Host-associated microbiomes are ubiquitous in nature, but highly variable in both space and time, and shaped by a diverse range of biotic and abiotic factors. This chapter summarises the numerous drivers of variation in microbiome structure and function across both plants and animals. Plants harbour distinct microbial communities in their rhizosphere, phyllosphere and endosphere. These communities interact with hosts in a different way, and in turn are shaped by a unique set of environmental factors. For example, the rhizosphere supports a particularly diverse microbial community shaped by plant exudates and signalling molecules to facilitate nutrient transfer to the host. Similarly, variation in animal microbiomes is driven by host genetic, life-history and environmental traits, including phylogeny, diet, age, metabolism and sociality. Several of these factors are also given more detailed treatment in later chapters. Particular attention is given to our current state of knowledge concerning initial colonisation and subsequent succession in microbial community composition in juveniles, the consequences of which remain one of the major outstanding questions in microbiome research.