The human microbiome, particularly in healthy individuals, is highly variable, with only a third of its genes found in most healthy people. Understanding this variability is crucial for identifying and correcting microbial configurations linked to disease. The healthy microbiome is defined by its composition, function, dynamics, and ecology. It includes a diverse range of bacteria, such as Bacteroidetes and Firmicutes, and is influenced by factors like geography, diet, and lifestyle. The microbiome's functional core includes essential metabolic and molecular functions, and its stability and resilience to perturbations are key characteristics. Studies have shown that the gut microbiome is the most studied body habitat, with significant interpersonal variation. The healthy microbiome also includes archaea, viruses, fungi, and other eukaryotes, which play roles in immune balance and host-microbe interactions. Geographical variation affects microbiome composition, with diet being a major contributor. Early-life factors, such as delivery mode and diet, significantly influence microbiome establishment. The healthy microbiome is characterized by a dynamic equilibrium, with the ability to resist perturbations and return to a healthy state. Research highlights the importance of understanding the microbiome's molecular functions, as up to 50% of microbial gene families remain uncharacterized. Future studies aim to integrate population-scale epidemiology with clinical research to better understand and manage the microbiome's role in health and disease. The healthy microbiome is essential for immune system development and disease prevention, and its study continues to advance personalized medicine and therapeutic interventions.The human microbiome, particularly in healthy individuals, is highly variable, with only a third of its genes found in most healthy people. Understanding this variability is crucial for identifying and correcting microbial configurations linked to disease. The healthy microbiome is defined by its composition, function, dynamics, and ecology. It includes a diverse range of bacteria, such as Bacteroidetes and Firmicutes, and is influenced by factors like geography, diet, and lifestyle. The microbiome's functional core includes essential metabolic and molecular functions, and its stability and resilience to perturbations are key characteristics. Studies have shown that the gut microbiome is the most studied body habitat, with significant interpersonal variation. The healthy microbiome also includes archaea, viruses, fungi, and other eukaryotes, which play roles in immune balance and host-microbe interactions. Geographical variation affects microbiome composition, with diet being a major contributor. Early-life factors, such as delivery mode and diet, significantly influence microbiome establishment. The healthy microbiome is characterized by a dynamic equilibrium, with the ability to resist perturbations and return to a healthy state. Research highlights the importance of understanding the microbiome's molecular functions, as up to 50% of microbial gene families remain uncharacterized. Future studies aim to integrate population-scale epidemiology with clinical research to better understand and manage the microbiome's role in health and disease. The healthy microbiome is essential for immune system development and disease prevention, and its study continues to advance personalized medicine and therapeutic interventions.