Next Generation Sequencing (NGS) technologies have helped to shed light on the expansive and diverse microbial communities that colonise the various tissues of plant and animal microbiomes such as gut, skin, and root. These communities play an important role in an organism’s health and the ecosystem they inhabit, impacting its productivity, fitness and disease resistance. Environmental researchers can use metagenomic sequencing to unveil the genetic dissections of microbiome diversity and function as well as its interactions with the host organism, increasing our understanding of how microbial perturbations can impact the host and its environment. Agricultural researchers may also use metagenomic analysis to assess how the microbiome impacts plants and animals through factors such as stress resistance, nutrient uptake, milk or meat production, and breeding.