The gut microbiota plays a critical role in human health, yet its taxonomic complexity, interpersonal variability, and resistance to change in adulthood present challenges for understanding the factors driving shifts in its composition and function. Here, we propose a hierarchy of ecological factors governing gut microbiota assembly, stability, and resilience. At the apex of this hierarchy is habitat filtering by host-derived electron acceptors, which dictates the ecological guilds that dominate distinct gut regions. Host dietary behavior shapes niche availability within these ecological guilds by regulating nutrient availability. Priority effects preserve taxonomic stability whereas microbial antagonism governs competition for open ecological positions. This framework highlights how host control over microbial energy metabolism directs microbiota self-assembly and maintains gut homeostasis.