Comparative biology of germ-free and conventional poultry

Interaction between the host and the enteric microbiome is highly complex. Microbial involvement in certain pathologies is moderately well established, but the contribution of the microbiome to animal welfare, behavior, sustainability, immune development, nutritional status, physiology, and maturation is less clear. A valuable experimental model to enable scientists to explore the role of the microbiome in various domains is to compare various phenotypes of a conventionally reared (CV) cohort with those in a germ-free (GF) state. A GF animal is one that is devoid of any detectable microbial life including bacteria, viruses, protozoa and parasites. The GF state is different from gnotobiotic animals where the microbiome is fully described, or ‘specific pathogen free’ (SPF) animals where a moderately normal microbiome is present but devoid of pathogenic microorganisms. Pioneering GF research in poultry in the late 1940s and 1950s has its origin in a need understand the mode of action of antibiotics. Early researchers quickly established that GF chicks responded differently to antibiotics than CV counterparts. The GF experimental model has since been exploited in many divergent fields including pathology, immunology, metabolism, anatomy, physiology, and others. The absence of a microbiome presents the host with a range of advantages and disadvantages. For example, GF chicks often grow more quickly and have lower feed conversion ratio (FCR) than their CV counterparts but may be less resilient to external stress and have a compromised immunological maturation rate. This review will summarize the literature on GF animal research with a special emphasis on poultry. The objective of the review is to establish a frame of reference to understand the extent of the role of the microbiome in animal health, welfare, nutrition, and growth, to provide opportunities for targeted modulation of the microbiome to achieve desired phenotypic responses whilst simultaneously minimizing unintended collateral effects.