The human microbiome, which consists of the total DNA content of microbes inhabiting the body, exhibits significant variability, with only a third of its genes found in a majority of healthy individuals. Understanding this variability in the "healthy microbiome" has been a major challenge in microbiome research. Several population-scale studies have documented the ranges and diversity of taxonomic compositions and functional potentials in healthy populations, along with possible driving factors such as geography, diet, and lifestyle. The review discusses various definitions of a 'healthy microbiome,' the current understanding of healthy microbial diversity, and gaps such as the characterization of molecular function and the development of ecological therapies. Key aspects include the functional core of the microbiome, its ecological properties, and temporal dynamics. The review also highlights the importance of early-life factors in shaping the microbiome and the role of diet and delivery mode in establishing a healthy microbiome. Additionally, it explores the concept of a healthy community ecology, the resistance and resilience of the microbiome to perturbations, and the potential for personalized medicine and therapeutic interventions based on the healthy microbiome.The human microbiome, which consists of the total DNA content of microbes inhabiting the body, exhibits significant variability, with only a third of its genes found in a majority of healthy individuals. Understanding this variability in the "healthy microbiome" has been a major challenge in microbiome research. Several population-scale studies have documented the ranges and diversity of taxonomic compositions and functional potentials in healthy populations, along with possible driving factors such as geography, diet, and lifestyle. The review discusses various definitions of a 'healthy microbiome,' the current understanding of healthy microbial diversity, and gaps such as the characterization of molecular function and the development of ecological therapies. Key aspects include the functional core of the microbiome, its ecological properties, and temporal dynamics. The review also highlights the importance of early-life factors in shaping the microbiome and the role of diet and delivery mode in establishing a healthy microbiome. Additionally, it explores the concept of a healthy community ecology, the resistance and resilience of the microbiome to perturbations, and the potential for personalized medicine and therapeutic interventions based on the healthy microbiome.