Pig microbial and immune traits respond to host evolutionary history and ecology across multiple scales (16S)

Animal ecology and evolution has long been known to shape host physiology, but more recently, the gut microbiome has been identified as a mediator between host ecology and evolution and host health. Gut microbiome responses to new animal genotypes and local environmental change during domestication may be linked to the appearance of specific host phenotypes that are adaptive (or not) to the domestic environment. Because ensuring the wellbeing of domestic animals is of the utmost importance for the agricultural sector, the influence of the gut microbiome on immune homeostasis and metabolism are particularly critical to understand. We investigated how domestication affects the gut microbiome and host immune state in multiple populations of free-ranging feral pigs, captive wild pigs, and free-ranging and captive domestic pigs. We observed that pig evolutionary history contributed to the repertoire of metabolic genes found in the gut microbiome, whereas domestication context explained the most variation in microbiome composition, pathogen and antibiotic resistance gene (ARG) abundances, and immune markers. We also documented population-level effects within domestication contexts, demonstrating that fine scale environmental variation also shaped host and microbe features. Our findings highlight that understanding which gut microbiome and immune traits respond to either host evolutionary history and/or local ecology will inform targeted interventions that manipulate the gut microbiome to achieve beneficial health outcomes.