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Abstract Purpose of ReviewThis review explores the application of classical ecological theory to host-associated microbiomes during initial colonization, maintenance, and recovery. We discuss unique challenges of applying these theories to host-associated microbiomes and host factors to consider going forward. Recent FindingsRecent studies applying community ecology principles to host microbiomes continue to demonstrate a role for both selective and stochastic processes in shaping host-associated microbiomes. However, ecological frameworks developed to describe dynamics during homeostasis do not necessarily apply during diseased or highly perturbed states, where large variations can potentially lead to alternate stable states. SummaryDespite providing valuable insights, the application of ecological theories to host-associated microbiomes has some unique challenges. The integration of host-specific factors, such as genotype or immune dynamics in ecological models or frameworks is crucial for understanding host microbiome assembly and stability, which could improve our ability to predict microbiome outcomes and improve host health.