Our knowledge and understanding of the structure and function of complex host-associated communities has grown exponentially in the last decade through improvements in sequencing technologies. Despite this, there are still many outstanding research questions, which will undoubtably lead to many more. Concerted effort is required to elucidate the composition and function of taxonomic groups other than bacteria that constitute host microbiomes, and to extend our current cataloguing efforts to non-model and field-based host organisms. Further to this, we need to continue to move beyond the 'who?' question provided by relatively cheap amplicon sequencing to gain a better understanding of 'what?' the microbiome is doing, using metatranscriptomics approaches. Critically, we need to understand how members of the microbiome interact to confer function. Given the current unprecedented environmental change, microbiome plasticity may prove vital to host resilience and fitness. Furthermore, there is considerable potential for microbial biotechnology to improve numerous aspects of humanity, although care must be taken to ensure environmental and social justice prevail.