Koch’s postulates originally proposed a one microorganism–one disease approach to disease; however, it is now clear that many diseases of plants and animals are associated with changes in the taxonomic composition and function of the microbiome, and that health and disease are mediated by a dynamic interplay between host factors, environmental factors, the host microbiota and pathogenic microorganisms. Commensal microbes can become pathogenic under certain conditions, and disease can arise from complex polymicrobial infections. Although causation and correlation can be difficult to untangle, it is clear that the host microbiome plays a key role in resisting colonisation by pathogens across all host taxa, from plants to animals to humans. This offers exciting possibilities for manipulating microbiomes in order to reduce pathogenic infection in a range of contexts, including agriculture, wildlife and human health, through the use of probiotics, prebiotics and microbiome transplants, among other approaches.

A classic example of microbiome function is its role in nutrient assimilation in both plants and animals, but other less obvious roles are becoming more apparent, particularly in terms of driving infectious and non-infectious disease outcomes and influencing host behaviour. However, numerous biotic and abiotic factors influence the composition of these communities, and host microbiomes can be susceptible to environmental change. How microbial communities will be altered by, and mitigate, the rapid environmental change we can expect in the next few decades remain to be seen. That said, given the enormous range of functional diversity conferred by microbes, there is currently something of a revolution in microbial bioengineering and biotechnology in order to address real-world problems including human and wildlife disease and crop and biofuel production. All of these concepts are explored in further detail throughout the book.

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.