Microbiota optimisation to promote health and fight disease in animals – a roadmap

Growing levels of meat consumption and the rising human population are placing global meat production systems under increasing pressure to maximise efficiency and animal productivity. Meeting these needs will require the effective prevention and mitigation of animal disease, which can place heavy burdens on productivity and impose direct economic costs via culling of affected animals. While antimicrobials have historically been our primary defence against animal disease, the growing threat of drug-resistant microbes is driving regulatory efforts to restrict their usage in animal production. These competing pressures have spurred fresh urgency in the identification and development of alternatives to antimicrobials that are capable of treating and/or preventing disease while avoiding the selection of drug-resistant microbes. With these developments in mind, the STAR IDAZ International Research Consortium recently conducted several expert workshops tasked with producing roadmaps that structure and organise ongoing research and outstanding questions in the field of antimicrobial alternatives. Here, we will explore the roadmap that addresses microbiota optimisation. This field of research focuses on understanding and modulating the microbial communities that colonise animals and the effects that these microbes have on animal development, productivity, and immunity. Recent studies have begun to shed light on the complex web of interactions linking host animals with their microbiota and the avenues by which they can be altered to promote health and productivity. This review will explore these studies through the lens of the STAR IDAZ microbiota optimisation roadmap and the European regulatory framework, discussing the fundamental biology of the microbiota, host-microbe interactions, and the various classes of microbiota optimisers – including dietary additives, probiotics, etc. – currently under development.