Emerging research on the gut-brain axis reveals that microbiome health affects stress responses, immune function, and emotional states in farm and companion animals — with direct welfare implications.
The gut-brain connection represents an emerging frontier in animal welfare science with potentially significant practical implications. If gut microbiome health affects emotional states, stress resilience, and cognitive function in farm animals — as it demonstrably does in rodent models — then management practices that disrupt microbiome development (early antibiotic use, rapid dietary changes, weaning stress) may be causing welfare harms beyond their direct physical effects. Conversely, management practices that support microbiome diversity — gradual dietary transitions, fermented feeds, diverse substrates, and reduced antibiotic use — may provide welfare benefits beyond their direct nutritional value. This research area is still developing; the welfare-relevant evidence is clearest in rodents and companion animals, with application to farm species requiring further validation. However, the precautionary principle supports microbiome-protective management where feasible.