Stress neurophysiology in poultry: A functional framework for the application of microbiome science in poultry production

Over the last two decades, scientific interest in the poultry microbiome has skyrocketed with a role ascribed for the microbiome in virtually every aspect of poultry health and production. While substantial progress has been made in revealing important correlations that can be used as a roadmap for utilization in a production setting, much remains to be understood in way of causality of the microbiome for the bird. In other words, correlation does not mean causation and there exists an overwhelming need to identify causal mechanisms if new microbiome-based modalities are to be implemented in poultry production. Therefore, this review discusses the need for function-driven hypotheses that provide an evidence-based framework when approaching poultry microbiome research. Considering that the impact of stress on both the bird and microbiome is well-appreciated across poultry species, pre-harvest stress is taken as a prototypical example of where the use of function-driven hypotheses can help bridge basic to applied microbiome-based science to benefit poultry production. Practical examples are provided and summarized herein, in which this approach can be applied ranging from areas of foodborne pathogen carriage to performance. Central to this aim is the interdisciplinary field of Microbial Endocrinology as it represents the intersection of microbiology and neurophysiology. Microbial Endocrinology has demonstrated that monoamine neurochemical systems can serve as mechanistic routes of host-microbe interaction, providing an evidence-based platform for identification of causal relationships between microbial taxa and the host. Interventions can therefore be designed to modulate these causal pathways to benefit the bird. While emphasis is given towards the nexus of gastrointestinal neurophysiology and the gut microbiome, this review also highlights the intersection of neurochemistry and the microbiome along the respiratory and reproductive tracts. The need for widespread adoption of best practices methodologies in microbiome research experimental design is integrated into function-driven hypotheses herein. It is anticipated that the cooperative use of directed hypotheses and the implementation of robust experimental design will accelerate the application of microbiome-based solutions in poultry production.