbra, Cal\u00e7ada Martim de Freitas, 3000-456 Coimbra, Portugal"}]},{"given":"In\u00eas","family":"Brand\u00e3o","sequence":"additional","affiliation":[{"name":"CATAA\u2014Agro-Food Technological Support Center, Industrial Zone of Castelo Branco, Rua A, 6000-459 Castelo Branco, Portugal"},{"name":"Center for Functional Ecology Science for People & the Planet, TERRA Associated Laboratory, Department of Life Sciences, University of Coimbra, Cal\u00e7ada Martim de Freitas, 3000-456 Coimbra, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9800-4186","authenticated-orcid":false,"given":"Christophe Esp\u00edrito","family":"Santo","sequence":"additional","affiliation":[{"name":"CATAA\u2014Agro-Food Technological Support Center, Industrial Zone of Castelo Branco, Rua A, 6000-459 Castelo Branco, Portugal"},{"name":"Center for Functional Ecology Science for People & the Planet, TERRA Associated Laboratory, Department of Life Sciences, University of Coimbra, Cal\u00e7ada Martim de Freitas, 3000-456 Coimbra, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5165-9513","authenticated-orcid":false,"given":"Ana","family":"Faria","sequence":"additional","affiliation":[{"name":"NOVA Medical School, Faculty of Medical Sciences, NMS, FCM, Nova University of Lisbon, 1169-056 Lisbon, Portugal"},{"name":"Comprehensive Health Research Center (CHRC), NOVA Medical School, Faculty of Medical Sciences, NMS, FCM, NOVA University Lisbon, 1169-056 Lisbon, Portugal"},{"name":"CINTESIS@RISE, NOVA Medical School, Faculty of Medical Sciences, NMS, FCM, NOVA University Lisbon, 1169-056 Lisbon, Portugal"}]},{"given":"Concei\u00e7\u00e3o","family":"Calhau","sequence":"additional","affiliation":[{"name":"NOVA Medical School, Faculty of Medical Sciences, NMS, FCM, Nova University of Lisbon, 1169-056 Lisbon, Portugal"},{"name":"CINTESIS@RISE, NOVA Medical School, Faculty of Medical Sciences, NMS, FCM, NOVA University Lisbon, 1169-056 Lisbon, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9327-2897","authenticated-orcid":false,"given":"Marta P.","family":"Silvestre","sequence":"additional","affiliation":[{"name":"NOVA Medical School, Faculty of Medical Sciences, NMS, FCM, Nova University of Lisbon, 1169-056 Lisbon, Portugal"},{"name":"Comprehensive Health Research Center (CHRC), NOVA Medical School, Faculty of Medical Sciences, NMS, FCM, NOVA University Lisbon, 1169-056 Lisbon, Portugal"},{"name":"CINTESIS@RISE, NOVA Medical School, Faculty of Medical Sciences, NMS, FCM, NOVA University Lisbon, 1169-056 Lisbon, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0320-1839","authenticated-orcid":false,"given":"Andr\u00e9","family":"Moreira-Ros\u00e1rio","sequence":"additional","affiliation":[{"name":"NOVA Medical School, Faculty of Medical Sciences, NMS, FCM, Nova University of Lisbon, 1169-056 Lisbon, Portugal"},{"name":"Comprehensive Health Research Center (CHRC), NOVA Medical School, Faculty of Medical Sciences, NMS, FCM, NOVA University Lisbon, 1169-056 Lisbon, Portugal"},{"name":"CINTESIS@RISE, NOVA Medical School, Faculty of Medical Sciences, NMS, FCM, NOVA University Lisbon, 1169-056 Lisbon, 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