The human gut microbiota is a diverse and dynamic ecosystem that has pleiotropic effects on host physiology. There is increasing evidence that the transition to an industrialized lifestyle has been accompanied by a gradual alteration of human gut microbiota, which is reflected at both compositional and functional levels and is associated with the emergence of chronic diseases. In early life, the gut microbiota undergoes highly dynamic evolution in response to environmental factors, which is less pronounced later in life. Gut microbiota may encounter various acute and continuous, and the response varies greatly between individuals and stressors. Growing interest in this topic has rapidly led to application of novel high resolution approaches that have increased insight into human gut microbiota stability, dynamics and response to disturbances. In the future, detailed longitudinal studies coupled with multi-omics based approaches and clinical outcomes, will help in the prediction of gut microbiome trajectories in response to disturbances and in the identification of preventive solutions to mitigate gut microbiota alterations.