Blurred Lines: Pathogens, Commensals, and the Healthy Gut

Detailed studies of the chicken microbiome have emerged in recent years, largely due to the impact of next-generation sequencing (NGS). We increasingly understand how the microbiome is important in health, in development of the gut and the immune system, and in maintenance of homeostasis. Manipulation of the microbiota directly through probiotics or antimicrobials or indirectly through feed and feed additives has long been used by the poultry industry to increase growth rates and feed conversion, to improve gut health, and to reduce the burden of pathogens and, in particular, to reduce the load of foodborne zoonotic pathogens such as Salmonella and Campylobacter. We can now begin to mechanistically determine how these treatments affect the microbiota and the wider host, and this understanding will allow us to use more targeted approaches in the future. In terms of food security, increasing yield is clearly a good thing. However, it is far from clear what represents a "healthy" microbiome, and the lines between what is a "harmless" commensal and what is a pathogen are often blurred. As such an understanding of the microbial ecology of the gut and how this is affected by manipulation of the microbiome or indeed treatment of "pathogens" is essential in ensuring that treatments intended to improve health and productivity do not in fact cause more problems.