The gut microbiome profoundly affects animal welfare through its roles in immunity, behavior, and stress responses, with implications for farming and companion animal care.
Microbiome science is revealing new dimensions of animal welfare. The composition of the gut microbiome affects behavior, stress reactivity, immune function, and potentially the capacity for positive emotional states - all core welfare concerns. In farm animals, early antibiotic use and hygiene practices that prevent normal social microbiome transmission can compromise the welfare-relevant functions of microbiomes established through evolutionary host-microbiome coevolution. Welfare-positive farm management that supports natural microbiome development through social contact, appropriate hygiene levels, and dietary diversity is supported by emerging microbiome science.