As pioneers of life, microorganisms have been established on our planet for c. 3.5 billion years. As a result, plants and animals have co-evolved with trillions of associated microorganisms for millions of years (Chisholm et al., Reference Chisholm, Coaker and Day2006), and multicellular organisms can be considered as meta-organisms; a complex of host cells plus many symbiotic species (Rohwer et al., Reference Rohwer, Seguritan, Azam and Knowlton2002). These communities have been termed the ‘microbiota’, and their associated genomes the ‘microbiome’. The microbiota can consist of algae, bacteria, archaea, fungi, protists and viruses, and collectively these microorganisms by far surpass the number of host cells (Bosch & McFall-Ngai, Reference Bosch and McFall-Ngai2011; Sender et al., Reference Sender, Fuchs and Milo2016). As a result of this co-evolution, significant interdependency has arisen between hosts and their associated microbiota, and host-associated microbiomes profoundly affect host biology and function (Gilbert et al., Reference Gilbert, Sapp and Tauber2012; McFall-Ngai et al., Reference McFall-Ngai, Hadfield and Bosch2013; Turner et al., Reference Turner, James and Poole2013). Across all meta-organisms, the host microbiota contributes significant functional diversity and performs critical roles through the provision of microbial ‘ecosystem services’, including the synthesis of important molecules required by the host, catabolism and bioconversion of complex polysaccharides, immune regulation and colonisation resistance from potentially pathogenic microorganisms (Lynch & Pedersen, Reference Lynch and Pedersen2016; Young, Reference Young2017). As such, multicellular organisms have become reliant on the genetic diversity of their microbiome, requiring the associated immune stimulation and products of microbial metabolism to function. For example, in the human microbiota,>10,000 different microbial strains are associated with the host, conferring around 8 million unique protein-encoding genes; 360 times more protein-coding genes than the human genome (Human Microbiome Consortium, 2012). Within this framework, the host and its microbiota together are defined as the ‘holobiont’, while the genomes of the host and microbiota within the holobiont represent the hologenome (Rosenberg & Zilber-Rosenberg, Reference Rosenberg and Zilber-Rosenberg2016). These selected relationships may be interpreted as evidence of a summed unit of evolutionary selection, whereby all the organisms that make up the intra-organismal ecosystem are under super-selection, shaping the evolution of each genotype. This has been termed the hologenome concept of evolution, and may define a level of selection in the evolution of both plants and animals (Bordenstein & Theis, Reference Bordenstein and Theis2015; Berg et al., Reference Berg, Rybakova and Grube2016; Osborne et al., Reference Osborne, De-Kayne and Bidartondo2018; Rosenberg & Zilber-Rosenberg, Reference Rosenberg and Zilber-Rosenberg2018). Although this concept remains the subject of debate (Douglas & Werren, Reference Douglas and Werren2016), it is compelling to view our shared journey through the world as a co-dependence, a symbiosis, in which both the microbes and the host are entirely dependent on each other.

Recent rapid advances in both nucleic acid sequencing technologies and the identification of proteins and metabolites have transformed our ability to characterise the structure and function of the host microbiome. These have allowed biologists to characterise complex microbial communities associated with a vast array of plant and animal taxa (including humans), offering increased insight into the role of microbes in host development and physiology (Grice & Segre, Reference Grice and Segre2012; McFall-Ngai et al., Reference McFall-Ngai, Hadfield and Bosch2013; Thompson et al., Reference Thompson, Rivera, Closek and Medina2015; Chen et al., Reference Chen, Teh and Sun2016; Esposti & Romero, Reference Esposti and Romero2017). Molecular tools such as amplicon sequencing (metabarcoding), metagenomics and metatranscriptomics can be used to construct species abundance and functional networks, and measure fine-scale changes in community microbiota with ever-increasing resolution, providing greater understanding of ecological trends between hosts and their microbiota. Such advances in DNA sequencing, proteomics and metabolomics, coupled with advances in computational analysis and modelling, have allowed unprecedented access to the microbiome, provoking new hypotheses on the role of microbiomes in health and disease (Autenrieth, Reference Autenrieth2017). Consequently, great progress has been made in our understanding of plant and animal holobionts. In Chapter 2, we outline and discuss the range of current methods available to researchers for characterising the composition and functional traits of host microbiomes.

One of the most well-studied and yet complex of all microbiomes is not in fact associated with plant or animal hosts, but with the soil that forms the basis of our terrestrial ecosystems. Soil microbiomes play numerous vital roles in the decomposition of soil organic matter and circulation of global carbon and nitrogen stores (Thakuria et al., Reference Thakuria, Schmidt and Finan2010). Moreover, soil microbiome composition is inherent to plant health and associated biodiversity (Fierer, Reference Fierer2017) and as such supports animal diversity and associated ecosystem health, as well as ultimately providing almost all human sustenance through crop production and livestock feed. Given the vital importance of soil health to ecosystem and human health, Chapter 3 is dedicated to understanding the diversity and function of soil microbiomes across a range of ecosystems and habitat types.

