Microbiome research has reframed biology by revealing humans, plants, and ecosystems as multispecies assemblages whose functions emerge from host–microbe interactions. Across gut, skin, oral, soil, and aquatic habitats, microbial communities regulate metabolism, immunity, development, and biogeochemical cycles. In human health, dysbiosis is associated with metabolic, inflammatory, neuropsychiatric, and infectious diseases, while targeted interventions—dietary fiber, pre/pro/postbiotics, bacteriophages, live biotherapeutic products, fecal microbiota transplantation (FMT), and engineered microbes—offer avenues for prevention and therapy. In nutrition, microbiome-mediated processing of macronutrients, micronutrients, and xenobiotics generates metabolites (e.g., short-chain fatty acids, bile acid derivatives, indoles) that shape glycemic control, satiety, and systemic inflammation, enabling precision nutrition strategies. Environmentally, plant- and soil-associated microbiomes enhance nutrient use efficiency, stress tolerance, and carbon sequestration, supporting sustainable agriculture and climate resilience. Methodological advances—long-read and single-cell sequencing, strain-resolved and multi-omic profiling, causal inference with gnotobiotics, and privacy-preserving data governance—are accelerating translation while exposing challenges of reproducibility, safety, equity, and regulation. This paper synthesizes current knowledge and outlines a roadmap for integrative, ethical, and scalable microbiome applications in medicine, food systems, and environmental stewardship.