<p>The gut microbiome is a complex ecosystem of trillions of microbes residing in the human gastrointestinal tract. This microbial community plays a pivotal role in human health by swaying various physiological processes like metabolism, immunomodulation, antimicrobial protection, and psychological health. Natural and biological products comprising herbal extracts, dietary fibers, probiotics, prebiotics, and synbiotics have long been documented for their potential to modulate gut microbiota composition and function. Understanding the interactions between natural products and gut microbiota can provide valuable insights into their health-promoting effects and therapeutic potential. Literature was systematically sourced, analyzed, and compiled through searches across databases such as Science Direct, Google Scholar, and PubMed. The search terms include “gut microbiome,” “Dysbiosis,” “probiotics,” “prebiotics,” “synbiotics,” “biological products,” “gut health,” “natural products,” “dietary fibers,” “resistant starches,” “clinical study reports,” “safety recommendations,” etc., and several combinations of these words. This article provides a deep insight into the overview of natural and biological products aimed at promoting a healthy gut microbiome. It underscores the functional roles of the gut microbiota, including nutrient metabolism, antimicrobial defense, and gastrointestinal tract integrity. Furthermore, it delves into the detailed mechanisms of action and clinical evidence supporting the use of probiotics, prebiotics, synbiotics, herbal extracts, and dietary fibers in modulating gut microbiota composition and function. The biological activity, detailed mechanism of action, safety, and their considerable potential as modulators of gut microbiota composition and function have been extensively studied. Further research is necessary to clarify the underlying mechanisms of action to investigate their clinical implications.</p>