Within a host organism there is a gradient in the strength of the interactions between individual microorganisms and the host, from dependence to independence, which highlights the huge ecological dynamics that shape these interactions. Different host species usually contain unique microbial assemblages (Davenport et al., Reference Davenport, Sanders and Song2017; Youngblut et al., Reference Youngblut, Reischer and Walters2019), and even within hosts, different regions can host different communities. For example, plants support different microbiota in their below-ground and above-ground components, and animals, including humans, have different communities associated with their skin, gut and other organs (Gopal & Gupta, Reference Gopal and Gupta2016; Gilbert et al., Reference Gilbert, Blaser and Caporaso2018). For both plants and animals, a range of intrinsic and extrinsic factors can influence microbiome composition, including host genetics, development stage, social interactions, behaviour, diet, environmental temperatures and other abiotic factors. The consequences of these for host function are just beginning to be understood, and we discuss these ideas in Chapter 4. Of these factors, diet and associated nutrition are particularly important. The animal microbiome generally reflects the lifestyle of the host (Douglas, Reference Douglas2015; Hammer & Bowers, Reference Hammer and Bowers2015; Macke et al., Reference Macke, Tasiemski and Massol2017), and host diet is one of the key factors that shape the composition and structure of the animal gut microbiome (Ley et al., Reference Ley, Hamady and Lozupone2008; McFall-Ngai et al., Reference McFall-Ngai, Hadfield and Bosch2013; Baldo et al., Reference Baldo, Pretus and Riera2017). Indeed, the gut microbiome of animals, including humans, has been most widely studied due to its key role in modulating nutritional intake from food sources, often accessing molecules that would otherwise be unavailable to the host. For example, ruminant guts contain unique cellulolytic bacteria that exude enzymes capable of breaking down tough grassy material (Flint et al., Reference Flint, Bayer and Rincon2008). Another classic example is that of aphid species, which carry Buchnera as an obligate bacterial symbiont that synthesises certain essential amino acids, thus allowing the host to feed on nutrient-poor phloem diets that would otherwise not sustain development (Oliver et al., Reference Oliver, Degnan, Burke and Moran2010). Similarly, the gut microbiome people from rural areas of Africa and South America have distinct gut microbiota for digestion of complex carbohydrates, whereas those of a large population of humans in the United States is optimised to process fat- and protein-rich diets (Yatsunenko et al., Reference Yatsunenko, Rey and Manary2012). Furthermore, recent studies in human microbiomes showed that disruption of particular microbiome functions may result in malnutrition, obesity and other metabolic syndromes (Grice & Segre, Reference Grice and Segre2012; Blaser et al., Reference Blaser, Cardon and Cho2016). Although devoid of a gut, plant nutrition is also intrinsically linked to the microbiome of both itself and its associated soil (Pii et al., Reference Pii, Mimmo and Tomasi2015). Indeed, plants have strong associations with a range of microbial partners, most notably mycorrhizal fungi and rhizobia bacteria, between which nutrients flow. Broadly speaking, plants provide microbial partners with carbon substrates in exchange for mobilising otherwise inaccessible nitrogen and phosphorous (Turner et al., Reference Turner, James and Poole2013). In Chapter 5, the interactions between microbiome composition and host nutrition for plants and animals is expanded upon.

Perhaps one of the more intriguing areas of research in this field involves the interactions between host microbiomes and host behaviours. Behaviours that can affect and be affected by microbiome composition and function can include foraging decisions, appetite and food choice. The role of microbiomes in synthesising and regulating hormone production as well as influencing reproductive behaviours is also a growing field of research. Furthermore, microbes interact with host mood and stress, and can have profound implications for memory and cognitive function, all of which can influence host health and disease susceptibility. There are also some remarkable examples of behavioural manipulation of the host by parasitic microbes to facilitate their dispersal and transmission. We explore this further in Chapter 6.

As discussed above, the traditional dogma of microorganisms as largely pathogenic no longer stands. Indeed, an increasing body of research is showing that host-associated microbes are in fact critical for preventing infectious and non-infectious disease. In Chapter 7, we examine the symbiotic interactions between hosts and their microbial communities, and highlight the broad suite of mechanisms by which the microbiome protects against invasion by bacterial, fungal and viral pathogens across plants and animals. This chapter also addresses the use of probiotics and microbiome manipulation (through microbiome transplants, personalised medicine, environmental management and host genotype selection) in order to prevent and treat human and wildlife diseases. This is particularly important in the context of the rapid increase in crop and wildlife diseases that we are currently experiencing, largely as a result of increased global trade and climate change (Tompkins et al., Reference Tompkins, Carver and Jones2015; Fisher et al., Reference Fisher, Gow and Gurr2016). Indeed, our planet is currently undergoing a plethora of extreme environmental changes, and the effect of these on host microbiome composition, as well as the potential for the microbiome to mitigate these changes for their hosts, are explored in Chapter 8. Furthermore, given the enormous and diverse functional power provided by microbes, the potential to harness these attributes to solve real-world problems, such as crop production, human and livestock health, antibiotic resistance, and biofuel production, is a highly active area of novel research. The field remains in its infancy; the application of microbes and microbially derived products is still fraught with problems, both biological and technical, in addition to a range of ethical considerations. We discuss this in more detail in Chapter 9. Finally, we conclude in Chapter 10 by bringing together research questions and future directions for the field of microbiome research inspired by our chapter authors. We hope you will enjoy reading this book as much as we enjoyed putting it together!