BackgroundThe human gut hosts complex microbial communities, which are linked to health and disease. The gut microbiota is continuously reshaped by multiple environmental factors, especially diet. Gut dysbiosis may promote various metabolic, neurological, intestinal, and cardiovascular diseases, and even tumor development. Probiotics have shown promising prophylactic, mitigating, or even curative effects when use as nutrient supplements or adjunctive therapy. These beneficial and/or symptom alleviation effects are often accompanied by gut microbiome and metabolome changes.Scope and approachDiffering from other published review articles, here we summarized the latest knowledge of evidence-based health-promoting effects of probiotics by scouring literature of recent animal and human probiotic intervention studies.Key findings and conclusionsTo elucidate the beneficial mechanisms of probiotics in enhancing intestinal homeostasis, intestinal barrier function, host immunity, and through modulating the gut microbiome and its metabolites. Meanwhile, we also discussed challenges in data analysis in clinical research of probiotics and data comparison between laboratories, and provides an outlook for future perspectives in the applications of probiotics.Key findings and conclusionsThe beneficial mechanisms of probiotics are achieved through enhancing intestinal homeostasis, intestinal barrier function, host immunity, and gut microbiome and metabolome modulation. Current challenges in data analysis and comparison in clinical research of probiotics are discussed. Finally, an outlook for future perspectives in the applications of probiotics is provided.