These nuts “help to support the gut microbiome,” Dr. Bedford said, and are “definitely good for gut health.”5. Along with bananas, apples are “definitely a good fruit for gut health,” Dr. Bedford noted, thanks to the fiber and prebiotics they contain. “Prebiotics are food for the good bacteria in your gut, helping them flourish and keeping a healthy balance of the microbiome.”10. OnionsOnions are another great prebiotic-rich food that help contribute to better gut health, according to Dr. Bedford. Prebiotics and probiotics are actually very different—but we depend on both for optimal gut health.