Health benefits and physiological actions of micronutrients, probiotics/prebiotics, phytochemicals, and their associated deficiency diseases: a systematic review of recent developments and applications

Micronutrients, probiotics/prebiotics, and phytochemicals influence physiological function, but benefits vary by baseline nutritional status, intervention, population, and outcome. This systematic review synthesizes evidence from primary research and high-quality reviews (2016–2026) on vitamins/minerals, probiotics/prebiotics, phytochemicals, and deficiency- or dysbiosis-related conditions. Following PRISMA 2020, searches covered PubMed/PMC, Scopus, ScienceDirect, Web of Science, Wiley Online Library, Taylor & Francis Online, MDPI, Frontiers, SAGE, Google Scholar, and WHO/FAO resources. Widespread micronutrient inadequacies were identified, particularly for iron, iodine, calcium, and vitamin E. Intervention evidence was strongest for correcting established deficiencies and selected strain- or outcome-specific probiotic applications. Evidence for extra-skeletal vitamin D effects, broad cardiometabolic prevention, phytochemical supplementation, and microbiome-mediated nutrient benefits was more heterogeneous and often observational or mechanistic rather than definitive clinical trials. Heterogeneity in populations, doses, formulations, comparators, outcomes, and designs precluded quantitative pooling; conclusions were therefore synthesized narratively according to evidence type and risk of bias. Evidence supports food-based dietary adequacy, targeted fortification/supplementation for demonstrated or high-risk deficiency, and cautious use of selected probiotics/prebiotics where strain- and outcome-specific evidence exists. Precision nutrition, biomarker-guided strategies, and microbiome-informed interventions remain insufficiently validated for population-wide implementation. More studies should prioritize adequately powered, long-term, preregistered trials with clinically meaningful outcomes and standardized reporting.