Abstract
BACKGROUND: The gut microbiota are increasingly recognised as key mediators of diet-related health outcomes. This systematic review primarily aimed to comprehensively evaluate associations between dietary interventions and gut microbiota in healthy and clinical adult populations, utilising controlled trials. Secondary outcomes included biological markers measured in blood, faecal, and urine samples. METHODS: A systematic literature search was conducted following the PRISMA guidelines, using the electronic databases PubMed, EMBASE, The Cochrane Central Register of Controlled Trials (CENTRAL), CINAHL (via EBSCOhost), and Scopus to gather controlled trials of dietary interventions that reported within-group changes from baseline for gut microbiota and biomarkers. Study screening, data extraction, and risk-of-bias assessment were conducted by two independent reviewers. RESULTS: Eighty studies met the eligibility criteria, trialling 13 distinct dietary interventions: Mediterranean, Western, Korean, Japanese, Nordic, low fermentable oligosaccharides, disaccharides, monosaccharides and polyols (FODMAP), ketogenic, gluten-free, calorie-restricted, macronutrient altered, animal- and plant-based, as well as diets high in functional nutrients and bioactive compounds. Dietary interventions were associated with within-group changes in taxonomy and particular biological markers; however, they were not consistently associated with changes in the alpha or beta diversity of the gut microbiota. The Mediterranean, Japanese, Korean, calorie-restricted, high-polyphenol, high-fibre, plant-based, low-fat, and low-protein diets were all associated with increased abundances of either short chain fatty acids (SCFA)- or lactic acid-producing bacteria or reduced abundance of opportunistic pathogenic bacteria. Some of these diets were also associated with reduced levels of inflammatory markers. In contrast, Western, animal-based, low FODMAP, ketogenic, and gluten-free diets were associated with a reduced abundance of SCFA-producing bacteria. There was substantial heterogeneity across studies in methodology and reporting. CONCLUSION: This systematic review identifies differential associations between a wide range of dietary interventions and gut microbiota and inflammatory outcomes, both beneficial and adverse. GRAPHICAL ABSTRACT: [Image: see text] SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12967-025-07428-9.