Domestication shapes the pig gut microbiome and immune traits from the scale of lineage to population

Animal ecology and evolution have long been known to shape host
physiology, but more recently, the gut microbiome has been identified as a
mediator between animal ecology and evolution and health. The gut
microbiome has been shown to differ between wild and domestic animals, but
the role of these differences for domestic animal evolution remains
unknown. Gut microbiome responses to new animal genotypes and local
environmental change during domestication may promote specific host
phenotypes that are adaptive (or not) to the domestic environment. Because
the gut microbiome supports host immune function, understanding the
effects of animal ecology and evolution on the gut microbiome and immune
phenotypes is critical. We investigated how domestication affects the gut
microbiome and host immune state in multiple pig populations across five
domestication contexts representing domestication status and current
living conditions: free-ranging wild, captive wild, free-ranging domestic,
captive domestic in research or industrial settings. We observed that
domestication context explained much of the variation in gut microbiome
composition, pathogen abundances, and immune markers, yet the main
differences in the repertoire of metabolic genes found in the gut
microbiome were between the wild and domestic genetic lineages. 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 host genetic lineage and/or scales
of local ecology could inform targeted interventions that manipulate the
gut microbiome to achieve beneficial health outcomes.