The human gut microbiota is a complex ecological community that influences normal physiology and susceptibility to diseases through its metabolic activities and interactions with the host. Understanding the factors that drive changes in the gut microbiota's composition and function is crucial for developing targeted therapies. The gut microbiota is highly diverse, varies between individuals, and fluctuates over time, especially during disease and early development. Ecological principles and advancements in sequencing technologies, such as proteomics and metabolomics, help in understanding host-microbe interactions and specific functions. Large-scale projects like MetaHIT and HMP have made significant progress in characterizing the healthy microbiota and identifying disease-associated disruptions. The gut microbiota's composition and function are influenced by age, genetics, environment, and diet. Infants have more volatile microbiomes, and dietary changes can significantly alter the microbiota. The gut microbiota's resilience to perturbations, such as antibiotics and dietary changes, varies among individuals. Understanding the mechanisms of resilience, including species richness and functional response diversity, is essential for developing strategies to maintain or restore a healthy microbiota. Feedback loops, both positive and negative, play a crucial role in stabilizing or destabilizing the microbiota. The success of fecal microbiota transplantation in treating recurrent Clostridium difficile-associated disease (CDAD) highlights the plasticity of the gut microbiota. Future research should focus on identifying species and feedback loops that promote a healthy microbiota and developing interventions to encourage transitions from unhealthy to healthy stable states.The human gut microbiota is a complex ecological community that influences normal physiology and susceptibility to diseases through its metabolic activities and interactions with the host. Understanding the factors that drive changes in the gut microbiota's composition and function is crucial for developing targeted therapies. The gut microbiota is highly diverse, varies between individuals, and fluctuates over time, especially during disease and early development. Ecological principles and advancements in sequencing technologies, such as proteomics and metabolomics, help in understanding host-microbe interactions and specific functions. Large-scale projects like MetaHIT and HMP have made significant progress in characterizing the healthy microbiota and identifying disease-associated disruptions. The gut microbiota's composition and function are influenced by age, genetics, environment, and diet. Infants have more volatile microbiomes, and dietary changes can significantly alter the microbiota. The gut microbiota's resilience to perturbations, such as antibiotics and dietary changes, varies among individuals. Understanding the mechanisms of resilience, including species richness and functional response diversity, is essential for developing strategies to maintain or restore a healthy microbiota. Feedback loops, both positive and negative, play a crucial role in stabilizing or destabilizing the microbiota. The success of fecal microbiota transplantation in treating recurrent Clostridium difficile-associated disease (CDAD) highlights the plasticity of the gut microbiota. Future research should focus on identifying species and feedback loops that promote a healthy microbiota and developing interventions to encourage transitions from unhealthy to healthy stable states.